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ORCIDBioinformatics, Volume 36
Volume 36, Number 1, January 2020
Genome Analysis
- Vahid Jalili
, Enis Afgan, James Taylor, Jeremy Goecks:
Cloud bursting galaxy: federated identity and access management. 1-9 - Peng Xu, Timothy Kennell Jr., Min Gao, Human Genome Structural Variation Consortium, Robert P. Kimberly, Zechen Chong:
MRLR: unraveling high-resolution meiotic recombination by linked reads. 10-16 - Adam Kaplan, Eric F. Lock, Mark Fiecas, Alzheimer's Disease Neuroimaging Initiative:
Bayesian GWAS with Structured and Non-Local Priors. 17-25
- Davoud Torkamaneh, Jérôme Laroche, Brian Boyle, François Belzile:
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing. 26-32 - Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan:
arcasHLA: high-resolution HLA typing from RNAseq. 33-40 - Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang:
Protein contact prediction using metagenome sequence data and residual neural networks. 41-48 - Chenwei Lou, Jian Zhao, Ruoyao Shi, Qian Wang, Wenyang Zhou, Yubo Wang, Guoqing Wang, Lan Huang, Xin Feng, Fengfeng Zhou:
sefOri: selecting the best-engineered sequence features to predict DNA replication origins. 49-55 - Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio:
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. 56-64 - Li Xing, Mary Lesperance, Xuekui Zhang:
Simultaneous prediction of multiple outcomes using revised stacking algorithms. 65-72 - Mohamed Chaabane, Robert M. Williams, Austin T. Stephens, Juw Won Park:
circDeep: deep learning approach for circular RNA classification from other long non-coding RNA. 73-80 - Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard:
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. 81-89 - Fabian Sievers, Desmond G. Higgins:
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. 90-95
- Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu:
P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking. 96-103 - Shuichiro Makigaki, Takashi Ishida:
Sequence alignment using machine learning for accurate template-based protein structure prediction. 104-111 - Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue:
iScore: a novel graph kernel-based function for scoring protein-protein docking models. 112-121 - Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex:
Positive multistate protein design. 122-130 - Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J. Lanczycki, Renata C. Geer, Thomas Madej, Lon Phan, Minghong Ward, Shennan Lu, Gabriele H. Marchler, Yanli Wang, Stephen H. Bryant, Lewis Y. Geer, Aron Marchler-Bauer:
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. 131-135 - Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen, Haiyan Liu:
Increasing the efficiency and accuracy of the ABACUS protein sequence design method. 136-144 - Angela Serra, Serli Önlü, Paola Festa, Vittorio Fortino, Dario Greco:
MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling. 145-153 - Tomer Meirson, David Bomze, Liron Gat Kahlon, Hava Gil-Henn, Abraham O. Samson:
A helical lock and key model of polyproline II conformation with SH3. 154-159 - Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse:
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity. 160-168
- Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi:
A dynamic programing approach to integrate gene expression data and network information for pathway model generation. 169-176 - John Ferguson, Joseph Chang:
An empirical Bayesian ranking method, with applications to high throughput biology. 177-185 - Erwan Bigan, Satish Sasidharan Nair, François-Xavier Lejeune, Hélissande Fragnaud, Frédéric Parmentier, Lucile Mégret, Marc Verny, Jeff Aaronson, Jim Rosinski, Christian Néri:
Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms. 186-196 - Xin Zhou, Xiaodong Cai:
Inference of differential gene regulatory networks based on gene expression and genetic perturbation data. 197-204 - Elizabeth Guruceaga, Alba Garín-Muga, Victor Segura:
MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides. 205-211
- Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette:
Mycorrhiza: genotype assignment using phylogenetic networks. 212-220 - Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu:
Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations. 221-231
- Axel Theorell, Katharina Nöh:
Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis. 232-240 - Rudolf Schill, Stefan Solbrig, Tilo Wettig, Rainer Spang:
Modelling cancer progression using Mutual Hazard Networks. 241-249
- Trang T. Le, Weixuan Fu, Jason H. Moore:
Scaling tree-based automated machine learning to biomedical big data with a feature set selector. 250-256 - Qian Li, Kate Fisher, Wenjun Meng, Bin Fang, Eric A. Welsh, Eric B. Haura, John M. Koomen, Steven A. Eschrich, Brooke L. Fridley, Yian Ann Chen:
GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. 257-263 - Alexander Junge, Lars Juhl Jensen:
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. 264-271 - Hannah F. Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider:
Deep learning on chaos game representation for proteins. 272-279 - John M. Giorgi, Gary D. Bader:
Towards reliable named entity recognition in the biomedical domain. 280-286 - Arne P. Raulf, Joshua Butke, Claus Küpper, Frederik Großerüschkamp, Klaus Gerwert, Axel Mosig:
Deep representation learning for domain adaptable classification of infrared spectral imaging data. 287-294 - Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser:
HUNER: improving biomedical NER with pretraining. 295-302 - Guoxian Yu, Keyao Wang, Carlotta Domeniconi, Maozu Guo, Jun Wang:
Isoform function prediction based on bi-random walks on a heterogeneous network. 303-310 - Nezar Abdennur, Leonid A. Mirny:
Cooler: scalable storage for Hi-C data and other genomically labeled arrays. 311-316
- Vincent Briane, Myriam Vimond, Cesar Augusto Valades-Cruz, Antoine Salomon, Christian Wunder, Charles Kervrann:
A sequential algorithm to detect diffusion switching along intracellular particle trajectories. 317-329
Bioimage Informatics
- Yan Zhao, Xing Chen, Jun Yin:
Adaptive boosting-based computational model for predicting potential miRNA-disease associations. 330
Volume 36, Number 2, January 2020
Genome Analysis
- William H. Majoros, Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, Cong Guo, William L. Lowe, Denise M. Scholtens, M. Geoffrey Hayes, Timothy E. Reddy, Andrew S. Allen:
Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. 331-338 - Ran Su, Jiahang Zhang, Xiaofeng Liu, Leyi Wei:
Identification of expression signatures for non-small-cell lung carcinoma subtype classification. 339-346 - Chan Wang, Jiyuan Hu, Martin J. Blaser, Huilin Li:
Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data. 347-355 - Terry Ma, Di Xiao, Xin Xing:
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies. 356-363 - Sierra S. Nishizaki, Natalie Ng, Shengcheng Dong, Robert S. Porter, Cody Morterud, Colten Williams, Courtney Asman, Jessica A Switzenberg, Alan P. Boyle:
Predicting the effects of SNPs on transcription factor binding affinity. 364-372 - Patrick Sorn, Christoph Holtsträter, Martin Löwer, Ugur Sahin, David Weber:
ArtiFuse - computational validation of fusion gene detection tools without relying on simulated reads. 373-379
- Alfredo Velasco II, Benjamin T. James, Vincent D. Wells, Hani Z. Girgis:
Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models. 380-387 - Cong Pian, Guang-Le Zhang, Fei Li, Xiaodan Fan:
MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model. 388-392 - Michele Berselli, Enrico Lavezzo, Stefano Toppo:
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable. 393-399 - Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin:
Haplotype-aware graph indexes. 400-407 - Martin C. Frith:
How sequence alignment scores correspond to probability models. 408-415 - Chloé Dimeglio, Stéphanie Raymond, Nicolas Jeanne, Christelle Reynès, Romain Carcenac, Caroline Lefebvre, Michelle Cazabat, Florence Nicot, Pierre Delobel, Jacques Izopet:
THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage. 416-421 - Maxat Kulmanov, Robert Hoehndorf:
DeepGOPlus: improved protein function prediction from sequence. 422-429
- Roberto Del Amparo, Alberto Vicens, Miguel Arenas:
The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation. 430-436
- Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen:
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. 437-448 - Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang:
DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing. 449-461 - Gregor Entzian, Martin Raden:
pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes. 462-469 - Badri Adhikari:
DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout. 470-477 - Zeyu Wen, Jiahua He, Sheng-You Huang:
Topology-independent and global protein structure alignment through an FFT-based algorithm. 478-486
- Adib Shafi, Tin Nguyen, Azam Peyvandi-Pour, Sorin Draghici:
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis. 487-495 - Wanwen Zeng, Yong Wang, Rui Jiang:
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network. 496-503 - Christelle Reynès, Guilhem Kister, Marine Rohmer, Tristan Bouschet, Annie Varrault, Emeric Dubois, Stéphanie Rialle, Laurent Journot, Robert Sabatier:
ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. 504-513 - Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot:
MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network. 514-523 - Zhiguang Huo, Shaowu Tang, Yongseok Park, George C. Tseng:
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications. 524-532 - Feiyang Ma, Matteo Pellegrini:
ACTINN: automated identification of cell types in single cell RNA sequencing. 533-538 - Li Chen, Feng Wang, Emily C. Bruggeman, Chao Li, Bing Yao:
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. 539-545 - Kyungsoo Kim, Sunmo Yang, Sang-Jun Ha, Insuk Lee:
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data. 546-551
- Lerato E. Magosi, Anuj Goel, Jemma C. Hopewell:
Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease. 552-557
- Mikel Hernaez, Charles Blatti, Olivier Gevaert:
Comparison of single and module-based methods for modeling gene regulatory networks. 558-567 - Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S. Dina, Xuequn Shang, David M. Kramer, Jin Chen:
Identifying emerging phenomenon in long temporal phenotyping experiments. 568-577 - Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He:
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics. 578-585 - Boseung Choi, Yu-Yu Cheng, Selahattin Cinar, William Ott, Matthew R. Bennett, Kresimir Josic, Jae Kyoung Kim:
Bayesian inference of distributed time delay in transcriptional and translational regulation. 586-593 - Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl:
Efficient parameterization of large-scale dynamic models based on relative measurements. 594-602 - Sameh K. Mohamed, Vít Novácek, Aayah Nounu:
Discovering protein drug targets using knowledge graph embeddings. 603-610
- Peiliang Lou, Antonio Jimeno-Yepes, Zai Zhang, Qinghua Zheng, Xiangrong Zhang, Chen Li:
BioNorm: deep learning-based event normalization for the curation of reaction databases. 611-620 - Siva Rajesh Kasa, Sakyajit Bhattacharya, Vaibhav Rajan:
Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping. 621-628 - Sami Tabib, Denis Larocque:
Non-parametric individual treatment effect estimation for survival data with random forests. 629-636 - Shankai Yan, Ka-Chun Wong:
Context awareness and embedding for biomedical event extraction. 637-643
Genome Analysis
- Ricardo N. Ramirez, Karni Bedirian, Simon M. Gray, Alos Diallo:
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data. 644-646
- Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick:
RAG-Web: RNA structure prediction/design using RNA-As-Graphs. 647-648
- Ramiro Magno, Ana-Teresa Maia:
gwasrapidd: an R package to query, download and wrangle GWAS catalog data. 649-650
Data and Text Mining
- Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. 651
Volume 36, Number 3, February 2020
Genome Analysis
- Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera, Shuang Wang:
A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes. 653-659 - Ren-Hua Chung, Chen-Yu Kang:
pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions. 660-665 - Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, Jing-Dong J. Han:
Accurate loop calling for 3D genomic data with cLoops. 666-675 - Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang, Sebastian Stintzing, Volker Heinemann, Heinz-Josef Lenz:
Partition: a surjective mapping approach for dimensionality reduction. 676-681 - Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Fast and accurate correction of optical mapping data via spaced seeds. 682-689 - Tianlei Xu, Peng Jin, Zhaohui S. Qin:
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. 690-697 - Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano:
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. 698-703
- Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song:
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. 704-712 - Mary A Wood, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Abhinav Nellore, Reid F. Thompson:
neoepiscope improves neoepitope prediction with multivariant phasing. 713-720 - Robert S. Harris, Paul Medvedev:
Improved representation of sequence bloom trees. 721-727 - Timothy J. Hackmann:
Accurate estimation of microbial sequence diversity with Distanced. 728-734 - M. B. B. Gutierres, C. B. C. Bonorino, Maurício Menegatti Rigo:
ChaperISM: improved chaperone binding prediction using position-independent scoring matrices. 735-741
- Yufeng Wu:
Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach. 742-750
- Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng:
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. 751-757 - Fergus Boyles, Charlotte M. Deane, Garrett M. Morris:
Learning from the ligand: using ligand-based features to improve binding affinity prediction. 758-764 - Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa, Marta Martínez, David Maluenda, Javier Mota, Amaya Jiménez, Javier Vargas, Roberto Marabini, Patrick M. Sexton, José María Carazo, Carlos Oscar Sánchez Sorzano:
Automatic local resolution-based sharpening of cryo-EM maps. 765-772
- Hannah De Los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett, Jennifer M. Hurley:
ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. 773-781 - Jiebiao Wang, Bernie Devlin, Kathryn Roeder:
Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression. 782-788 - Pengchao Ye, Wenbin Ye, Congting Ye, Shuchao Li, Lishan Ye, Guoli Ji, Xiaohui Wu:
scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size. 789-797 - Priyam Das, Christine B. Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani:
NExUS: Bayesian simultaneous network estimation across unequal sample sizes. 798-804 - Wenjiang Deng, Tian Mou, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Trung-Nghia Vu:
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data. 805-812 - Godwin Woo, Michael Fernández, Michael Hsing, Nathan A. Lack, Ayse Derya Cavga, Artem Cherkasov:
DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules. 813-818 - Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F. Xiao-Feng Qin, Aiping Wu:
Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes. 819-827
- José Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen, Rasmus Nielsen, Anna-Sapfo Malaspinas:
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. 828-841 - Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin, Lida Chatzi, Graham Casey, Duncan C. Thomas, David V. Conti:
A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits. 842-850
- Yu-An Huang, Pengwei Hu, Keith C. C. Chan, Zhu-Hong You:
Graph convolution for predicting associations between miRNA and drug resistance. 851-858 - Hongyang Li, Yuanfang Guan:
Machine learning empowers phosphoproteome prediction in cancers. 859-864 - Noemi Di Nanni, Matteo Gnocch