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ORCIDBioinformatics, Volume 35
Volume 35, Number 1, January 2019
Genome Analysis
- Nilotpal Sanyal
, Min-Tzu Lo, Karolina Kauppi, Srdjan Djurovic, Ole A. Andreassen, Valen E. Johnson, Chi-Hua Chen:
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies. 1-11
- Nelson Gil, András Fiser:
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. 12-19 - Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach:
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. 20-27
- Kieran R. Campbell, Christopher Yau:
A descriptive marker gene approach to single-cell pseudotime inference. 28-35 - Eleonora Lusito, Barbara Felice, Giovanni D'Ario, Alessandro Ogier, Francesca Montani, Pier Paolo Di Fiore, Fabrizio Bianchi:
Unraveling the role of low-frequency mutated genes in breast cancer. 36-46 - Sumon Ahmed, Magnus Rattray, Alexis Boukouvalas:
GrandPrix: scaling up the Bayesian GPLVM for single-cell data. 47-54 - Marjan Farahbod, Paul Pavlidis:
Differential coexpression in human tissues and the confounding effect of mean expression levels. 55-61 - Andrea Rau, Michael Flister, Hallgeir Rui, Paul L. Auer:
Exploring drivers of gene expression in the Cancer Genome Atlas. 62-68
- Christian X. Weichenberger, Johannes Rainer, Cristian Pattaro, Peter P. Pramstaller, Francisco S. Domingues:
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. 69-76
- Lei Han, Lei Li, Feng Wen, Lei Zhong, Tong Zhang, Xiu-Feng Wan:
Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus. 77-87 - Barnali Das, Abhijeet Rajendra Patil, Pralay Mitra:
A network-based zoning for parallel whole-cell simulation. 88-94 - Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin J. Callahan, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J. Wong, Cecele Quaintance, Anthony Culos, Natalie Stanley, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul H. Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D. Winn, Maurice L. Druzin, Ronald Gibbs, Gary L. Darmstadt, David B. Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry P. Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour:
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. 95-103 - Fangping Wan, Lixiang Hong, An Xiao, Tao Jiang, Jianyang Zeng:
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. 104-111
- Jianwen Fang:
Tightly integrated genomic and epigenomic data mining using tensor decomposition. 112-118
Genome Analysis
- Jerome Kelleher, Mike Lin, Carl H. Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y. González, David K. Jackson, Aaron Kemp, John Marshall, Andrew Nowak, Alexander Senf, Jaime M. Tovar-Corona, Alexander Vikhorev, Thomas M. Keane, GA4GH Streaming Task Team:
htsget: a protocol for securely streaming genomic data. 119-121 - Velimir Gayevskiy, Tony Roscioli, Marcel E. Dinger, Mark J. Cowley:
Seave: a comprehensive web platform for storing and interrogating human genomic variation. 122-125 - Zhaohui Gu, Charles Mullighan:
ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations. 126-129 - André Gohr, Manuel Irimia:
Matt: Unix tools for alternative splicing analysis. 130-132 - Sebastian Deorowicz, Adam Gudys, Maciej Dlugosz, Marek Kokot, Agnieszka Danek:
Kmer-db: instant evolutionary distance estimation. 133-136 - Patrick K. Kimes, Alejandro Reyes:
Reproducible and replicable comparisons using SummarizedBenchmark. 137-139 - Marc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort:
WAVES: a web application for versatile enhanced bioinformatic services. 140-142
- Levent Albayrak, Kamil Khanipov, George Golovko, Yuriy Fofanov:
Broom: application for non-redundant storage of high throughput sequencing data. 143-145 - Seyed Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
Cryfa: a secure encryption tool for genomic data. 146-148
- Salvatore Cosentino, Wataru Iwasaki:
SonicParanoid: fast, accurate and easy orthology inference. 149-151
- Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk:
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. 152-155
- Jamil Najafov, Ayaz Najafov:
GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution. 156-159
- Shijia Zhu, Tongqi Qian, Yujin Hoshida, Yuan Shen, Jing Yu, Ke Hao:
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data. 160-163 - Corbin Quick, Christian Fuchsberger, Daniel Taliun, Gonçalo R. Abecasis, Michael Boehnke, Hyun Min Kang:
emeraLD: rapid linkage disequilibrium estimation with massive datasets. 164-166
- Pierre Salvy, Georgios Fengos, Meriç Ataman, Thomas Pathier, Keng C. Soh, Vassily Hatzimanikatis:
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. 167-169
- Jean-Michel Claverie, Thi Ngan Ta:
ACDtool: a web-server for the generic analysis of large data sets of counts. 170-171
- Chuan Jiao, Pengpeng Yan, Cuihua Xia, Zhaoming Shen, Zexi Tan, Yanyan Tan, Kangli Wang, Yi Jiang, Lingling Huang, Rujia Dai, Yu Wei, Yan Xia, Qingtuan Meng, Yanmei Ouyang, Liu Yi, Fangyuan Duan, Jiacheng Dai, Shunan Zhao, Chunyu Liu, Chao Chen:
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. 172-174 - Zeyu Wen, Jiahua He, Huanyu Tao, Sheng-You Huang:
PepBDB: a comprehensive structural database of biological peptide-protein interactions. 175-177
- Paolo Inglese, Gonçalo D. S. Correia, Zoltan Takats, Jeremy K. Nicholson, Robert C. Glen:
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data. 178-180
Volume 35, Number 2, January 2019
Genome Analysis
- Joeri J. Meijsen, Alexandros Rammos, Archie Campbell, Caroline Hayward, David J. Porteous, Ian J. Deary, Riccardo E. Marioni, Kristin K. Nicodemus:
Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study. 181-188 - Malene Juul, Tobias Madsen, Qianyun Guo, Johanna Bertl, Asger Hobolth, Manolis Kellis, Jakob Skou Pedersen:
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. 189-199 - Bianca Dumitrascu, Gregory Darnell, Julien Ayroles, Barbara E. Engelhardt:
Statistical tests for detecting variance effects in quantitative trait studies. 200-210 - Chris-André Leimeister, Thomas Dencker, Burkhard Morgenstern:
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. 211-218 - Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng:
Metagenomic binning through low-density hashing. 219-226
- Sebastian Deorowicz, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz:
CoMSA: compression of protein multiple sequence alignment files. 227-234
- Yu-Chen Lo, Tianyun Liu, Kari M. Morrissey, Satoko Kakiuchi-Kiyota, Adam R. Johnson, Fabio Broccatelli, Yu Zhong, Amita Joshi, Russ B. Altman:
Computational analysis of kinase inhibitor selectivity using structural knowledge. 235-242 - Miha Skalic, Alejandro Varela-Rial, José Jiménez, Gerard Martínez-Rosell, Gianni De Fabritiis:
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks. 243-250
- Jiaan Dai, Wei Jiang, Fengchao Yu, Weichuan Yu:
Xolik: finding cross-linked peptides with maximum paired scores in linear time. 251-257 - Emmanuel Curis, Cindie Courtin, Pierre Alexis Geoffroy, Jean-Louis Laplanche, Bruno Saubaméa, Cynthia Marie-Claire:
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios. 258-265
- Matthias P. Gerstl, Stefan Müller, Georg Regensburger, Jürgen Zanghellini:
Flux tope analysis: studying the coordination of reaction directions in metabolic networks. 266-273 - Clément Frainay, Sandrine Aros, Maxime Chazalviel, Thomas Garcia, Florence Vinson, Nicolas Weiss, Benoit Colsch, Frédéric Sedel, Dominique Thabut, Christophe Junot, Fabien Jourdan:
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. 274-283 - Olivia Eriksson, Alexandra Jauhiainen, Sara Maad Sasane, Andrei Kramer, Anu G. Nair, Carolina Sartorius, Jeanette Hellgren Kotaleski:
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models. 284-292
- Piotr Klukowski, Mario Schubert:
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. 293-300 - Etienne Becht, Yannick Simoni, Elaine Coustan-Smith, Maximilien Evrard, Yang Cheng, Lai Guan Ng, Dario Campana, Evan W. Newell:
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting. 301-308 - Masashi Tsubaki, Kentaro Tomii, Jun Sese:
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences. 309-318
- Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang:
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. 319-328
Genome Analysis
- Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet:
GeneSpy, a user-friendly and flexible genomic context visualizer. 329-331
- David Jakubec, Jirí Vondrásek, Robert D. Finn:
3DPatch: fast 3D structure visualization with residue conservation. 332-334 - Sebastian Uhrig, Holger Klein:
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data. 335-336 - James K. Bonfield, Shane A. McCarthy, Richard Durbin:
Crumble: reference free lossy compression of sequence quality values. 337-339
- Dana Wyman, Ali Mortazavi:
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts. 340-342 - Sara B. Linker, Jonathan Y. Hsu, Adela Pfaff, Debha Amatya, Shu-Meng Ko, Sarah Voter, Quinn Wong, Fred H. Gage:
BrainImageR: spatiotemporal gene set analysis referencing the human brain. 343-345
- Soumita Ghosh, Abhik Datta, Kaisen Tan, Hyungwon Choi:
SLIDE - a web-based tool for interactive visualization of large-scale - omics data. 346-348
- David R. Damerell, Claire Strain-Damerell, Sefa Garsot, Stephen P. Joyce, Paul Barrett, Brian D. Marsden:
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications. 349-351
Databases and Ontologies
- Hojjat Naderi-Meshkin, Xin Lai, Raheleh Amirkhah, Julio Vera, John E. J. Rasko, Ulf Schmitz:
Exosomal lncRNAs and cancer: connecting the missing links. 352-360
Volume 35, Number 3, February 2019
Systems Biology
- Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang:
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. 361-364
Genome Analysis
- Nora von Thenen, Erman Ayday, A. Ercüment Çiçek:
Re-identification of individuals in genomic data-sharing beacons via allele inference. 365-371
- Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich:
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. 372-379 - Wei Zheng, Qi Mao, Robert J. Genco, Jean Wactawski-Wende, Michael Buck, Yunpeng Cai, Yijun Sun:
A parallel computational framework for ultra-large-scale sequence clustering analysis. 380-388 - Xinguo Lu, Xin Qian, Xing Li, Qiumai Miao, Shaoliang Peng:
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters. 389-397 - Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC. 398-406 - Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles:
Dynamic compression schemes for graph coloring. 407-414 - Chen Sun, Paul Medvedev:
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. 415-420 - Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles:
Scaling read aligners to hundreds of threads on general-purpose processors. 421-432 - Avdesh Mishra, Pujan Pokhrel, Md. Tamjidul Hoque:
StackDPPred: a stacking based prediction of DNA-binding protein from sequence. 433-441 - Jeffrey M. Yunes, Patricia C. Babbitt:
Effusion: prediction of protein function from sequence similarity networks. 442-451
- Marcin Kowiel, Dariusz Brzezinski, Przemyslaw J. Porebski, Ivan G. Shabalin, Mariusz Jaskolski, Wladek Minor:
Automatic recognition of ligands in electron density by machine learning. 452-461 - Justina Jankauskaite, Brian Jiménez-García, Justas Dapkunas, Juan Fernández-Recio, Iain H. Moal:
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. 462-469 - Rubén Sánchez García, Carlos Oscar Sánchez Sorzano, José María Carazo, Joan Segura:
BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. 470-477
- Rasmus Henningsson, Magnus Fontes:
SMSSVD: SubMatrix Selection Singular Value Decomposition. 478-486 - Shiquan Sun, Jiaqiang Zhu, Sahar Mozaffari, Carole Ober, Mengjie Chen, Xiang Zhou:
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. 487-496
- Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot:
Random walk with restart on multiplex and heterogeneous biological networks. 497-505
- Bruce A. Corliss, H. Clifton Ray, James T. Patrie, Jennifer Mansour, Sam Kesting, Janice H. Park, Gustavo K. Rohde, Paul A. Yates, Kevin A. Janes, Shayn M. Peirce:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. 506-514
Genome Analysis
- Caralyn Reisle, Karen L. Mungall, Caleb Choo, Daniel Paulino, Dustin W. Bleile, Amir Muhammadzadeh, Andrew J. Mungall, Richard A. Moore, Inna Shlafman, Robin Coope, Stephen Pleasance, Yussanne Ma, Steven J. M. Jones:
MAVIS: merging, annotation, validation, and illustration of structural variants. 515-517 - Haiming Tang, Robert D. Finn, Paul D. Thomas:
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. 518-520
- Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer, Erik Bongcam-Rudloff:
Simulating Illumina metagenomic data with InSilicoSeq. 521-522 - Robert Lanfear, Miriam Schalamun, David Kainer, Weiwen Wang, Benjamin Schwessinger:
MinIONQC: fast and simple quality control for MinION sequencing data. 523-525
- Emmanuel Paradis, Klaus Schliep:
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. 526-528
- Zongxiao He, Lu Wang, Andrew Thomas DeWan, Suzanne M. Leal:
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data. 529-531
- Kieu Trinh Do, David J. N. P. Rasp, Gabi Kastenmüller, Karsten Suhre, Jan Krumsiek:
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. 532-534 - Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes:
gMCS: fast computation of genetic minimal cut sets in large networks. 535-537
- Zainab Noor, Jemma X. Wu, Dana Pascovici, Abidali Mohamedali, Mark P. Molloy, Mark S. Baker, Shoba Ranganathan:
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries. 538-539
Data and Text Mining
- Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard:
polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. 540
Volume 35, Number 4, February 2019
Sequence Analysis
- Reuben J. Pengelly, Andrew Collins:
Linkage disequilibrium maps to guide contig ordering for genome assembly. 541-545
Genome Analysis
- Justin Miller, Brandon D. Pickett, Perry G. Ridge:
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. 546-552 - Zi Yang, George Michailidis:
Quantifying heterogeneity of expression data based on principal components. 553-559 - Timothy J. Peters, Hugh J. French, Stephen T. Bradford, Ruth Pidsley, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A. Giles, Aaron L. Statham, Helen Speirs, Terence P. Speed, Susan J. Clark:
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. 560-570 - Jack M. Fu, Elizabeth J. Leslie, Alan F. Scott, Jeffrey C. Murray, Mary L. Marazita, Terri H. Beaty, Robert B. Scharpf, Ingo Ruczinski:
Detection of de novo copy number deletions from targeted sequencing of trios. 571-578 - Markus Fricke, Ruman Gerst, Bashar Ibrahim, Michael Niepmann, Manja Marz:
Global importance of RNA secondary structures in protein-coding sequences. 579-583
- Bansho Masutani, Shinichi Morishita:
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer. 584-592 - Wenying He, Cangzhi Jia, Quan Zou:
4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction. 593-601
- Jiazhou Chen, Hong Peng, Guoqiang Han, Hongmin Cai, Jiulun Cai:
HOGMMNC: a higher order graph matching with multiple network constraints model for gene-drug regulatory modules identification. 602-610 - Magdalena E. Strauß, John E. Reid, Lorenz Wernisch:
GPseudoRank: a permutation sampler for single cell orderings. 611-618 - Sungwon Jung:
KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein-protein interactions. 619-627
- Miao-Xin Li, Lin Jiang, Timothy Shin Heng Mak, Johnny S. H. Kwan, Chao Xue, Peikai Chen, Henry Chi-Ming Leung, Liqian Cui, Tao Li, Pak Chung Sham:
A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia. 628-635
- Beibei Ru, Yin Tong, Jiangwen Zhang:
MR4Cancer: a web server prioritizing master regulators for cancer. 636-642 - Eunji Kim, Ivan Ivanov, Edward R. Dougherty:
Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. 643-649
- Tatiana Radchenko, Fabien Fontaine, Luca Morettoni, Ismael Zamora:
WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source. 650-655
- Magnus Palmblad, Anna-Lena Lamprecht, Jon C. Ison, Veit Schwämmle:
Automated workflow composition in mass spectrometry-based proteomics. 656-664 - Richard Wilton, Sarah J. Wheelan, Alexander S. Szalay, Steven L. Salzberg:
The Terabase Search Engine: a large-scale relational database of short-read sequences. 665-670
Genome Analysis
- Xiaofei Zhao:
BinDash, software for fast genome distance estimation on a typical personal laptop. 671-673 - Jonathan Laperle, Simon Hébert-Deschamps, Joanny Raby, David A. de Lima Morais, Michel Barrette, David Bujold, Charlotte Bastin, Marc-Antoine Robert, Jean-François Nadeau, Marie Harel, Alexei Nordell-Markovits, Alain Veilleux, Guillaume Bourque, Pierre-Étienne Jacques:
The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets. 674-676
- Szymon Grabowski, Wojciech Bieniecki:
copMEM: finding maximal exact matches via sampling both genomes. 677-678 - Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux:
VisioProt-MS: interactive 2D maps from intact protein mass spectrometry. 679-681 - Matthew Higgins, Matt Ravenhall, Daniel Ward, Jody Phelan, Amy Ibrahim, Matthew S. Forrest, Taane G. Clark, Susana G. Campino:
PrimedRPA: primer design for recombinase polymerase amplification assays. 682-684
- Eoin Fahy, Jorge Álvarez-Jarreta, Christopher J. Brasher, An Nguyen, Jade I Hawksworth, Patricia Rodrigues, Sven Meckelmann, Stuart M. Allen, Valerie B. O'Donnell:
LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics. 685-687 - Ian Walsh, Terry Nguyen-Khuong, Katherine Wongtrakul-Kish, Shi Jie Tay, Daniel Chew, Tasha José, Christopher H. Taron, Pauline M. Rudd:
GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions. 688-690 - Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao:
PredMP: a web server for de novo prediction and visualization of membrane proteins. 691-693 - Mateusz Kurcinski, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Aleksander Kuriata, Andrzej Kolinski, Sebastian Kmiecik:
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility. 694-695
- Gwendolien Sergeant, Lennart Martens, Marleen Van Troys, Paola Masuzzo:
DoRes within CellMissy: dose-response analysis on cell migration and related data. 696-697 - Zhiwei Zhou, Xiaotao Shen, Xi Chen, Jia Tu, Xin Xiong, Zheng-Jiang Zhu:
LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility - mass spectrometry based lipidomics. 698-700 - Shaoli Das, Xiang Deng, Kevin Camphausen, Uma T. Shankavaram:
DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers. 701-702
- Rocío Nieto-Arellano, Héctor Sánchez-Iranzo:
zfRegeneration: a database for gene expression profiling during regeneration. 703-705
- Hengyang Lu, Jiabing Li, Melisa A. Martinez-Paniagua, Irfan N. Bandey, Amit Amritkar, Harjeet Singh, David Mayerich, Navin Varadarajan, Badrinath Roysam:
TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids. 706-708
Databases and Ontologies
- Bo Peng, Man Chong Leong, Huann-Sheng Chen, Melissa Rotunno, Katy R. Brignole, John Clarke, Leah E. Mechanic:
Genetic Simulation Resources and the GSR Certification Program. 709-710
Systems Biology
- Florian Schmidt, Marcel H. Schulz:
On the problem of confounders in modeling gene expression. 711-719
Systems Biology
- Bruce A. Corliss, H. Clifton Ray, James T. Patrie, Jennifer Mansour, Sam Kesting, Janice H. Park, Gustavo K. Rohde, Paul A. Yates, Kevin A. Janes, Shayn M. Peirce:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. 720-721
Volume 35, Number 5, March 2019
Data and Text Mining
- Zheng Zhang, Zhaozhong Zhu, Wenjun Chen, Zena Cai, Beibei Xu, Zhiying Tan, Aiping Wu, Xingyi Ge, Xinhong Guo, Zhongyang Tan, Zanxian Xia, Haizhen Zhu, Taijiao Jiang, Yousong Peng:
Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors. 723-728
Genome Analysis
- Marco Masseroli, Arif Canakoglu, Pietro Pinoli, Abdulrahman Kaitoua, Andrea Gulino, Olha Horlova, Luca Nanni, Anna Bernasconi, Stefano Perna, Eirini Stamoulakatou, Stefano Ceri:
Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data. 729-736
- Angelika Merkel, Marcos Fernández-Callejo, Eloi Casals, Santiago Marco-Sola, Ronald P. Schuyler, Ivo Glynne Gut, Simon C. Heath:
gemBS: high throughput processing for DNA methylation data from bisulfite sequencing. 737-742 - Thomas Shafee, Marilyn A. Anderson:
A quantitative map of protein sequence space for the cis-defensin superfamily. 743-752 - Aashish Jain, Daisuke Kihara:
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. 753-759 - Lizhen Shi, Xiandong Meng, Elizabeth Tseng, Michael Mascagni, Zhong Wang:
SpaRC: scalable sequence clustering using Apache Spark. 760-768
- Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu:
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. 769-777
- Darlene Lu, Yorghos Tripodis, Louis C. Gerstenfeld, Serkalem Demissie:
Clustering of temporal gene expression data with mixtures of mixed effects models with a penalized likelihood. 778-786 - Yuanyuan Bian, Chong He, Jie Hou, Jianlin Cheng, Jing Qiu:
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects. 787-797
- Gerton Lunter:
Haplotype matching in large cohorts using the Li and Stephens model. 798-806 - Zhenwei Dai, Sunny Hei Wong, Jun Yu, Yingying Wei:
Batch effects correction for microbiome data with Dirichlet-multinomial regression. 807-814
- Z. S. Wallace, Sara Brin Rosenthal, Kathleen M. Fisch, Trey Ideker, Roman Sásik:
On entropy and information in gene interaction networks. 815-822 - Shila Ghazanfar, Dario Strbenac, John T. Ormerod, Jean Yee Hwa Yang, Ellis Patrick:
DCARS: differential correlation across ranked samples. 823-829 - Alejandro Fernández Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R. Banga:
Benchmarking optimization methods for parameter estimation in large kinetic models. 830-838
- Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack, Marco Capuccini, Joachim Burman, Kim Kultima, Ola Spjuth:
Container-based bioinformatics with Pachyderm. 839-846
- Jie Yuan, Jiajian Zhou, Huating Wang, Hao Sun:
SKmDB: an integrated database of next generation sequencing information in skeletal muscle. 847-855 - Víctor H. Tierrafría, Citlalli Mejía-Almonte, J. M. Camacho-Zaragoza, Heladia Salgado, K. Alquicira, Chu Ishida, Socorro Gama-Castro, Julio Collado-Vides:
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. 856-864
Genome Analysis
- Adam D. Scott, Kuan-Lin Huang, Amila Weerasinghe, R. Jay Mashl, Qingsong Gao, Fernanda Martins Rodrigues, Matthew A. Wyczalkowski, Li Ding:
CharGer: clinical Characterization of Germline variants. 865-867 - Niko Popitsch:
VARAN-GIE: curation of genomic interval sets. 868-870
- Michael Vilsker, Yumna Moosa, Sam Nooij, Vagner Fonseca, Yoika Ghysens, Korneel Dumon, Raf Pauwels, Luiz Carlos Alcantara, Ewout Vanden Eynden, Anne-Mieke Vandamme, Koen Deforche, Tulio de Oliveira:
Genome Detective: an automated system for virus identification from high-throughput sequencing data. 871-873
- Agnes Meyder, Stefanie Kampen, Jochen Sieg, Rainer Fährrolfes, Nils-Ole Friedrich, Florian Flachsenberg, Matthias Rarey:
StructureProfiler: an all-in-one tool for 3D protein structure profiling. 874-876
- Tahmid Mehdi, Swneke D. Bailey, Paul Guilhamon, Mathieu Lupien:
C3D: a tool to predict 3D genomic interactions between cis-regulatory elements. 877-879 - Daniel Toro-Domínguez, Jordi Martorell-Marugan, Raúl López-Domínguez, Adrián García-Moreno, Víctor González-Rumayor, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez:
ImaGEO: integrative gene expression meta-analysis from GEO database. 880-882
- Yan Zhao, Li Ma, Sukun Jiang, George D. Song, Shaohua He, Hong Li, Qing Song:
AncestryView: data-driven visualization of whole-genome local-ancestry. 883-885 - Samuel Neuenschwander, Frédéric Michaud, Jérôme Goudet:
QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time. 886-888
- George Minadakis, Margarita Zachariou, Anastasis Oulas, George M. Spyrou:
PathwayConnector: finding complementary pathways to enhance functional analysis. 889-891 - Jennifer Hannig, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch:
isiKnock: in silico knockouts in signaling pathways. 892-894 - Andrew Keller, Juan D. Chavez, James E. Bruce:
Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks. 895-897 - Cheng Chang, Mansheng Li, Chaoping Guo, Yuqing Ding, Kaikun Xu, Mingfei Han, Fuchu He, Yunping Zhu:
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis. 898-900
- Hugo Varet, Jean-Yves Coppée:
checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes. 901-902
Volume 35, Number 6, March 2019
Genome Analysis
- Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony:
Characterizing protein-DNA binding event subtypes in ChIP-exo data. 903-913 - Loredana M. Genovese, Marco M. Mosca, Marco Pellegrini, Filippo Geraci:
Dot2dot: accurate whole-genome tandem repeats discovery. 914-922
- Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu:
Protease target prediction via matrix factorization. 923-929 - Hong Su, Mengchen Liu, Saisai Sun, Zhenling Peng, Jianyi Yang:
Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods. 930-936 - Kliment Olechnovic, Bohdan Monastyrskyy, Andriy Kryshtafovych, Ceslovas Venclovas:
Comparative analysis of methods for evaluation of protein models against native structures. 937-944 - Kai-Chun Chang, Emmanuel Oluwatobi Salawu, Yuan-Yu Chang, Jin-Der Wen, Lee-Wei Yang:
Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. 945-952
- Tiehang Duan, José P. Pinto, Xiaohui Xie:
Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures. 953-961 - Itamar Kanter, Piero Dalerba, Tomer Kalisky:
A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors. 962-971 - Lin Shi, Johan A. Westerhuis, Johan Rosén, Rikard Landberg, Carl Brunius:
Variable selection and validation in multivariate modelling. 972-980 - Tyler J. Gorrie-Stone, Melissa C. Smart, Ayden Saffari, Karim Malki, Eilis J. Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C. Schalkwyk:
Bigmelon: tools for analysing large DNA methylation datasets. 981-986 - Nurgazy Sulaimanov, Sunil Kumar, Frédéric Burdet, Mark Ibberson, Marco Pagni, Heinz Koeppl:
Inferring gene expression networks with hubs using a degree weighted Lasso approach. 987-994 - Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. 995-1001
- Brent Kirkpatrick, Shufei Ge, Liangliang Wang:
Efficient computation of the kinship coefficients. 1002-1008
- Mahsa Ghanbari, Julia Lasserre, Martin Vingron:
The Distance Precision Matrix: computing networks from non-linear relationships. 1009-1017 - Eun Jeong Min, Sandra E. Safo, Qi Long:
Penalized co-inertia analysis with applications to -omics data. 1018-1025 - Daniel Morgan, Andreas Tjärnberg, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer:
A generalized framework for controlling FDR in gene regulatory network inference. 1026-1032
- Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung:
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. 1033-1039 - Qichao Tu, Lu Lin, Lei Cheng, Ye Deng, Zhili He:
NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. 1040-1048
Genome Analysis
- Jason M. Inman, Granger G. Sutton, Erin Beck, Lauren M. Brinkac, Thomas H. Clarke, Derrick E. Fouts:
Large-scale comparative analysis of microbial pan-genomes using PanOCT. 1049-1050 - Wai Yee Wong, Oleg Simakov:
RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation. 1051-1052
- Fei Song, Chunmei Cui, Lin Gao, Qinghua Cui:
miES: predicting the essentiality of miRNAs with machine learning and sequence features. 1053-1054
- Hendrik Schultheis, Carsten Kuenne, Jens Preussner, Rene Wiegandt, Annika Fust, Mette Bentsen, Mario Looso:
WIlsON: Web-based Interactive Omics VisualizatioN. 1055-1057 - José Fernández Navarro, Joakim Lundeberg, Patrik L. Ståhl:
ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets. 1058-1060
- Biao Zeng, Greg Gibson:
PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness. 1061-1063 - Stephen C. Watts, Scott C. Ritchie, Michael Inouye, Kathryn E. Holt:
FastSpar: rapid and scalable correlation estimation for compositional data. 1064-1066
- Hongbin Yang, Chaofeng Lou, Lixia Sun, Jie Li, Yingchun Cai, Zhuang Wang, Weihua Li, Guixia Liu, Yun Tang:
admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. 1067-1069 - Anamaria Crisan, Tamara Munzner, Jennifer L. Gardy:
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews. 1070-1072
- Thomas R. Sibley, Evan J. Silberman, James I. Mullins:
ISDB: a database toolkit for storing and analyzing viral integration site data. 1073-1075 - K. Joeri van der Velde, Floris Imhann, Bart Charbon, Chao Pang, David van Enckevort, Mariska Slofstra, Ruggero Barbieri, Rudi Alberts, Dennis Hendriksen, Fleur D. L. Kelpin, Mark de Haan, Tommy de Boer, Sido Haakma, Connor Stroomberg, Salome Scholtens, Gert-Jan van de Geijn, Eleonora A. M. Festen, Rinse K. Weersma, Morris A. Swertz:
MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians. 1076-1078 - Pablo Mier, Miguel A. Andrade-Navarro:
Traitpedia: a collaborative effort to gather species traits. 1079-1081
Databases and Ontologies
- Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad:
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. 1082
Volume 35, Number 7, April 2019
Genome Analysis
- Pariya Behrouzi, Ernst C. Wit:
De novo construction of polyploid linkage maps using discrete graphical models. 1083-1093 - Changchun Xie, Yuet-Kin Leung, Aimin Chen, Ding-Xin Long, Catherine Hoyo, Shuk-Mei Ho:
Differential methylation values in differential methylation analysis. 1094-1097
- Emilio Fenoy, José M. G. Izarzugaza, Vanessa Isabell Jurtz, Søren Brunak, Morten Nielsen:
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. 1098-1107 - Shixiong Zhang, Xiangtao Li, Qiuzhen Lin, Ka-Chun Wong:
Synergizing CRISPR/Cas9 off-target predictions for ensemble insights and practical applications. 1108-1115 - Stavros Makrodimitris, Roeland C. H. J. van Ham, Marcel J. T. Reinders:
Improving protein function prediction using protein sequence and GO-term similarities. 1116-1124 - Manal Kalkatawi, Arturo Magana-Mora, Boris R. Jankovic, Vladimir B. Bajic:
DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions. 1125-1132 - Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon:
RNAdetect: efficient computational detection of novel non-coding RNAs. 1133-1141 - Min Li, Li Tang, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
SCOP: a novel scaffolding algorithm based on contig classification and optimization. 1142-1150
- Lucas Czech, Pierre Barbera, Alexandros Stamatakis:
Methods for automatic reference trees and multilevel phylogenetic placement. 1151-1158 - Ivana Pilizota, Clément-Marie Train, Adrian M. Altenhoff, Henning Redestig, Christophe Dessimoz:
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. 1159-1166
- Jinmyung Jung, Yeeok Kang, Hyojung Paik, Mijin Kwon, Hasun Yu, Doheon Lee:
Deconvoluting essential gene signatures for cancer growth from genomic expression in compound-treated cells. 1167-1173
- Anwoy Kumar Mohanty, Dana Vuzman, Laurent C. Francioli, Christopher Cassa, Ágnes Tóth-Petróczy, Shamil R. Sunyaev:
novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data. 1174-1180 - Haohan Wang, Benjamin J. Lengerich, Bryon Aragam, Eric P. Xing:
Precision Lasso: accounting for correlations and linear dependencies in high-dimensional genomic data. 1181-1187
- Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone:
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. 1188-1196 - Zicheng Hu, Benjamin S. Glicksberg, Atul J. Butte:
Robust prediction of clinical outcomes using cytometry data. 1197-1203 - Andrew J. Sedgewick, Kristina Buschur, Ivy Shi, Joseph D. Ramsey, Vineet K. Raghu, Dimitris V. Manatakis, Yingze Zhang, Jessica Bon, Divay Chandra, Chad Karoleski, Frank C. Sciurba, Peter Spirtes, Clark Glymour, Panayiotis V. Benos:
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis. 1204-1212
- Erin Oerton, Ian Roberts, Patrick S. H. Lewis, Tim Guilliams, Andreas Bender:
Understanding and predicting disease relationships through similarity fusion. 1213-1220
- Axel Theorell, Johannes Seiffarth, Alexander Grünberger, Katharina Nöh:
When a single lineage is not enough: Uncertainty-Aware Tracking for spatio-temporal live-cell image analysis. 1221-1228
Phylogenetics
- Joseph T. Miller, Rebecca Pirzl, Dan Rosauer, Garry Jolley-Rogers, Temi Varghese:
Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity. 1229-1230
- Jan Jelínek, Josef Pánek:
cpPredictor: a web server for template-based prediction of RNA secondary structure. 1231-1233 - Yi He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor F. Muñoz:
Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts. 1234-1236 - Miha Skalic, Gerard Martínez-Rosell, José Jiménez, Gianni De Fabritiis:
PlayMolecule BindScope: large scale CNN-based virtual screening on the web. 1237-1238 - Sabri Hamad, Gianluca Adornetto, J. Jesús Naveja, Aakash Chavan Ravindranath, Johannes Raffler, Mónica Campillos:
HitPickV2: a web server to predict targets of chemical compounds. 1239-1240 - Sergio Decherchi, Andrea Spitaleri, John E. Stone, Walter Rocchia:
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. 1241-1243
- Jiangshan J. Shen, Chao Yang, Yong-Fei Wang, Ting-You Wang, Mengbiao Guo, Yu-Lung Lau, Xuejun Zhang, Yujun Sheng, Wanling Yang:
HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels. 1244-1246
- Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan:
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. 1247-1248
- Kai Li, Marc Vaudel, Bing Zhang, Yan Ren, Bo Wen:
PDV: an integrative proteomics data viewer. 1249-1251 - Graham M. Hughes, Emma C. Teeling:
AGILE: an assembled genome mining pipeline. 1252-1254 - Matthieu Marbac, Mohammed Sedki:
VarSelLCM: an R/C++ package for variable selection in model-based clustering of mixed-data with missing values. 1255-1257
- Gabriele Sales, Enrica Calura, Chiara Romualdi:
metaGraphite-a new layer of pathway annotation to get metabolite networks. 1258-1260
- Nathan Heath Patterson, Ethan Yang, Elizabeth-Ann Kranjec, Pierre Chaurand:
Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes. 1261-1262
Volume 35, Number 8, April 2019
Genome Analysis
- Roozbeh Dehghannasiri, Linda Szabo, Julia Salzman:
Ambiguous splice sites distinguish circRNA and linear splicing in the human genome. 1263-1268
Genome Analysis
- Yuchen Yang, Ruth Huh, Houston W. Culpepper, Yuan Lin, Michael I. Love, Yun Li:
SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data. 1269-1277 - Xuesi Dong, Lijuan Lin, Ruyang Zhang, Yang Zhao, David C. Christiani, Yongyue Wei, Feng Chen:
TOBMI: trans-omics block missing data imputation using a k-nearest neighbor weighted approach. 1278-1283 - Jaroslav Budis, Juraj Gazdarica, Ján Radvánszky, Gábor Szücs, Marcel Kucharík, Lucia Strieskova, Iveta Gazdaricova, Maria Harsanyova, Frantisek Duris, Gabriel Minarik, Martina Sekelska, Bálint Nagy, Ján Turna, Tomás Szemes:
Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing. 1284-1291
- Hussein Al-Asadi, Kushal K. Dey, John Novembre, Matthew Stephens:
Inference and visualization of DNA damage patterns using a grade of membership model. 1292-1298 - Chang Xu, Xiujing Gu, Raghavendra Padmanabhan, Zhong Wu, Quan Peng, John DiCarlo, Yexun Wang:
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers. 1299-1309 - Jaroslav Budis, Marcel Kucharík, Frantisek Duris, Juraj Gazdarica, Michaela Zrubcová, Andrej Ficek, Tomás Szemes, Brona Brejová, Ján Radvánszky:
Dante: genotyping of known complex and expanded short tandem repeats. 1310-1317 - Patrick V. Holec, Joseph Berleant, Mark Bathe, Michael E. Birnbaum:
A Bayesian framework for high-throughput T cell receptor pairing. 1318-1325 - Leyi Wei, Shasha Luan, Luis Augusto Eijy Nagai, Ran Su, Quan Zou:
Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species. 1326-1333
- Maciej Wójcikowski, Michal Kukielka, Marta M. Stepniewska-Dziubinska, Pawel Siedlecki:
Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions. 1334-1341 - Daniel Wiegreffe, Daniel Alexander, Peter F. Stadler, Dirk Zeckzer:
RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. 1342-1349
- Kevin Y. X. Wang, Alexander M. Menzies, Ines P. Silva, James S. Wilmott, Yibing Yan, Matthew Wongchenko, Richard F. Kefford, Richard A. Scolyer, Georgina V. Long, Garth Tarr, Samuel Müller, Jean Yee Hwa Yang:
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays. 1350-1357 - Trang T. Le, Ryan J. Urbanowicz, Jason H. Moore, Brett A. McKinney:
STatistical Inference Relief (STIR) feature selection. 1358-1365
- Bin Guo, Baolin Wu:
Powerful and efficient SNP-set association tests across multiple phenotypes using GWAS summary data. 1366-1372 - Qiuying Sha, Zhenchuan Wang, Xiao Zhang, Shuanglin Zhang:
A clustering linear combination approach to jointly analyze multiple phenotypes for GWAS. 1373-1379
- Silvia Calderazzo, Marco Brancaccio, Bärbel Finkenstädt:
Filtering and inference for stochastic oscillators with distributed delays. 1380-1387 - Ishita K. Khan, Aashish Jain, Reda Rawi, Halima Bensmail, Daisuke Kihara:
Prediction of protein group function by iterative classification on functional relevance network. 1388-1394
- Yuan Luo, Chengsheng Mao, Yiben Yang, Fei Wang, Faraz S. Ahmad, Donna Arnett, Marguerite R. Irvin, Sanjiv J. Shah:
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization. 1395-1403
- Albert Casanovas, Óscar Gallardo, Montserrat Carrascal, Joaquin Abian:
TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. 1404-1413
Genome Analysis
- Cheng-Kai Shiau, Jia-Hsin Huang, Huai-Kuang Tsai:
CATANA: a tool for generating comprehensive annotations of alternative transcript events. 1414-1415 - Tuan Trieu, Oluwatosin Oluwadare, Julia Wopata, Jianlin Cheng:
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. 1416-1418 - Nengjun Yi, Zaixiang Tang, Xinyan Zhang, Boyi Guo:
BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology. 1419-1421 - Evgeny Anatskiy, Devon Patrick Ryan, Björn A. Grüning, Laura Arrigoni, Thomas Manke, Ulrike Bönisch:
Parkour LIMS: high-quality sample preparation in next generation sequencing. 1422-1424
- Benjamin D. Lee:
Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. 1425-1426
- Oana M. Enache, David L. Lahr, Ted E. Natoli, Lev Litichevskiy, David Wadden, Corey Flynn, Joshua Gould, Jacob K. Asiedu, Rajiv Narayan, Aravind Subramanian:
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices. 1427-1429 - Xian Liu, Mingfei Han, Chen Zhao, Cheng Chang, Yunping Zhu, Changhui Ge, Ronghua Yin, Yiqun Zhan, Changyan Li, Miao Yu, Fuchu He, Xiaoming Yang:
KeggExp: a web server for visual integration of KEGG pathways and expression profile data. 1430-1432
- Junfang Chen, Dietmar Lippold, Josef Frank, William Rayner, Andreas Meyer-Lindenberg, Emanuel Schwarz:
Gimpute: an efficient genetic data imputation pipeline. 1433-1435
- Minoo Ashtiani, Mehdi Mirzaie, Mohieddin Jafari:
CINNA: an R/CRAN package to decipher Central Informative Nodes in Network Analysis. 1436-1437
- Yi Zhang, Mohith Manjunath, Yeonsung Kim, Joerg Heintz, Jun S. Song:
SequencEnG: an interactive knowledge base of sequencing techniques. 1438-1440 - Alejandro Brenes, Angus I. Lamond:
The Encyclopedia of Proteome Dynamics: the KinoViewer. 1441-1442
Databases and Ontologies
- Bansho Masutani, Shinichi Morishita:
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer. 1443
Volume 35, Number 9, May 2019
Genome Analysis
- (Withdrawn) RETRACTED: LFQC: a lossless compression algorithm for FASTQ files. e1-e7
Genome Analysis
- Chen Cao, Lauren Mak, Guangxu Jin, Paul Gordon, Kai Ye, Quan Long:
PRESM: personalized reference editor for somatic mutation discovery in cancer genomics. 1445-1452 - Hai Yang, Rui Chen, Quan Wang, Qiang Wei, Ying Ji, Guangze Zheng, Xue Zhong, Nancy J. Cox, Bingshan Li:
De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. 1453-1460
- Pieter Meysman, Nicolas De Neuter, Sofie Gielis, Danh Bui Thi, Benson Ogunjimi, Kris Laukens:
On the viability of unsupervised T-cell receptor sequence clustering for epitope preference. 1461-1468 - Chao-Qin Feng, Zhao-Yue Zhang, Xiao-Juan Zhu, Yan Lin, Wei Chen, Hua Tang, Hao Lin:
iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators. 1469-1477 - Néli José da Fonseca Jr., Marcelo Querino Lima Afonso, Lucas Carrijo de Oliveira, Lucas Bleicher:
A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection. 1478-1485 - Dengke Zhao, William D. Baez, Kurt Fredrick, Ralf Bundschuh:
RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling. 1486-1493 - Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin:
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. 1494-1502
- Wen Torng, Russ B. Altman:
High precision protein functional site detection using 3D convolutional neural networks. 1503-1512 - Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli:
A natural upper bound to the accuracy of predicting protein stability changes upon mutations. 1513-1517
- Alexander M. Crowell, Casey S. Greene, Jennifer J. Loros, Jay C. Dunlap:
Learning and Imputation for Mass-spec Bias Reduction (LIMBR). 1518-1526 - Jianghong Yang, Ao Li, Yongqiang Li, Xiangqian Guo, Minghui Wang:
A novel approach for drug response prediction in cancer cell lines via network representation learning. 1527-1535 - Chih-Hsu Lin, Daniel M. Konecki, Meng Liu, Stephen J. Wilson, Huda Nassar, Angela D. Wilkins, David F. Gleich, Olivier Lichtarge:
Multimodal network diffusion predicts future disease-gene-chemical associations. 1536-1543
- Florian Plaza Oñate, Emmanuelle Le Chatelier, Mathieu Almeida, Alessandra C. L. Cervino, Franck Gauthier, Frédéric Magoulès, S. Dusko Ehrlich, Matthieu Pichaud:
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. 1544-1552 - Sampo Pyysalo, Simon Baker, Imran Ali, Stefan Haselwimmer, Tejas Shah, Andrew Young, Yufan Guo, Johan Högberg, Ulla Stenius, Masashi Narita, Anna Korhonen:
LION LBD: a literature-based discovery system for cancer biology. 1553-1561
- Adriano Barbosa-Silva, Dorina Bratfalean, Wei Gu, Venkata P. Satagopam, Paul Houston, Lauren B. Becnel, Serge Eifes, Fabien Richard, Andreas Tielmann, Sascha Herzinger, Kavita Rege, Rudi Balling, Paul Peeters:
Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART. 1562-1565 - Shengsong Xie, Qin Zhu, Wubin Qu, Zhong Xu, Xiangdong Liu, Xinyun Li, Shijun Li, Wubin Ma, Yiliang Miao, Lisheng Zhang, Xiaoyong Du, Wuzi Dong, Haiwei Li, Changzhi Zhao, Yunlong Wang, Yaping Fang, Shuhong Zhao:
sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs. 1566-1572
Genome Analysis
- Li Chen, Ye Wang, Bing Yao, Amit Mitra, Xu Wang, Xiao Qin:
TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction. 1573-1575
- Xavier Bofill-De Ros, Kevin Chen, Susanna Chen, Nikola Tesic, Dusan Randjelovic, Nikola Skundric, Svetozar Nesic, Vojislav Varjacic, Elizabeth H. Williams, Raunaq Malhotra, Minjie Jiang, Shuo Gu:
QuagmiR: a cloud-based application for isomiR big data analytics. 1576-1578 - Tamsen Dunn, Gwenn Berry, Dorothea Emig-Agius, Yu Jiang, Serena Lei, Anita Iyer, Nitin Udar, Han-Yu Chuang, Jeff Hegarty, Michael Dickover, Brandy Klotzle, Justin Robbins, Marina Bibikova, Marc Peeters, Michael Strömberg:
Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data. 1579-1581 - Thomas A. Hopf, Anna G. Green, Benjamin Schubert, Sophia Mersmann, Charlotta Schärfe, John Ingraham, Ágnes Tóth-Petróczy, Kelly Brock, Adam J. Riesselman, Perry Palmedo, Chan Kang, Robert P. Sheridan, Eli J. Draizen, Christian Dallago, Chris Sander, Debora S. Marks:
The EVcouplings Python framework for coevolutionary sequence analysis. 1582-1584
- Anna Vangone, Jörg Schaarschmidt, Panagiotis I. Koukos, Cunliang Geng, Nevia Citro, Mikael E. Trellet, Li C. Xue, Alexandre M. J. J. Bonvin:
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. 1585-1587 - Sebastian Stolzenberg:
PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles. 1588-1590 - Gideon Lapidoth, Jake Parker, Jaime Prilusky, Sarel Jacob Fleishman:
AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains. 1591-1593
- Marco Trevisan-Herraz, Navratan Bagwan, Fernando García-Marqués, José Manuel Rodriguez, Inmaculada Jorge, Iakes Ezkurdia, Elena Bonzon-Kulichenko, Jesús Vázquez:
SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments. 1594-1596 - Tianzhou Ma, Zhiguang Huo, Anche Kuo, Li Zhu, Zhou Fang, Xiangrui Zeng, Chien-Wei Lin, Silvia Liu, Lin Wang, Peng Liu, Tanbin Rahman, Lun-Ching Chang, Sunghwan Kim, Jia Li, Yongseok Park, Chi Song, Steffi Oesterreich, Etienne Sibille, George C. Tseng:
MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis. 1597-1599
- Maxwell Lewis Neal, Christopher T. Thompson, Karam G. Kim, Ryan C. James, Daniel L. Cook, Brian E. Carlson, John H. Gennari:
SemGen: a tool for semantics-based annotation and composition of biosimulation models. 1600-1602 - Le Yuan, Yu Tian, Shaozhen Ding, Yanfang Liu, Fu Chen, Tong Zhang, Weizhong Tu, Junni Chen, Qian-Nan Hu:
PrecursorFinder: a customized biosynthetic precursor explorer. 1603-1604 - Maria Suprun, Mayte Suárez-Fariñas:
PlateDesigner: a web-based application for the design of microplate experiments. 1605-1607 - Florian Schmidt, Fabian Kern, Peter Ebert, Nina Baumgarten, Marcel H. Schulz:
TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis. 1608-1609
- Marcus A. Badgeley, Manway Liu, Benjamin S. Glicksberg, Mark M. Shervey, John R. Zech, Khader Shameer, Joseph Lehar, Eric K. Oermann, Michael V. McConnell, Thomas M. Snyder, Joel T. Dudley:
CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis. 1610-1612
Sequence Analysis
- Nidhi Shah, Michael G. Nute, Tandy J. Warnow, Mihai Pop:
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. 1613-1614
Genome Analysis
- Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve:
Colocalization analyses of genomic elements: approaches, recommendations and challenges. 1615-1624
Volume 35, Number 10, May 2019
Genome Analysis
- Hadi Fanaee-T, Magne Thoresen:
Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization. 1625-1633 - Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, Michal Ziv-Ukelson:
CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes. 1634-1643 - Can Yang, Xiang Wan, Xinyi Lin, Mengjie Chen, Xiang Zhou, Jin Liu:
CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information. 1644-1652 - Hao Ding, Michael F. Sharpnack, Chao Wang, Kun Huang, Raghu Machiraju:
Integrative cancer patient stratification via subspace merging. 1653-1659
- Hailin Hu, An Xiao, Sai Zhang, Yangyang Li, Xuanling Shi, Tao Jiang, Linqi Zhang, Lei Zhang, Jianyang Zeng:
DeepHINT: understanding HIV-1 integration via deep learning with attention. 1660-1667
- Anamaria Crisan, Jennifer L. Gardy, Tamara Munzner:
A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT. 1668-1676 - Ki-Hok Liao, Wing-Kai Hon, Chuan Yi Tang, Wen-Ping Hsieh:
MetaSMC: a coalescent-based shotgun sequence simulator for evolving microbial populations. 1677-1685
- Saisai Sun, Qi Wu, Zhenling Peng, Jianyi Yang:
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles. 1686-1691 - Gang Hu, Zhonghua Wu, Christopher J. Oldfield, Chen Wang, Lukasz A. Kurgan:
Quality assessment for the putative intrinsic disorder in proteins. 1692-1700
- Divya Niveditha, Sudeshna Mukherjee, Syamantak Majumder, Rajdeep Chowdhury, Shibasish Chowdhury:
A global transcriptomic pipeline decoding core network of genes involved in stages leading to acquisition of drug-resistance to cisplatin in osteosarcoma cells. 1701-1711 - Hui-Zeng Sun, Ke Zhao, Mi Zhou, Yanhong Chen, Le Luo Guan:
Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle. 1712-1719
- Louis Raynal, Jean-Michel Marin, Pierre Pudlo, Mathieu Ribatet, Christian P. Robert, Arnaud Estoup:
ABC random forests for Bayesian parameter inference. 1720-1728 - Mingwei Dai, Xiang Wan, Hao Peng, Yao Wang, Yue Liu, Jin Liu, Zongben Xu, Can Yang:
Joint analysis of individual-level and summary-level GWAS data by leveraging pleiotropy. 1729-1736
- Da Chen Emily Koo, Richard Bonneau:
Towards region-specific propagation of protein functions. 1737-1744 - Xuan Wang, Yu Zhang, Xiang Ren, Yuhao Zhang, Marinka Zitnik, Jingbo Shang, Curtis P. Langlotz, Jiawei Han:
Cross-type biomedical named entity recognition with deep multi-task learning. 1745-1752
- Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C. Berrios, Peter B. Tran, Jonathan M. Galazka, Sylvain V. Costes:
GeneLab: Omics database for spaceflight experiments. 1753-1759
Genome Analysis
- Weihua Pan, Stefano Lonardi:
Accurate detection of chimeric contigs via Bionano optical maps. 1760-1762 - Pieter J. K. Libin, Koen Deforche, Ana B. Abecasis, Kristof Theys:
VIRULIGN: fast codon-correct alignment and annotation of viral genomes. 1763-1765
- Tony E. Lewis, Ian Sillitoe, Jonathan G. Lees:
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly. 1766-1767 - Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, William J. Salerno, Gerard D. Schellenberg, Li-San Wang:
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. 1768-1770
- Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis:
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes. 1771-1773
- Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P. Lewis, Bruck Taddese, Jinwoo Leem, Charlotte M. Deane:
SCALOP: sequence-based antibody canonical loop structure annotation. 1774-1776 - Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou:
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. 1777-1779
- Jason R. Phillips, Daniel L. Svoboda, Arpit Tandon, Shyam Patel, Alex Sedykh, Deepak Mav, Byron Kuo, Carole L. Yauk, Longlong Yang, Russell S. Thomas, Jeff S. Gift, J. Allen Davis, Louis Olszyk, B. Alex Merrick, Richard S. Paules, Fred Parham, Trey Saddler, Ruchir R. Shah, Scott S. Auerbach:
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow. 1780-1782
- Arthur T. O. Melo, Iago Hale:
Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP. 1783-1785 - Chi Zhang, Shan-Shan Dong, Jun-Yang Xu, Weiming He, Tie-Lin Yang:
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. 1786-1788
- Chongyang Tan, Wei Cui, Xinping Cui, Kang Ning:
Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling. 1789-1791 - Minzhe Zhang, Sangin Lee, Bo Yao, Guanghua Xiao, Lin Xu, Yang Xie:
DIGREM: an integrated web-based platform for detecting effective multi-drug combinations. 1792-1794 - Yann Beauxis, Grégory Genta-Jouve:
MetWork: a web server for natural products anticipation. 1795-1796
- Han Cao, Jiayu Zhou, Emanuel Schwarz:
RMTL: an R library for multi-task learning. 1797-1798 - Axel J. Soto, Piotr Przybyla, Sophia Ananiadou:
Thalia: semantic search engine for biomedical abstracts. 1799-1801
- Georges Hattab, Tim W. Nattkemper:
SeeVis - 3D space-time cube rendering for visualization of microfluidics image data. 1802-1804
Volume 35, Number 11, June 2019
Genome Analysis
- Beibei Ru, Jianlong Sun, Qingzheng Kang, Yin Tong, Jiangwen Zhang:
A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. 1805-1812 - Anton Pirogov, Peter Pfaffelhuber, Angelika Börsch-Haubold, Bernhard Haubold:
High-complexity regions in mammalian genomes are enriched for developmental genes. 1813-1819
- Wei Zheng, Le Yang, Robert J. Genco, Jean Wactawski-Wende, Michael Buck, Yijun Sun:
SENSE: Siamese neural network for sequence embedding and alignment-free comparison. 1820-1828 - Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach:
Alignment-free clustering of UMI tagged DNA molecules. 1829-1836 - Zhen Cao, Shihua Zhang:
Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction. 1837-1843 - Loris Nanni, Sheryl Brahnam:
Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins. 1844-1851
- Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab:
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. 1852-1861 - Rui Borges, João Paulo Machado, Cidália Gomes, Ana Paula Rocha, Agostinho Antunes:
Measuring phylogenetic signal between categorical traits and phylogenies. 1862-1869
- Sebastian Daberdaku, Carlo Ferrari:
Antibody interface prediction with 3D Zernike descriptors and SVM. 1870-1876
- Yumi Kawamura, Shinsuke Koyama, Ryo Yoshida:
Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing. 1877-1884 - Anna Papiez, Michal Marczyk, Joanna Polanska, Andrzej Polanski:
BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm. 1885-1892 - Ruiqing Zheng, Min Li, Xiang Chen, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks. 1893-1900
- Mary D. Fortune, Chris Wallace:
simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics. 1901-1906 - Tzipi Braun, Antonio V. Bordería, Cyril Barbezange, Marco Vignuzzi, Yoram Louzoun:
Long-term context-dependent genetic adaptation of the viral genetic cloud. 1907-1915
- Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Nikita Harvey, Beatriz Jiménez, Kazuhiro Sonomura, Taka-Aki Sato, Fumihiko Matsuda, Pierre A. Zalloua, Dominique Gauguier, Jeremy K. Nicholson, Marc-Emmanuel Dumas:
pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra. 1916-1922 - Yonghyun Nam, Jong Ho Jhee, Junhee Cho, Ji-Hyun Lee, Hyunjung Shin:
Disease gene identification based on generic and disease-specific genome networks. 1923-1930
- Milton Pividori, Andres Cernadas, Luis A. de Haro, Fernando Carrari, Georgina Stegmayer, Diego H. Milone:
Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization. 1931-1939
- Johannes Leuschner, Maximilian Schmidt, Pascal Fernsel, Delf Lachmund, Tobias Boskamp, Peter Maass:
Supervised non-negative matrix factorization methods for MALDI imaging applications. 1940-1947 - Meiling Wang, Xiaoke Hao, Jiashuang Huang, Wei Shao, Daoqiang Zhang:
Discovering network phenotype between genetic risk factors and disease status via diagnosis-aligned multi-modality regression method in Alzheimer's disease. 1948-1957
Genome Analysis
- Xu Ren, Pei Fen Kuan:
methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. 1958-1959 - Roberto Vera Alvarez, Lorinc Sándor Pongor, Leonardo Mariño-Ramírez, David Landsman:
TPMCalculator: one-step software to quantify mRNA abundance of genomic features. 1960-1962 - Rebecca Rose, Olga Golosova, Dmitrii Sukhomlinov, Aleksey Tiunov, Mattia Prosperi:
Flexible design of multiple metagenomics classification pipelines with UGENE. 1963-1965
- Ashish Jain, Geetu Tuteja:
TissueEnrich: Tissue-specific gene enrichment analysis. 1966-1967
- Abbas A. Rizvi, Ezgi Karaesmen, Martin Morgan, Leah Preus, Junke Wang, Michael Sovic, Theresa Hahn, Lara E. Sucheston-Campbell:
gwasurvivr: an R package for genome-wide survival analysis. 1968-1970 - Milton Pividori, Hae Kyung Im:
ukbREST: efficient and streamlined data access for reproducible research in large biobanks. 1971-1973
- Tiago Chedraoui Silva, Simon G. Coetzee, Nicole Gull, Lijing Yao, Dennis J. Hazelett, Houtan Noushmehr, De-Chen Lin, Benjamin P. Berman:
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. 1974-1977
- Christos Kopanos, Vasilis Tsiolkas, Alexandros Kouris, Charles E. Chapple, Monica Albarca Aguilera, Richard Meyer, Andreas Massouras:
VarSome: the human genomic variant search engine. 1978-1980 - Matthew C. Canver, Daniel E. Bauer, Takahiro Maeda, Luca Pinello:
DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens. 1981-1984
Databases and Ontologies
- Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, William J. Salerno, Gerard D. Schellenberg, Li-San Wang:
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. 1985
Volume 35, Number 12, June 2019
Genome analysis
- Zhi-Kai Yang, Hao Luo, Yanming Zhang, Baijing Wang, Feng Gao:
Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome. 1987-1991
Genome analysis
- Eva-Maria Huessler, Martin Schäfer, Holger Schwender, Pablo Landgraf:
BayMAP: a Bayesian hierarchical model for the analysis of PAR-CLIP data. 1992-2000 - Eran Barash, Neta Sal-Man, Sivan Sabato, Michal Ziv-Ukelson:
BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM. 2001-2008 - Md-Nafiz Hamid, Iddo Friedberg:
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. 2009-2016
- Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow:
Bastion3: a two-layer ensemble predictor of type III secreted effectors. 2017-2028 - Mark Howison, Mia Coetzer, Rami Kantor:
Measurement error and variant-calling in deep Illumina sequencing of HIV. 2029-2035 - Miguel Correa Marrero, Richard G. H. Immink, Dick de Ridder, Aalt D. J. van Dijk:
Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis. 2036-2042 - Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys, Szymon Grabowski:
Whisper: read sorting allows robust mapping of DNA sequencing data. 2043-2050 - Li Xue, Bin Tang, Wei Chen, Jiesi Luo:
DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence. 2051-2057 - Wei Shi, Jianhua Chen, Mao Luo, Min Chen:
High efficiency referential genome compression algorithm. 2058-2065 - Yuansheng Liu, Zu-Guo Yu, Marcel E. Dinger, Jinyan Li:
Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression. 2066-2074 - Fu-Ying Dao, Hao Lv, Fang Wang, Chao-Qin Feng, Hui Ding, Wei Chen, Hao Lin:
Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique. 2075-2083
- Anqi Zhu, Joseph G. Ibrahim, Michael I. Love:
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. 2084-2092 - Gregory J. Hunt, Saskia Freytag, Melanie Bahlo, Johann Gagnon-Bartsch:
dtangle: accurate and robust cell type deconvolution. 2093-2099
- Mengshi Zhou, Yang Chen, Rong Xu:
A Drug-Side Effect Context-Sensitive Network approach for drug target prediction. 2100-2107 - Mahdi Shafiee Kamalabad, Alexander Martin Heberle, Kathrin Thedieck, Marco Grzegorczyk:
Partially non-homogeneous dynamic Bayesian networks based on Bayesian regression models with partitioned design matrices. 2108-2117 - Jacob D. Davis, Eberhard O. Voit:
Metrics for regulated biochemical pathway systems. 2118-2124
- João C. Marques, Michael B. Orger:
Clusterdv: a simple density-based clustering method that is robust, general and automatic. 2125-2132
- Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. 2133-2140
- Hao Yuan, Lei Cai, Zhengyang Wang, Xia Hu, Shaoting Zhang, Shuiwang Ji:
Computational modeling of cellular structures using conditional deep generative networks. 2141-2149
Genome analysis
- Robert D. Stewart, Marc D. Auffret, Timothy J. Snelling, Rainer Roehe, Mick Watson:
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). 2150-2152 - Arthur Zwaenepoel, Yves Van de Peer:
wgd - simple command line tools for the analysis of ancient whole-genome duplications. 2153-2155 - Marek S. Wiewiórka, Anna Lesniewska, Agnieszka Szmurlo, Kacper Stepien, Mateusz Borowiak, Michal J. Okoniewski, Tomasz Gambin:
SeQuiLa: an elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals. 2156-2158
- Thomas Moerman, Sara Aibar Santos, Carmen Bravo González-Blas, Jaak Simm, Yves Moreau, Jan Aerts, Stein Aerts:
GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. 2159-2161
- Regev Schweiger, Yaniv Erlich, Shai Carmi:
FactorialHMM: fast and exact inference in factorial hidden Markov models. 2162-2164
- Alireza Khatamian, Evan O. Paull, Andrea Califano, Jiyang Yu:
SJARACNe: a scalable software tool for gene network reverse engineering from big data. 2165-2166
Systems biology
- (Withdrawn) RETRACTED: Analysis and prediction of β-turn types using multinomial logistic regression and artificial neural network. e8-e15
Volume 35, Number 13, July 2019
Genome Analysis
- Axel Poulet, Ben Li, Tristan Dubos, Juan Carlos Rivera-Mulia, David M. Gilbert, Zhaohui S. Qin:
RT States: systematic annotation of the human genome using cell type-specific replication timing programs. 2167-2176 - Richard C. Brown, Gerton Lunter:
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs. 2177-2184 - Rodrigo Santamaría, Roberto Therón, Laura Durán, Alicia García-Holgado, Sara González, Mar Sánchez, Francisco Antequera:
Genome-wide search of nucleosome patterns using visual analytics. 2185-2192
- Alexander Payne, Nadine Holmes, Vardhman K. Rakyan, Matthew Loose:
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. 2193-2198 - Carine Rey, Philippe Veber, Bastien Boussau, Marie Sémon:
CAARS: comparative assembly and annotation of RNA-Seq data. 2199-2207 - Ioannis A. Tamposis, Konstantinos D. Tsirigos, Margarita C. Theodoropoulou, Panagiota I. Kontou, Pantelis G. Bagos:
Semi-supervised learning of Hidden Markov Models for biological sequence analysis. 2208-2215 - Abdurrahman Elbasir, Balasubramanian Moovarkumudalvan, Khalid Kunji, Prasanna R. Kolatkar, Raghvendra Mall, Halima Bensmail:
DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction. 2216-2225
- Ameen Eetemadi, Ilias Tagkopoulos:
Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships. 2226-2234 - Jun Li, Alicia T. Lamere:
DiPhiSeq: robust comparison of expression levels on RNA-Seq data with large sample sizes. 2235-2242
- Eran Elhaik, Desmond M. Ryan:
Pair Matcher (PaM): fast model-based optimization of treatment/case-control matches. 2243-2250 - Bin Guo, Baolin Wu:
Integrate multiple traits to detect novel trait-gene association using GWAS summary data with an adaptive test approach. 2251-2257
- T. Van Du Tran, Sébastien Moretti, Alix T. Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni:
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. 2258-2266 - Fiorenza Gianì, Giulia Russo, Marzio Pennisi, Laura Sciacca, Francesco Frasca, Francesco Pappalardo:
Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. 2267-2275
- Samaneh Kouchaki, Yang Yang, Timothy M. Walker, A. Sarah Walker, Daniel J. Wilson, Timothy E. A Peto, Derrick W. Crook, CRyPTIC Consortium, David A. Clifton:
Application of machine learning techniques to tuberculosis drug resistance analysis. 2276-2282
- Jamie Soul, Tim E. Hardingham, Ray P. Boot-Handford, Jean-Marc Schwartz:
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. 2283-2290
- Henrik Failmezger, Ezgi Dursun, Sebastian Dümcke, Max Endele, Don Poron, Timm Schroeder, Anne Krug, Achim Tresch:
Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging. 2291-2299
Genome Analysis
- Yasminka A Jakubek, F. Anthony San Lucas, Paul Scheet:
Directional allelic imbalance profiling and visualization from multi-sample data with RECUR. 2300-2302 - Olga Kunyavskaya, Andrey D. Prjibelski:
SGTK: a toolkit for visualization and assessment of scaffold graphs. 2303-2305 - Jikai Zhang, Haidong Lan, Yuandong Chan, Yuan Shang, Bertil Schmidt, Weiguo Liu:
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. 2306-2308 - Moritz Schaefer, Djork-Arné Clevert, Bertram Weiss, Andreas Steffen:
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. 2309-2310 - Laurent Lacroix:
G4HunterApps. 2311-2312 - Gang Peng, Rashaun Wilson, Yishuo Tang, TuKiet T. Lam, Angus C. Nairn, Kenneth R. Williams, Hongyu Zhao:
ProteomicsBrowser: MS/proteomics data visualization and investigation. 2313-2314 - Jannah Shamsani, Stephen H. Kazakoff, Irina M. Armean, Will McLaren, Michael T. Parsons, Bryony A Thompson, Tracy A. O'Mara, Sarah E. Hunt, Nicola Waddell, Amanda B. Spurdle:
A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. 2315-2317 - Matthew D. Czajkowski, Daniel P. Vance, Steven A. Frese, Giorgio Casaburi:
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets. 2318-2319
- Ritika Ramani, Katie Krumholz, Yi-Fei Huang, Adam C. Siepel:
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. 2320-2322
- Jacob D. Durrant:
BlendMol: advanced macromolecular visualization in Blender. 2323-2325
- Tobias Jakobi, Alexey Uvarovskii, Christoph Dieterich:
circtools - a one-stop software solution for circular RNA research. 2326-2328 - Saeid Parvandeh, Brett A. McKinney:
EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks. 2329-2331
- Federico Baldini, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele:
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. 2332-2334 - Bob Chen, Charles A. Herring, Ken S. Lau:
pyNVR: investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. 2335-2337 - Hongyang Li, Shuai Hu, Nouri Neamati, Yuanfang Guan:
TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction. 2338-2339
- Taras Sych, Thomas Schubert, Romain Vauchelles, Josef Madl, Ramin Omidvar, Roland Thuenauer, Ludovic Richert, Yves Mély, Winfried Römer:
GUV-AP: multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles. 2340-2342
Data and Text Mining
- Stefano Nembrini:
Bias in the intervention in prediction measure in random forests: illustrations and recommendations. 2343-2345
Data and Text Mining
- Siamak Zamani Dadaneh, Mingyuan Zhou, Xiaoning Qian:
Bayesian negative binomial regression for differential expression with confounding factors. 2346 - Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. 2347 - Zhenwei Dai, Sunny Hei Wong, Jun Yu, Yingying Wei:
Batch effects correction for microbiome data with Dirichlet-multinomial regression. 2348
Volume 35, Number 14, July 2019
Sequence Analysis
- Vikram Alva, Andrei N. Lupas:
Histones predate the split between bacteria and archaea. 2349-2353
Genome Analysis
- Alexander J. Nash, Boris Lenhard:
A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates. 2354-2361 - Catharina Lippmann, Alfred Ultsch, Jörn Lötsch:
Computational functional genomics-based reduction of disease-related gene sets to their key components. 2362-2370 - Zhihao Xia, Yu Li, Bin Zhang, Zhongxiao Li, Yuhui Hu, Wei Chen, Xin Gao:
DeeReCT-PolyA: a robust and generic deep learning method for PAS identification. 2371-2379
- Chang Sik Kim, Sumitra Mohan, Mahmood Ayub, Dominic G. Rothwell, Caroline Dive, Ged Brady, Crispin J. Miller:
In silico error correction improves cfDNA mutation calling. 2380-2385 - Duolin Wang, Yanchun Liang, Dong Xu:
Capsule network for protein post-translational modification site prediction. 2386-2394 - Xiaoying Wang, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma:
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. 2395-2402
- Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks. 2403-2410 - Seung Hwan Hong, Keehyoung Joo, Jooyoung Lee:
ConDo: protein domain boundary prediction using coevolutionary information. 2411-2417 - David Simoncini, Kam Y. J. Zhang, Thomas Schiex, Sophie Barbe:
A structural homology approach for computational protein design with flexible backbone. 2418-2426 - Amaya Jiménez, Slavica Jonic, Tomás Majtner, Joaquín Otón, Jose Luis Vilas, David Maluenda, Javier Mota, Erney Ramírez-Aportela, Marta Martínez, Yaiza Rancel, Joan Segura, Rubén Sánchez García, Roberto Melero, Laura del Cano, Pablo Conesa, Lars Skjaerven, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano:
Validation of electron microscopy initial models via small angle X-ray scattering curves. 2427-2433 - Shinichiro Tsuchiya, Issaku Yamada, Kiyoko F. Aoki-Kinoshita:
GlycanFormatConverter: a conversion tool for translating the complexities of glycans. 2434-2440
- Yang Shi, Mengqiao Wang, Weiping Shi, Ji-Hyun Lee, Huining Kang, Hui Jiang:
Accurate and efficient estimation of small P-values with the cross-entropy method: applications in genomic data analysis. 2441-2448
- Andrew Parton, Victoria McGilligan, Melody Chemaly, Maurice O'Kane, Steven Watterson:
New models of atherosclerosis and multi-drug therapeutic interventions. 2449-2457
- Johanna Schwarz, Dominik Heider:
GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making. 2458-2465
- Jimmy Ka Ho Chiu, Rick Twee-Hee Ong:
ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases. 2466-2474
- Xiongtao Ruan, Robert F. Murphy:
Evaluation of methods for generative modeling of cell and nuclear shape. 2475-2485
Genome Analysis
- Hong-Dong Li, Tianjian Bai, Erin Sandford, Margit Burmeister, Yuanfang Guan:
BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets. 2486-2488 - Tobias Rausch, Markus Hsi-Yang Fritz, Jan O. Korbel, Vladimir Benes:
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. 2489-2491 - Tania Cuppens, Thomas E. Ludwig, Pascal Trouvé, Emmanuelle Génin:
GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype. 2492-2494 - Gregory McInnes, Yosuke Tanigawa, Chris DeBoever, Adam Lavertu, Julia Eve Olivieri, Matthew Aguirre, Manuel A. Rivas:
Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics. 2495-2497
- Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, Mohammad R. K. Mofrad:
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. 2498-2500 - Jiamin Sun, Hao Liu, Jianxiao Liu, Shikun Cheng, Yong Peng, Qinghua Zhang, Jianbing Yan, Haijun Liu, Ling-Ling Chen:
CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. 2501-2503
- Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz:
iHam and pyHam: visualizing and processing hierarchical orthologous groups. 2504-2506
- Aleix Lafita, Pengfei Tian, Robert B. Best, Alex Bateman:
TADOSS: computational estimation of tandem domain swap stability. 2507-2508
- Thomas Sherman, Jack M. Fu, Robert B. Scharpf, Alexandre Bureau, Ingo Ruczinski:
Detection of rare disease variants in extended pedigrees using RVS. 2509-2511 - Bongsong Kim, Xinbin Dai, Wenchao Zhang, Zhaohong Zhuang, Darlene L. Sanchez, Thomas Lübberstedt, Yun Kang, Michael K. Udvardi, William D. Beavis, Shizhong Xu, Patrick X. Zhao:
GWASpro: a high-performance genome-wide association analysis server. 2512-2514
- Héléna A. Gaspar, Christopher Hübel, Gerome Breen:
Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes. 2515-2517
- Adrián Bazaga, Alfonso Valencia, María-José Rementeria:
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. 2518-2520 - Zheng Kuang, Ying Wang, Lei Li, Xiaozeng Yang:
miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants. 2521-2522 - Sergio Castillo-Lara, Josep F. Abril:
PPaxe: easy extraction of protein occurrence and interactions from the scientific literature. 2523-2524
Structural Bioinformatics
- Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli:
On the biases in predictions of protein stability changes upon variations: the INPS test case. 2525-2527
Structural Bioinformatics
- Wei Zhang, Jianzhu Ma, Trey Ideker:
Classifying tumors by supervised network propagation. 2528
ISMB/ECCB 2019 PROCEEDINGS
- Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac:
ISMB/ECCB 2019 Proceedings. i1-i2
- ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE. i3
- Martin Strazar, Lan Zagar, Jaka Kokosar, Vesna Tanko, Ales Erjavec, Pavlin G. Policar, Anze Staric, Janez Demsar, Gad Shaulsky, Vilas Menon, Andrew Lemire, Anup Parikh, Blaz Zupan:
scOrange - a tool for hands-on training of concepts from single-cell data analytics. i4-i12
- Camilo Valdes, Vitalii Stebliankin, Giri Narasimhan:
Large scale microbiome profiling in the cloud. i13-i22 - Sahar Tavakoli, Shibu Yooseph:
Learning a mixture of microbial networks using minorization-maximization. i23-i30 - Erfan Sayyari, Ban Kawas, Siavash Mirarab:
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. i31-i40
- Wei Vivian Li, Jingyi Jessica Li:
A statistical simulator scDesign for rational scRNA-seq experimental design. i41-i50 - Martin D. Muggli, Bahar Alipanahi, Christina Boucher:
Building large updatable colored de Bruijn graphs via merging. i51-i60 - Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen, Pavel A. Pevzner:
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. i61-i70 - André Hennig, Kay Nieselt:
Efficient merging of genome profile alignments. i71-i80 - Ali Ghaffaari, Tobias Marschall:
Fully-sensitive seed finding in sequence graphs using a hybrid index. i81-i89 - Song-Yao Zhang, Shao-Wu Zhang, Xiao-Nan Fan, Teng Zhang, Jia Meng, Yufei Huang:
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. i90-i98 - Qiao Liu, Hairong Lv, Rui Jiang:
hicGAN infers super resolution Hi-C data with generative adversarial networks. i99-i107 - Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje:
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts. i108-i116 - Krister M. Swenson, Mathieu Blanchette:
Large-scale mammalian genome rearrangements coincide with chromatin interactions. i117-i126 - Guillaume Marçais, Dan F. DeBlasio, Prashant Pandey, Carl Kingsford:
Locality-sensitive hashing for the edit distance. i127-i135 - Hirak Sarkar, Avi Srivastava, Rob Patro:
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level. i136-i144 - Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi:
Selfish: discovery of differential chromatin interactions via a self-similarity measure. i145-i153 - Lisa Handl, Adrin Jalali, Michael Scherer, Ralf Eggeling, Nico Pfeifer:
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data. i154-i163
- Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka:
ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra. i164-i172 - Avanti Shrikumar, Eva Prakash, Anshul Kundaje:
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs. i173-i182 - Hao Yang, Hao Chi, Wen-Feng Zeng, Wen-Jing Zhou, Si-Min He:
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework. i183-i190 - Michio Iwata, Longhao Yuan, Qibin Zhao, Yasuo Tabei, Francois Berenger, Ryusuke Sawada, Sayaka Akiyoshi, Momoko Hamano, Yoshihiro Yamanishi:
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm. i191-i199 - Yan Gao, Bo Liu, Yadong Wang, Yi Xing:
TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. i200-i207 - Dan Guo, Kylie A. Bemis, Catherine Rawlins, Jeffrey N. Agar, Olga Vitek:
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues. i208-i217
- Teppo Mikael Niinimäki, Mikko A. Heikkilä, Antti Honkela, Samuel Kaski:
Representation transfer for differentially private drug sensitivity prediction. i218-i224
- Xiao Yang, Yasushi Saito, Arjun A. Rao, Hyunsung John Kim, Pranav Singh, Eric Scott, Matthew Larson, Wenying Pan, Mohini Desai, Earl Hubbell:
Alignment-free filtering for cfNA fusion fragments. i225-i232 - Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang:
Efficient haplotype matching between a query and a panel for genealogical search. i233-i241 - Vikas Bansal:
Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes. i242-i248
- Renmin Han, Zhipeng Bao, Xiangrui Zeng, Tongxin Niu, Fa Zhang, Min Xu, Xin Gao:
A joint method for marker-free alignment of tilt series in electron tomography. i249-i259 - Ruogu Lin, Xiangrui Zeng, Kris Kitani, Min Xu:
Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms. i260-i268 - Ameni Trabelsi, Mohamed Chaabane, Asa Ben-Hur:
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. i269-i277 - Haoyang Zeng, David K. Gifford:
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding. i278-i283 - Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang:
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. i284-i294 - Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A. Hendrix, David H. Mathews:
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. i295-i304 - Muhao Chen, Chelsea J.-T. Ju, Guangyu Zhou, Xuelu Chen, Tianran Zhang, Kai-Wei Chang, Carlo Zaniolo, Wei Wang:
Multifaceted protein-protein interaction prediction based on Siamese residual RCNN. i305-i314 - Azat M. Tagirdzhanov, Alexander Shlemov, Alexey A. Gurevich:
NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches. i315-i323 - Jiansheng Wu, Ben Liu, Wallace K. B. Chan, Weijian Wu, Tao Pang, Haifeng Hu, Shancheng Yan, Xiaoyan Ke, Yang Zhang:
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. i324-i332 - Zichao Yan, Eric Lécuyer, Mathieu Blanchette:
Prediction of mRNA subcellular localization using deep recurrent neural networks. i333-i342 - Jian Zhang, Lukasz A. Kurgan:
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. i343-i353 - Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, Rolf Backofen:
ShaKer: RNA SHAPE prediction using graph kernel. i354-i359 - Dinithi Sumanaweera, Lloyd Allison, Arun Siddharth Konagurthu:
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors. i360-i369
- Jiafan Zhu, Xinhao Liu, Huw A. Ogilvie, Luay Nakhleh:
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. i370-i378 - Sahand Khakabimamaghani, Salem Malikic, Jeffrey Tang, Dujian Ding, Ryan D. Morin, Leonid Chindelevitch, Martin Ester:
Collaborative intra-tumor heterogeneity detection. i379-i388 - Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel:
Estimating the predictability of cancer evolution. i389-i397 - Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky:
Inference of clonal selection in cancer populations using single-cell sequencing data. i398-i407 - Nuraini Aguse, Yuanyuan Qi, Mohammed El-Kebir:
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees. i408-i416 - Erin K. Molloy, Tandy J. Warnow:
TreeMerge: a new method for improving the scalability of species tree estimation methods. i417-i426
- Héctor Climente-González, Chloé-Agathe Azencott, Samuel Kaski, Makoto Yamada:
Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data. i427-i435 - Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf-Herman Fridman, Markus List, Tatsiana Aneichyk:
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. i436-i445 - Anika Cheerla, Olivier Gevaert:
Deep learning with multimodal representation for pancancer prognosis prediction. i446-i454 - Mengyun Yang, Huimin Luo, Yaohang Li, Jianxin Wang:
Drug repositioning based on bounded nuclear norm regularization. i455-i463 - Caroline Labelle, Anne Marinier, Sébastien Lemieux:
Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose-response experiments. i464-i473 - Lei Du, Kefei Liu, Lei Zhu, Xiaohui Yao, Shannon L. Risacher, Lei Guo, Andrew J. Saykin, Li Shen:
Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: a longitudinal study of the ADNI cohort. i474-i483 - Jakob Richter, Katrin Madjar, Jörg Rahnenführer:
Model-based optimization of subgroup weights for survival analysis. i484-i491 - Welles Robinson, Roded Sharan, Mark D. M. Leiserson:
Modeling clinical and molecular covariates of mutational process activity in cancer. i492-i500 - Hossein Sharifi-Noghabi, Olga I. Zolotareva, Colin C. Collins, Martin Ester:
MOLI: multi-omics late integration with deep neural networks for drug response prediction. i501-i509 - Soufiane Mourragui, Marco Loog, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels:
PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors. i510-i519 - Do-Hoon Lee, Sangseon Lee, Sun Kim:
PRISM: methylation pattern-based, reference-free inference of subclonal makeup. i520-i529 - Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma:
Rotation equivariant and invariant neural networks for microscopy image analysis. i530-i537 - Bojian Yin, Marleen Balvert, Rick A. A. van der Spek, Bas E. Dutilh, Sander M. Bohté, Jan Veldink, Alexander Schönhuth:
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. i538-i547
- Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki:
Bayesian metabolic flux analysis reveals intracellular flux couplings. i548-i557 - Alexis Baudin, Soumya Paul, Cui Su, Jun Pang:
Controlling large Boolean networks with single-step perturbations. i558-i567 - Sumit Mukherjee, Thanneer M. Perumal, Kenneth Daily, Solveig K. Sieberts, Larsson Omberg, Christoph Preuss, Gregory W. Carter, Lara M. Mangravite, Benjamin A. Logsdon:
Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation. i568-i576 - Mathias Cardner, Nathalie Meyer-Schaller, Gerhard Christofori, Niko Beerenwinkel:
Inferring signalling dynamics by integrating interventional with observational data. i577-i585 - Aline Marguet, Marc Lavielle, Eugenio Cinquemani:
Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data. i586-i595 - Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz:
Large-scale inference of competing endogenous RNA networks with sparse partial correlation. i596-i604 - Jerzy Tiuryn, Ewa Szczurek:
Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects. i605-i614 - Reza Miraskarshahi, Hooman Zabeti, Tamon Stephen, Leonid Chindelevitch:
MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks. i615-i623 - Mitchell J. Wagner, Aditya Pratapa, T. M. Murali:
Reconstructing signaling pathways using regular language constrained paths. i624-i633 - Torsten Gross, Matthew Wongchenko, Yibing Yan, Nils Blüthgen:
Robust network inference using response logic. i634-i642
- Author Index. i643-i644
Volume 35, Number 15, August 2019
Genome Analysis
- Sarah N. Mapelli, Sara Napoli, Giuseppina Pisignano, Ramon Garcia-Escudero, Giuseppina M. Carbone, Carlo V. Catapano:
Deciphering the complexity of human non-coding promoter-proximal transcriptome. 2529-2534
Genome Analysis
- Dipan Shaw, Hao Chen, Tao Jiang:
DeepIsoFun: a deep domain adaptation approach to predict isoform functions. 2535-2544
- Joseph Mingrone, Edward Susko, Joseph P. Bielawski:
ModL: exploring and restoring regularity when testing for positive selection. 2545-2554 - Arthur Gilly, Lorraine Southam, Daniel Suveges, Karoline Kuchenbaecker, Rachel Moore, Giorgio E. M. Melloni, Konstantinos Hatzikotoulas, Aliki-Eleni Farmaki, Graham Ritchie, Jeremy Schwartzentruber, Petr Danecek, Britt Kilian, Martin O. Pollard, Xiangyu Ge, Emmanouil Tsafantakis, George V. Dedoussis, Eleftheria Zeggini:
Very low-depth whole-genome sequencing in complex trait association studies. 2555-2561
- Asher Moshe, Tal Pupko:
Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices. 2562-2568
- Mattia Miotto, Pier Paolo Olimpieri, Lorenzo Di Rienzo, Francesco Ambrosetti, Pietro Corsi, Rosalba Lepore, Gian Gaetano Tartaglia, Edoardo Milanetti:
Insights on protein thermal stability: a graph representation of molecular interactions. 2569-2577 - Eduardo Mayol, Mercedes Campillo, Arnau Cordomí, Mireia Olivella:
Inter-residue interactions in alpha-helical transmembrane proteins. 2578-2584 - Claire Marks, Charlotte M. Deane:
Increasing the accuracy of protein loop structure prediction with evolutionary constraints. 2585-2592
- Ziwei Chen, Shaokun An, Xiangqi Bai, Fuzhou Gong, Liang Ma, Lin Wan:
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data. 2593-2601 - Jie Hao, Wei Cao, Jian Huang, Xin Zou, Zeguang Han:
Optimal Gene Filtering for Single-Cell data (OGFSC) - a gene filtering algorithm for single-cell RNA-seq data. 2602-2609
- Wenqiang Shi, Oriol Fornes, Wyeth W. Wasserman:
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. 2610-2617
- Annika Röhl, Tanguy Riou, Alexander Bockmayr:
Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection. 2618-2625 - Rongting Huang, Yuanhua Huang, Yubin Guo, Shangwei Ji, Ming Lu, Tingting Li:
Systematic characterization and prediction of post-translational modification cross-talk between proteins. 2626-2633 - Meshari Alazmi, Hiroyuki Kuwahara, Othman Soufan, Lizhong Ding, Xin Gao:
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. 2634-2643
- Topaz Gilad, José Reyes, Jia-Yun Chen, Galit Lahav, Tammy Riklin Raviv:
Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy. 2644-2653
Genome Analysis
- Guoli Ji, Wenbin Ye, Yaru Su, Moliang Chen, Guangzao Huang, Xiaohui Wu:
AStrap: identification of alternative splicing from transcript sequences without a reference genome. 2654-2656 - Sunyoung Shin, Rebecca Hudson, Christopher Harrison, Mark Craven, Sündüz Keles:
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. 2657-2659 - Lucian P. Smith, Jon A Yamato, Mary K. Kuhner:
CNValidator: validating somatic copy-number inference. 2660-2662
- Carlos de Lannoy, Judith Risse, Dick de Ridder:
poreTally: run and publish de novo nanopore assembler benchmarks. 2663-2664 - Christopher M. Gibb, Robert Jackson, Sabah Mohammed, Jinan Fiaidhi, Ingeborg Zehbe:
Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data. 2665-2667 - Swaine L. Chen:
Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets. 2668-2670 - Josephine Burgin, Corentin Molitor, Fady R. Mohareb:
MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment. 2671-2673 - Shubham Chandak, Kedar Tatwawadi, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
SPRING: a next-generation compressor for FASTQ data. 2674-2676
- Mirco Michel, David Menéndez Hurtado, Arne Elofsson:
PconsC4: fast, accurate and hassle-free contact predictions. 2677-2679
- Felipe Llinares-López, Laetitia Papaxanthos, Damian Roqueiro, Dean A. Bodenham, Karsten M. Borgwardt:
CASMAP: detection of statistically significant combinations of SNPs in association mapping. 2680-2682 - Ehsan Ullah, Michaël Aupetit, Arun Das, Abhishek Patil, Nooral Al Muftah, Reda Rawi, Mohamad Saad, Halima Bensmail:
KinVis: a visualization tool to detect cryptic relatedness in genetic datasets. 2683-2685
- Asa Thibodeau, Dong-Guk Shin:
TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators. 2686-2689
- Céline Trébeau, Jacques Boutet de Monvel, Fabienne Wong Jun Tai, Christine Petit, Raphaël Etournay:
DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments. 2690-2691
Genome Analysis
- Boris Vishnepolsky, Malak Pirtskhalava:
Comment on: 'Empirical comparison of web-based antimicrobial peptide prediction tools'. 2692-2694 - Musa Nur Gabere, William Stafford Noble:
Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'. 2695-2696
- Raúl A González-Pech, Timothy G. Stephens, Cheong Xin Chan:
Commonly misunderstood parameters of NCBI BLAST and important considerations for users. 2697-2698 - Thomas L. Madden, Ben Busby, Jian Ye:
Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows. 2699-2700
- Stefano Nembrini:
On what to permute in test-based approaches for variable importance measures in Random Forests. 2701-2705
Volume 35, Number 16, August 2019
Sequence Analysis
- Justin R. Klesmith, Benjamin J. Hackel:
Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit. 2707-2712 - Igor E. Eliseev, Ivan N. Terterov, Anna N. Yudenko, Olga V. Shamova:
Linking sequence patterns and functionality of alpha-helical antimicrobial peptides. 2713-2717
- Tamir Tuller, Alon Diament, Avital Yahalom, Assaf Zemach, Shimshi Atar, Daniel A. Chamovitz:
The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. 2718-2723
Genome Analysis
- Leopold Carron, Jean Baptiste Morlot, Vincent Matthys, Annick Lesne, Julien Mozziconacci:
Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps. 2724-2729 - Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev:
Promoter analysis and prediction in the human genome using sequence-based deep learning models. 2730-2737
- Blake Hewelt, Haiqing Li, Mohit Kumar Jolly, Prakash Kulkarni, Isa Mambetsariev, Ravi Salgia:
The DNA walk and its demonstration of deterministic chaos - relevance to genomic alterations in lung cancer. 2738-2748 - Jialin Yu, Shaoping Shi, Fang Zhang, Guodong Chen, Man Cao:
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization. 2749-2756 - Balachandran Manavalan, Shaherin Basith, Tae Hwan Shin, Leyi Wei, Gwang Lee:
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation. 2757-2765 - Fenglin Luo, Minghui Wang, Yu Liu, Xing-Ming Zhao, Ao Li:
DeepPhos: prediction of protein phosphorylation sites with deep learning. 2766-2773 - Alice Cheng, Charles E. Grant, William S. Noble, Timothy L. Bailey:
MoMo: discovery of statistically significant post-translational modification motifs. 2774-2782 - Houxiang Zhu, Chun Liang:
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity. 2783-2789 - Jan Ludwiczak, Aleksander Winski, Krzysztof Szczepaniak, Vikram Alva, Stanislaw Dunin-Horkawicz:
DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences. 2790-2795 - Wei Chen, Hao Lv, Fulei Nie, Hao Lin:
i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome. 2796-2800
- Mikhail Karasikov, Guillaume Pagès, Sergei Grudinin:
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment. 2801-2808
- Xiangtao Li, Shixiong Zhang, Ka-Chun Wong:
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning. 2809-2817 - Jinyan Chan, Xuan Wang, Jacob A. Turner, Nicole E. Baldwin, Jinghua Gu:
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. 2818-2826
- Yinsheng Zhou, Han Zhang, Yaning Yang:
CSHAP: efficient haplotype frequency estimation based on sparse representation. 2827-2833
- Yang Yang, Mingyu Zhou, Qingwei Fang, Hong-Bin Shen:
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model. 2834-2842
Genome Analysis
- Hung Nguyen, Sangam Shrestha, Sorin Draghici, Tin Nguyen:
PINSPlus: a tool for tumor subtype discovery in integrated genomic data. 2843-2846 - Jos B. Poell, Matias Mendeville, Daoud Sie, Arjen Brink, Ruud H. Brakenhoff, Bauke Ylstra:
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data. 2847-2849 - Georgette Tanner, David R. Westhead, Alastair P. Droop, Lucy F. Stead:
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing. 2850-2852
- Giorgio Gonnella, Niklas Niehus, Stefan Kurtz:
GfaViz: flexible and interactive visualization of GFA sequence graphs. 2853-2855 - Milot Mirdita, Martin Steinegger, Johannes Söding:
MMseqs2 desktop and local web server app for fast, interactive sequence searches. 2856-2858 - Linfang Jin, Jinhuo Lai, Yang Zhang, Ying Fu, Shuhang Wang, Heng Dai, Bingding Huang:
BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads. 2859-2861
- Milad Miladi, Soheila Montaseri, Rolf Backofen, Martin Raden:
Integration of accessibility data from structure probing into RNA-RNA interaction prediction. 2862-2864
- Tallulah S. Andrews, Martin Hemberg:
M3Drop: dropout-based feature selection for scRNASeq. 2865-2867
- Paula Tataru, Thomas Bataillon:
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species. 2868-2869
- Xiaotao Shen, Zheng-Jiang Zhu:
MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery. 2870-2872 - Hoon Hong, Alexey Ovchinnikov, Gleb Pogudin, Chee Yap:
SIAN: software for structural identifiability analysis of ODE models. 2873-2874 - Diego A. A. Morais, Rita M. C. Almeida, Rodrigo J. S. Dalmolin:
Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction. 2875-2876
- Samir Kanaan-Izquierdo, Andrey Ziyatdinov, Maria Araceli Burgueño, Alexandre Perera-Lluna:
Multiview: a software package for multiview pattern recognition methods. 2877-2879 - Dries Vaneechoutte, Klaas Vandepoele:
Curse: building expression atlases and co-expression networks from public RNA-Seq data. 2880-2881
- Lihua Liu, David R. Damerell, Leonidas Koukouflis, Yufeng Tong, Brian D. Marsden, Matthieu Schapira:
UbiHub: a data hub for the explorers of ubiquitination pathways. 2882-2884
Databases and Ontologies
- Yuan Luo, Chengsheng Mao, Yiben Yang, Fei Wang, Faraz S. Ahmad, Donna Arnett, Marguerite R. Irvin, Sanjiv J. Shah:
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization. 2885
Volume 35, Number 17, September 2019
Genome Analysis
- Bandana Kumari, Ravindra Kumar, Manish Kumar:
Identifying residues that determine palmitoylation using association rule mining. 2887-2890
Genome Analysis
- Feifei Xiao, Xizhi Luo, Ning Hao, Yue Niu, Xiangjun Xiao, Guoshuai Cai, Christopher I. Amos, Heping Zhang:
An accurate and powerful method for copy number variation detection. 2891-2898 - Zhong Zhuang, Xiaotong Shen, Wei Pan:
A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data. 2899-2906 - David Heller, Martin Vingron:
SVIM: structural variant identification using mapped long reads. 2907-2915 - John C. Stansfield, Kellen Garrison Cresswell, Mikhail G. Dozmorov:
multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments. 2916-2923 - Mark R. Zucker, Lynne V. Abruzzo, Carmen D. Herling, Lynn L. Barron, Michael J. Keating