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ORCIDBioinformatics, Volume 37
Volume 37, Number 1, April 2021
- M. K. Sobczyk
, Tom R. Gaunt, Lavinia Paternoster:
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. 1-8 - Aditya Gorla, Brandon Jew, Luke Zhang, Jae Hoon Sul:
xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery. 9-16 - Benjamin Jean-Marie Tremblay, Briallen Lobb, Andrew C. Doxey:
PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. 17-22 - Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský:
SoluProt: prediction of soluble protein expression in Escherichia coli. 23-28 - Jordi Silvestre-Ryan, Yujie Wang, Mehak Sharma, Stephen Lin, Yolanda Shen, Shihab Dider, Ian H. Holmes:
Machine Boss: rapid prototyping of bioinformatic automata. 29-35 - Hong Su, Zhenling Peng, Jianyi Yang:
Recognition of small molecule-RNA binding sites using RNA sequence and structure. 36-42 - Zhengyang Dong, Gil Alterovitz:
netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. 43-49 - Meiling Liu, Yang Liu, Michael C. Wu, Li Hsu, Qianchuan He:
A method for subtype analysis with somatic mutations. 50-56 - Anja C. Gumpinger, Bastian Rieck, Dominik G. Grimm, Karsten M. Borgwardt:
Network-guided search for genetic heterogeneity between gene pairs. 57-65 - Cunmei Ji, Zhen Gao, Xu Ma, Qing-Wen Wu, Jian-Cheng Ni, Chunhou Zheng:
AEMDA: inferring miRNA-disease associations based on deep autoencoder. 66-72 - Sara Omranian, Angela Angeleska, Zoran Nikoloski:
PC2P: parameter-free network-based prediction of protein complexes. 73-81 - Chuang Liu, Zhen Han, Zi-Ke Zhang, Ruth Nussinov, Feixiong Cheng:
A network-based deep learning methodology for stratification of tumor mutations. 82-88 - Rachel Torchet, Karen Druart, Luis Checa Ruano, Alexandra Moine-Franel, Hélène Borges, Olivia Doppelt-Azeroual, Bryan Brancotte, Fabien Mareuil, Michael Nilges, Hervé Ménager, Olivier Sperandio:
The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators. 89-96 - Afshin Khadangi, Thomas Boudier, Vijay Rajagopal:
EM-stellar: benchmarking deep learning for electron microscopy image segmentation. 97-106 - Renmin Han, Guojun Li, Xin Gao:
Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints. 107-117 - Jianglin Feng, Nathan C. Sheffield:
IGD: high-performance search for large-scale genomic interval datasets. 118-120 - Anna Abramova, Adriana Osinska, Haveela Kunche, Emil Burman, Johan Bengtsson-Palme:
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data. 121-122 - Jonathan Jacob Weinstein, Adi Goldenzweig, Shlomoyakir Hoch, Sarel Jacob Fleishman:
PROSS 2: a new server for the design of stable and highly expressed protein variants. 123-125 - A. K. M. Firoj Mahmud, Nicolas Delhomme, Soumyadeep Nandi, Maria Fällman:
ProkSeq for complete analysis of RNA-Seq data from prokaryotes. 126-128 - Alireza Ani, Peter J. van der Most, Harold Snieder, Ahmad Vaez, Ilja M. Nolte:
GWASinspector: comprehensive quality control of genome-wide association study results. 129-130 - Maria Suprun, Randall J. Ellis, Hugh A. Sampson, Mayte Suárez-Fariñas:
bbeaR: an R package and framework for epitope-specific antibody profiling. 131-133 - Wei He, Helen Wang, Yanjun Wei, Zhiyun Jiang, Yitao Tang, Yiwen Chen, Han Xu:
GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. 134-136 - Josep Marín-Llaó, Sarah Mubeen, Alexandre Perera-Lluna, Martin Hofmann-Apitius, Sergio Picart-Armada, Daniel Domingo-Fernández:
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms. 137-139 - Evgeny S. Zhvansky, Anatoly A. Sorokin, Denis S. Bormotov, Konstantin V. Bocharov, Denis S. Zavorotnyuk, Daniil G. Ivanov, Eugene N. Nikolaev, Igor A. Popov:
The software for interactive evaluation of mass spectra stability and reproducibility. 140-142 - John Zobolas, Vasundra Touré, Martin Kuiper, Steven Vercruysse:
UniBioDicts: Unified access to Biological Dictionaries. 143-144 - Georgios N. Dimitrakopoulos, Maria I. Klapa, Nicholas K. Moschonas:
PICKLE 3.0: enriching the human meta-database with the mouse protein interactome extended via mouse-human orthology. 145-146
Volume 37, Number 2, April 2021
- Dimitrios V. Vavoulis, Anthony Cutts, Jenny C. Taylor, Anna Schuh:
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data. 147-154 - Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang, Fengzhu Sun:
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. 155-161 - Amelia Villegas-Morcillo, Stavros Makrodimitris, Roeland C. H. J. van Ham, Angel M. Gomez, Victoria E. Sánchez, Marcel J. T. Reinders:
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. 162-170 - Dan Zhang, Zhao-Chun Xu, Wei Su, Yu-He Yang, Hao Lv, Hui Yang, Hao Lin:
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features. 171-177 - Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova:
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. 178-184 - Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu:
Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms. 185-191 - Gabriel E. Hoffman, Panos Roussos:
Dream: powerful differential expression analysis for repeated measures designs. 192-201 - Samuel Melton, Sharad Ramanathan:
Discovering a sparse set of pairwise discriminating features in high-dimensional data. 202-212 - Saptarshi Sinha, Sourabh Samaddar, Sujoy K. Das Gupta, Soumen Roy:
Network approach to mutagenesis sheds insight on phage resistance in mycobacteria. 213-220 - Marzieh Ayati, Mark R. Chance, Mehmet Koyutürk:
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. 221-228 - Gustavo Hernandez-Mejia, Esteban A. Hernández-Vargas:
Uncovering antibody cross-reaction dynamics in influenza A infections. 229-235 - Mario Sänger, Ulf Leser:
Large-scale entity representation learning for biomedical relationship extraction. 236-242 - Elena Tutubalina, Ilseyar Alimova, Zulfat Miftahutdinov, Andrey Sakhovskiy, Valentin Malykh, Sergey I. Nikolenko:
The Russian Drug Reaction Corpus and neural models for drug reactions and effectiveness detection in user reviews. 243-249 - William G. La Cava, Heather Williams, Weixuan Fu, Steven Vitale, Durga Srivatsan, Jason H. Moore:
Evaluating recommender systems for AI-driven biomedical informatics. 250-256 - Octavio Morante-Palacios, Esteban Ballestar:
shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays. 257-259 - Lifen Liu, Ge Zhang, Shoupeng He, Xuehai Hu:
TSPTFBS: a Docker image for trans-species prediction of transcription factor binding sites in plants. 260-262 - Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J. Park:
BamSnap: a lightweight viewer for sequencing reads in BAM files. 263-264 - Chenxin Li, Mingxuan Gao, Wenxian Yang, Chuanqi Zhong, Rongshan Yu:
Diamond: a multi-modal DIA mass spectrometry data processing pipeline. 265-267 - Jordan Douglas:
UglyTrees: a browser-based multispecies coalescent tree visualizer. 268-269 - Andy M. C. Lau, Jürgen Claesen, Kjetil Hansen, Argyris Politis:
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry. 270-272 - Tiansheng Zhu, Hao Chen, Xishan Yan, Zhicheng Wu, Xiaoxu Zhou, Qi Xiao, Weigang Ge, Qiushi Zhang, Chao Xu, Luang Xu, Guan Ruan, Zhangzhi Xue, Chunhui Yuan, Guo-Bo Chen, Tiannan Guo:
ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets. 273-275 - Daniel Sumner Magruder, Anna-Maria Liebhoff, Jörn Bethune, Stefan Bonn:
Interactive gene networks with KNIT. 276-278 - Prashant Singh, Fredrik Wrede, Andreas Hellander:
Scalable machine learning-assisted model exploration and inference using Sciope. 279-281 - Trang T. Le, Jason H. Moore:
treeheatr: an R package for interpretable decision tree visualizations. 282-284 - Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang:
CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. 285-287 - Yi Liu, Benjamin L. Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Oliver Lloyd, Marina Vabistsevits, Tom R. Gaunt:
Erratum to: EpiGraphDB: a database and data mining platform for health data science. 288
Volume 37, Number 3, April 2021
- Luyu Xie, Limsoon Wong:
PDR: a new genome assembly evaluation metric based on genetics concerns. 289-295 - Yue Fan, Huanhuan Zhu, Yanyi Song, Qinke Peng, Xiang Zhou:
Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses. 296-302 - Shani Cohen, Lior Rokach, Yair Motro, Jacob Moran-Gilad, Isana Veksler-Lublinsky:
minMLST: machine learning for optimization of bacterial strain typing. 303-311 - Xizhi Luo, Fei Qin, Guoshuai Cai, Feifei Xiao:
Integrating genomic correlation structure improves copy number variations detection. 312-317 - Florian Mock, Adrian Viehweger, Emanuel Barth, Manja Marz:
VIDHOP, viral host prediction with deep learning. 318-325 - Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova:
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. 326-333 - Pep Amengual-Rigo, Juan Fernández-Recio, Victor Guallar:
UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. 334-341 - Oliver P. Watson, Isidro Cortes-Ciriano, James A. Watson:
A semi-supervised learning framework for quantitative structure-activity regression modelling. 342-350 - Joshua M. Toth, Paul J. DePietro, Juergen Haas, William A. McLaughlin:
ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques. 351-359 - Federico Baldassarre, David Menéndez Hurtado, Arne Elofsson, Hossein Azizpour:
GraphQA: protein model quality assessment using graph convolutional networks. 360-366 - Andrew J. Bass, John D. Storey:
The optimal discovery procedure for significance analysis of general gene expression studies. 367-374 - Rajinder Gupta, Yannick Schrooders, Marcha Verheijen, Adrian Roth, Jos Kleinjans, Florian Caiment:
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. 375-381 - Liya Wang, Zhenyuan Lu, Michael Regulski, Yinping Jiao, Junping Chen, Doreen Ware, Zhanguo Xin:
BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations. 382-387 - Woosub Shin, Joseph L. Hellerstein:
Isolating structural errors in reaction networks in systems biology. 388-395 - Shuzhen Kuang, Yanzhang Wei, Liangjiang Wang:
Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells. 396-403 - Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu:
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations. 404-412 - Maria Nattestad, Robert Aboukhalil, Chen-Shan Chin, Michael C. Schatz:
Ribbon: intuitive visualization for complex genomic variation. 413-415 - Wanson Choi, Yang Luo, Soumya Raychaudhuri, Buhm Han:
HATK: HLA analysis toolkit. 416-418 - Thiago L. A. Miller, Fernanda Orpinelli Rego, José Leonel L. Buzzo, Pedro A. F. Galante:
sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies. 419-421 - Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn A. Grüning, Fidel Ramírez, Thomas Manke:
pyGenomeTracks: reproducible plots for multivariate genomic datasets. 422-423 - Konrad Diedrich, Joel Graef, Katrin Schöning-Stierand, Matthias Rarey:
GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. 424-425 - Silver A. Wolf, Lennard Epping, Sandro Andreotti, Knut Reinert, Torsten Semmler:
SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria. 426-428 - Quanxue Li, Wentao Dai, Jixiang Liu, Qingqing Sang, Yi-Xue Li, Yuan-Yuan Li:
DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures in cancer. 429-430 - Nils Kurzawa, André Mateus, Mikhail M. Savitski:
Rtpca: an R package for differential thermal proximity coaggregation analysis. 431-433 - Ailin Ren, Dachuan Zhang, Yu Tian, Pengli Cai, Tong Zhang, Qian-Nan Hu:
Transcriptor: a comprehensive platform for annotation of the enzymatic functions of transcripts. 434-435 - Sarah E. I. Perez, Aria S. Hahn, Martin Krzywinski, Steven J. Hallam:
Hive Panel Explorer: an interactive network visualization tool. 436-437
Volume 37, Number 4, May 2021
- Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble:
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. 439-447 - Maximilian Collatz, Florian Mock, Emanuel Barth, Martin Hölzer, Konrad Sachse, Manja Marz:
EpiDope: a deep neural network for linear B-cell epitope prediction. 448-455 - Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni:
Shark: fishing relevant reads in an RNA-Seq sample. 464-472 - Borja Freire, Susana Ladra, José R. Paramá, Leena Salmela:
Inference of viral quasispecies with a paired de Bruijn graph. 473-481 - Vyacheslav Tretyachenko, Václav Vorácek, Radko Soucek, Kosuke Fujishima, Klára Hlouchová:
CoLiDe: Combinatorial Library Design tool for probing protein sequence space. 482-489 - Mu Gao, Jeffrey Skolnick:
A novel sequence alignment algorithm based on deep learning of the protein folding code. 490-496 - Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
Text mining for modeling of protein complexes enhanced by machine learning. 497-505 - Pietro Di Lena, Pierre Baldi:
Fold recognition by scoring protein maps using the congruence coefficient. 506-513 - Chubing Zeng, Duncan C. Thomas, Juan Pablo Lewinger:
Incorporating prior knowledge into regularized regression. 514-521 - Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S. Omenn, Jianxin Wang:
IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation. 522-530 - Christopher N. Foley, Amy M. Mason, Paul D. W. Kirk, Stephen Burgess:
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates. 531-541 - Lun Hu, Jun Zhang, Xiangyu Pan, Hong Yan, Zhu-Hong You:
HiSCF: leveraging higher-order structures for clustering analysis in biological networks. 542-550 - Arthur M. Lesk, Arun Siddharth Konagurthu:
Neighbourhoods in the yeast regulatory network in different physiological states. 551-558 - Heeva Baharlou, Nicolas P. Canete, Kirstie M. Bertram, Kerrie J. Sandgren, Anthony Cunningham, Andrew N. Harman, Ellis Patrick:
AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images. 559-567 - M. A. Kühl, B. Stich, D. C. Ries:
Mutation-Simulator: fine-grained simulation of random mutations in any genome. 568-569 - Anuradha Jagadeesan, S. Sunna Ebenesersdóttir, Valdis B. Guðmundsdóttir, Elisabet Linda Thordardottir, Kristjan H. S. Moore, Agnar Helgason:
HaploGrouper: a generalized approach to haplogroup classification. 570-572 - Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu:
RabbitQC: high-speed scalable quality control for sequencing data. 573-574 - Xin Li, Haiyan Hu, Xiaoman Li:
mixtureS: a novel tool for bacterial strain genome reconstruction from reads. 575-577 - Kevin Troulé, Hugo López-Fernández, Santiago García-Martín, Miguel Reboiro-Jato, Carlos Carretero-Puche, Jordi Martorell-Marugan, Guillermo Martín-Serrano, Pedro Carmona-Saez, Daniel Glez-Peña, Fátima Al-Shahrour, Gonzalo Gómez-López:
DREIMT: a drug repositioning database and prioritization tool for immunomodulation. 578-579 - Sunil Nagpal, Bhusan K. Kuntal, Sharmila S. Mande:
NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams. 580-582 - Benjamin L. Elsworth, Tom R. Gaunt:
MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature. 583-585 - Daniel Robert Korn, Tesia M. Bobrowski, Michael Li, Yaphet Kebede, Patrick Wang, Phillips Owen, Gaurav Vaidya, Eugene N. Muratov, Rada Chirkova, Chris Bizon, Alexander Tropsha:
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. 586-587
Volume 37, Number 5, May 2021
- Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. 589-595 - Michael Menzel, Sabine Hurka, Stefan Glasenhardt, Andreas Gogol-Döring:
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling. 596-602 - Priyesh Agrawal, Debasisa Mohanty:
A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides. 603-611 - Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers:
Finding long tandem repeats in long noisy reads. 612-621 - Cristian D. Loaiza, Rakesh Kaundal:
PredHPI: an integrated web server platform for the detection and visualization of host-pathogen interactions using sequence-based methods. 622-624 - Dhaivat Joshi, Shunfu Mao, Sreeram Kannan, Suhas N. Diggavi:
QAlign: aligning nanopore reads accurately using current-level modeling. 625-633 - Ruoyi Cai, Cécile Ané:
Assessing the fit of the multi-species network coalescent to multi-locus data. 634-641 - Shijia Wang, Liangliang Wang:
Particle Gibbs sampling for Bayesian phylogenetic inference. 642-649 - Xu Shi, Andrew F. Neuwald, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. 650-658 - Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand:
selectBoost: a general algorithm to enhance the performance of variable selection methods. 659-668 - Juan Pablo Prada, Gaby Wangorsch, Kirstin Kucka, Isabell Lang, Thomas Dandekar, Harald Wajant:
A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2. 669-676 - Gabriel J. Kowalczyk, J. Agustin Cruz, Yue Guo, Qiuhong Zhang, Natalie Sauerwald, Robin E. C. Lee:
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells. 677-683 - Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text. 684-692 - Ahmet Süreyya Rifaioglu, Rengül Çetin-Atalay, Deniz Cansen Kahraman, Tunca Dogan, Maria Jesus Martin, Volkan Atalay:
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. 693-704 - Rosa L. Allesøe, Camilla K. Lemvigh, My V. T. Phan, Philip T. L. C. Clausen, Alfred F. Florensa, Marion Koopmans, Ole Lund, Matthew Cotten:
Automated download and clean-up of family-specific databases for kmer-based virus identification. 705-710 - Zongli Xu, Changchun Xie, Jack A. Taylor, Liang Niu:
ipDMR: identification of differentially methylated regions with interval P-values. 711-713 - Niema Moshiri:
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes. 714-716 - Michaela Frye, Susanne Bornelöv:
CONCUR: quick and robust calculation of codon usage from ribosome profiling data. 717-719 - Omer Sabary, Yoav Orlev, Roy Shafir, Leon Anavy, Eitan Yaakobi, Zohar Yakhini:
SOLQC: Synthetic Oligo Library Quality Control tool. 720-722 - Emanuela Iovino, Marco Seri, Tommaso Pippucci:
unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level. 723-725 - Markku Kuismin, Mikko J. Sillanpää:
MCPeSe: Monte Carlo penalty selection for graphical lasso. 726-727 - Xiuwen Zheng, J. Wade Davis:
SAIGEgds - an efficient statistical tool for large-scale PheWAS with mixed models. 728-730 - Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek:
TRTools: a toolkit for genome-wide analysis of tandem repeats. 731-733 - Matthew I. J. Raybould, Aleksandr Kovaltsuk, Claire Marks, Charlotte M. Deane:
CoV-AbDab: the coronavirus antibody database. 734-735
Volume 37, Number 6, May 2021
- Rui Yin, Zihan Luo, Pei Zhuang, Zhuoyi Lin, Chee Keong Kwoh:
VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments. 737-743 - Melanie Kirsche, Arun Das, Michael C. Schatz:
Sapling: accelerating suffix array queries with learned data models. 744-749 - Runbin Tang, Zuguo Yu, Yuanlin Ma, Yaoqun Wu, Yi-Ping Phoebe Chen, Limsoon Wong, Jinyan Li:
Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning. 750-758 - Xin Bai, Jie Ren, Yingying Fan, Fengzhu Sun:
KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate. 759-766 - Hannah De Los Santos, Kristin P. Bennett, Jennifer M. Hurley:
MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data. 767-774 - Liang Chen, Qiuyan He, Yuyao Zhai, Minghua Deng:
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation. 775-784 - Mingming Gong, Peng Liu, Frank C. Sciurba, Petar Stojanov, Dacheng Tao, George C. Tseng, Kun Zhang, Kayhan Batmanghelich:
Unpaired data empowers association tests. 785-792 - Julie Jiang, Li-Ping Liu, Soha Hassoun:
Learning graph representations of biochemical networks and its application to enzymatic link prediction. 793-799 - Jeffrey N. Law, Shiv D. Kale, T. M. Murali:
Accurate and efficient gene function prediction using a multi-bacterial network. 800-806 - Andres M. Cifuentes-Bernal, Vu Viet Hoang Pham, Xiaomei Li, Lin Liu, Jiuyong Li, Thuc Duy Le:
A pseudotemporal causality approach to identifying miRNA-mRNA interactions during biological processes. 807-814 - Meng Wang, Lihua Jiang, Ruiqi Jian, Joanne Y. Chan, Qing Liu, Michael Snyder, Hua Tang:
RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. 815-821 - Abdur Rahman Mohd Abul Basher, Steven J. Hallam:
Leveraging heterogeneous network embedding for metabolic pathway prediction. 822-829 - Kexin Huang, Cao Xiao, Lucas M. Glass, Jimeng Sun:
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. 830-836 - Ahmad Borzou, Rovshan G. Sadygov:
A novel estimator of the interaction matrix in Graphical Gaussian Model of omics data using the entropy of non-equilibrium systems. 837-844 - Sergio Picart-Armada, Wesley K. Thompson, Alfonso Buil, Alexandre Perera-Lluna:
The effect of statistical normalization on network propagation scores. 845-852 - Jun Chen, Azza Althagafi, Robert Hoehndorf:
Predicting candidate genes from phenotypes, functions and anatomical site of expression. 853-860 - Paula A. Marin Zapata, Sina Roth, Dirk Schmutzler, Thomas Wolf, Erica Manesso, Djork-Arné Clevert:
Self-supervised feature extraction from image time series in plant phenotyping using triplet networks. 861-867 - Heather Manching, Randall J. Wisser:
SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation. 868-870 - Russell Lewis McLaughlin:
REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data. 871-872 - Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. 873-875 - Thomas Peacock, James M. Heather, Tahel Ronel, Benny Chain:
Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation? 876-878 - Cui Su, Jun Pang:
CABEAN: a software for the control of asynchronous Boolean networks. 879-881 - Massimo Andreatta, Santiago J. Carmona:
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data. 882-884 - Blaz Skrlj, Nika Erzen, Nada Lavrac, Tanja Kunej, Janez Konc:
CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets. 885-887
Volume 37, Number 7, May 2021
- Felix Kallenborn, Andreas Hildebrandt, Bertil Schmidt:
CARE: context-aware sequencing read error correction. 889-895 - Yiwei Li, Geoffrey Brian Golding, Lucian Ilie:
DELPHI: accurate deep ensemble model for protein interaction sites prediction. 896-904 - Marleen Balvert, Xiao Luo, Ernestina Hauptfeld, Alexander Schönhuth, Bas E. Dutilh:
OGRE: Overlap Graph-based metagenomic Read clustEring. 905-912 - Xiaopeng Jin, Qing Liao, Hang Wei, Jun Zhang, Bin Liu:
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection. 913-920 - Sylvain Träger, Giorgio Tamò, Deniz Aydin, Giulia Fonti, Martina Audagnotto, Matteo Dal Peraro:
CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. 921-928 - Tomer Meirson, David Bomze, Gal Markel:
Structural basis of SARS-CoV-2 spike protein induced by ACE2. 929-936 - Yang Liu, Weikang Gong, Yanpeng Zhao, Xueqing Deng, Shan Zhang, Chunhua Li:
aPRBind: protein-RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks. 937-942 - Maria Kadukova, Karina dos Santos Machado, Pablo Chacón, Sergei Grudinin:
KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. 943-950 - Stephen Todd, Peter Todd, Simon J. McGowan, James R. Hughes, Yasutaka Kakui, Frederic Fol Leymarie, William H. Latham, Stephen Taylor:
CSynth: an interactive modelling and visualization tool for 3D chromatin structure. 951-955 - Alan Zammit, Leon S. Helwerda, René C. L. Olsthoorn, Fons J. Verbeek, Alexander P. Gultyaev:
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. 956-962 - Daniel Osório, James J. Cai:
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. 963-967 - Dongshunyi Li, Jun Ding, Ziv Bar-Joseph:
Identifying signaling genes in spatial single-cell expression data. 968-975 - Tao Jiang, Yuanyuan Li, Alison A. Motsinger-Reif:
Knockoff boosted tree for model-free variable selection. 976-983 - Weiguang Mao, Javad Rahimikollu, Ryan Hausler, Maria Chikina:
DataRemix: a universal data transformation for optimal inference from gene expression datasets. 984-991 - Gen Li, Swagata Pahari, Adithya Krishna Murthy, Siqi Liang, Robert Fragoza, Haiyuan Yu, Emil Alexov:
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. 992-999 - Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac:
Classification in biological networks with hypergraphlet kernels. 1000-1007 - Jinmyung Jung:
Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells. 1008-1014 - Quang Tran, Alexej Abyzov:
LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. 1015-1017 - Martin Hölzer, Manja Marz:
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. 1018-1020 - Shixu He, Zhibo Huang, Xiaohan Wang, Lin Fang, Shengkang Li, Yong Zhang, Gengyun Zhang:
SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters. 1021-1023 - Po-E Li, Adán Myers y Gutiérrez, Karen Davenport, Mark Flynn, Bin Hu, Chien-Chi Lo, Elais Player Jackson, Migun Shakya, Yan Xu, Jason D. Gans, Patrick S. G. Chain:
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. 1024-1025 - Néli J. Fonseca-Júnior, Marcelo Q. L. Afonso, Lucas Carrijo de Oliveira, Lucas Bleicher:
CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis. 1026-1028 - Kui Xu, Nan Liu, Jingle Xu, Chunlong Guo, Lingyun Zhao, Hongwei Wang, Qiangfeng Cliff Zhang:
VRmol: an integrative web-based virtual reality system to explore macromolecular structure. 1029-1031 - Jan Niclas Wolf, Marcus Keßler, Jörg Ackermann, Ina Koch:
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. 1032-1034 - Jessica Ewald, Othman Soufan, Jianguo Xia, Niladri Basu:
FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data. 1035-1036 - Quan Do, Bich Hai Ho, Pierre Larmande:
PyRice: a Python package for querying Oryza sativa databases. 1037-1038
Volume 37, Number 8, May 2021
- Nan Hao, Huawei Xin, Xiaowei Shi, Jie Xin, Haijuan Zhang, Shaofen Guo, Zhen Wang, Chunxiang Hao:
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. 1039-1044 - Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J. Park:
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. 1045-1051 - Weiwei Zhang, Hao Wu, Ziyi Li:
Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. 1052-1059 - Lijun Cai, Xuanbai Ren, Xiangzheng Fu, Li Peng, Mingyu Gao, Xiangxiang Zeng:
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor. 1060-1067 - Babak Saremi, Moritz Kohls, Pamela Liebig, Ursula Siebert, Klaus Jung:
Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files. 1068-1075 - Borja Pitarch, Juan A. G. Ranea, Florencio Pazos:
Protein residues determining interaction specificity in paralogous families. 1076-1082 - Vaibhav Rajan, Ziqi Zhang, Carl Kingsford, Xiuwei Zhang:
Maximum likelihood reconstruction of ancestral networks by integer linear programming. 1083-1092 - Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang:
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks. 1093-1098 - Sayoni Das, Harry M. Scholes, Neeladri Sen, Christine A. Orengo:
CATH functional families predict functional sites in proteins. 1099-1106 - Johannes Smolander, Sini Junttila, Mikko S. Venäläinen, Laura L. Elo:
ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data. 1107-1114 - Ting Jin, Nam D. Nguyen, Flaminia Talos, Daifeng Wang:
ECMarker: interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. 1115-1124 - Li Liu, Pramod Chandrashekar, Biao Zeng, Maxwell D. Sanderford, Sudhir Kumar, Greg Gibson:
TreeMap: a structured approach to fine mapping of eQTL variants. 1125-1134 - Bilal Shaker, Myeong-Sang Yu, Jin Sook Song, Sunjoo Ahn, Jae Yong Ryu, Kwang-Seok Oh, Dokyun Na:
LightBBB: computational prediction model of blood-brain-barrier penetration based on LightGBM. 1135-1139 - Thin Nguyen, Hang Le, Thomas P. Quinn, Tri Nguyen, Thuc Duy Le, Svetha Venkatesh:
GraphDTA: predicting drug-target binding affinity with graph neural networks. 1140-1147 - Julio Aracena, Luis Cabrera-Crot, Lilian Salinas:
Finding the fixed points of a Boolean network from a positive feedback vertex set. 1148-1155 - Peiliang Lou, Yuxin Dong, Antonio Jimeno-Yepes, Chen Li:
A representation model for biological entities by fusing structured axioms with unstructured texts. 1156-1163 - Raghu Chandramohan, Nipun Kakkar, Angshumoy Roy, D. Williams Parsons:
reconCNV: interactive visualization of copy number data from high-throughput sequencing. 1164-1167 - Arnav Moudgil, Daofeng Li, Silas Hsu, Deepak Purushotham, Ting Wang, Robi D. Mitra:
The qBED track: a novel genome browser visualization for point processes. 1168-1170 - Xiaolei Zhang, Matthew Wakeling, James S. Ware, Nicola Whiffin:
Annotating high-impact 5′untranslated region variants with the UTRannotator. 1171-1173 - Alessandro Pedretti, Angelica Mazzolari, Silvia Gervasoni, Laura Fumagalli, Giulio Vistoli:
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects. 1174-1175 - Hongzhao Shao, Stephen Boulton, Cristina Olivieri, Hebatallah Mohamed, Madoka Akimoto, Manu Veliparambil Subrahmanian, Gianluigi Veglia, John L. Markley, Giuseppe Melacini, Woonghee Lee:
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. 1176-1177 - Derek W. Brown, Timothy A. Myers, Mitchell J. Machiela:
PCAmatchR: a flexible R package for optimal case-control matching using weighted principal components. 1178-1181 - Dachuan Zhang, Tong Zhang, Sheng Liu, Dandan Sun, Shaozhen Ding, Xingxiang Cheng, Pengli Cai, Ailin Ren, Mengying Han, Dongliang Liu, Cancan Jia, Linlin Gong, Rui Zhang, Huadong Xing, Weizhong Tu, Junni Chen, Qian-Nan Hu:
SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model. 1182-1183 - Lu-Chi Liu, Ming-Yang Ho, Bo-Han Su, San-Yuan Wang, Ming-Tsung Hsu, Yufeng J. Tseng:
PanGPCR: predictions for multiple targets, repurposing and side effects. 1184-1186 - Maxat Kulmanov, Robert Hoehndorf:
DeepGOPlus: improved protein function prediction from sequence. 1187
Volume 37, Number 9, June 2021
- Sisheng Liu, Jinpeng Liu, Yanqi Xie, Tingting Zhai, Eugene W. Hinderer, Arnold J. Stromberg, Nathan L. Vanderford, Jill M. Kolesar, Hunter N. B. Moseley, Li Chen, Chunming Liu, Chi Wang:
MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations. 1189-1197 - Peter Ebert, Marcel H. Schulz:
Fast detection of differential chromatin domains with SCIDDO. 1198-1205 - Arnab Mallik, Lucian Ilie:
ALeS: adaptive-length spaced-seed design. 1206-1210 - Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto:
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. 1211-1217 - Louis Becquey, Eric Angel, Fariza Tahi:
RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures. 1218-1224 - Yidan Eden Sun, Heather J. Zhou, Jingyi Jessica Li:
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. 1225-1233 - Cynthia Z. Ma, Michael R. Brent:
Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. 1234-1245 - Laura Baumgartner, J. J. Reagh, Miguel Ángel González Ballester, Jérôme Noailly:
Simulating intervertebral disc cell behaviour within 3D multifactorial environments. 1246-1253 - Narmada Sambaturu, Vaidehi Pusadkar, Sridhar Hannenhalli, Nagasuma Chandra:
PathExt: a general framework for path-based mining of omics-integrated biological networks. 1254-1262 - Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio, Luca Pasquini, Antti Häkkinen, Elenora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Mauro Biffoni, Anniina Färkkilä, Sampsa Hautaniemi:
Agile workflow for interactive analysis of mass cytometry data. 1263-1268 - Giulia Simoni, Chanchala Kaddi, Mengdi Tao, Federico Reali, Danilo Tomasoni, Corrado Priami, Karim Azer, Susana Neves-Zaph, Luca Marchetti:
A robust computational pipeline for model-based and data-driven phenotype clustering. 1269-1277 - Victor Barreto Mesquita, Florêncio Mendes Oliveira Filho, Paulo Canas Rodrigues:
Detection of crossover points in detrended fluctuation analysis: an application to EEG signals of patients with epilepsy. 1278-1284 - Yue Wang, Kunqi Chen, Zhen Wei, Frans Coenen, Jionglong Su, Jia Meng:
MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. 1285-1291 - Anthony Westbrook, Elizabeth Varki, W. Kelley Thomas:
RepeatFS: a file system providing reproducibility through provenance and automation. 1292-1296 - Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin, Víctor González-Ruiz, Serge Rudaz, Julien Boccard:
Network principal component analysis: a versatile tool for the investigation of multigroup and multiblock datasets. 1297-1303 - Yi Liu, Benjamin L. Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Oliver Lloyd, Marina Vabistsevits, Tom R. Gaunt:
EpiGraphDB: a database and data mining platform for health data science. 1304-1311 - Chayan Kumar Saha, Rodrigo Sanches Pires, Harald Brolin, Maxence Delannoy, Gemma Catherine Atkinson:
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation. 1312-1314 - Heng Li, Jiazhen Rong:
Bedtk: finding interval overlap with implicit interval tree. 1315-1316 - Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson:
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities. 1317-1318 - Shanwen Sun, Lei Xu, Quan Zou, Guohua Wang:
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method. 1319-1321 - Fairlie Reese, Ali Mortazavi:
Swan: a library for the analysis and visualization of long-read transcriptomes. 1322-1323 - Wei Huang, Ping Zheng, Zhenhai Cui, Zhuo Li, Yifeng Gao, Helong Yu, You Tang, Xiaohui Yuan, Zhiwu Zhang:
MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes. 1324-1326 - Vivek Kohar, Danya Gordin, Ataur Katebi, Herbert Levine, José N. Onuchic, Mingyang Lu:
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. 1327-1329 - Tobias Newmiwaka, Benjamin Engelhardt, Philipp Wendland, Dominik Kahl, Holger Fröhlich, Maik Kschischo:
SEEDS: data driven inference of structural model errors and unknown inputs for dynamic systems biology. 1330-1331 - Daniel Domingo-Fernández, Shounak Baksi, Bruce Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology. 1332-1334 - Loane Danès, Nicolas Tchitchek, Christophe Bécavin:
Bacnet: a user-friendly platform for building multi-omics websites. 1335-1336 - Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning:
Scool: a new data storage format for single-cell Hi-C data. 1337 - Johan Nyström-Persson, Gabriel Keeble-Gagnère, Niamat Zawad:
Compact and evenly distributed k-mer binning for genomic sequences. 1338
Volume 37, Number 10, June 2021
- Xiang-He Meng, Hong-Mei Xiao, Hong-Wen Deng:
Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants. 1339-1344 - Mojtaba Bahrami, Malosree Maitra, Corina Nagy, Gustavo Turecki, Hamid R. Rabiee, Yue Li:
Deep feature extraction of single-cell transcriptomes by generative adversarial network. 1345-1351 - Victor Alexandre Padilha, Omer S. Alkhnbashi, Van Dinh Tran, Shiraz A. Shah, André C. P. L. F. de Carvalho, Rolf Backofen:
Casboundary: automated definition of integral Cas cassettes. 1352-1359 - Samuel M. Nicholls, Wayne Aubrey, Kurt De Grave, Leander Schietgat, Christopher J. Creevey, Amanda Clare:
On the complexity of haplotyping a microbial community. 1360-1366 - Swarnendu Tripathi, Nikita R. Dsouza, Raul Urrutia, Michael T. Zimmermann:
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. 1367-1375 - Norberto Sánchez-Cruz, José L. Medina-Franco, Jordi Mestres, Xavier Barril:
Extended connectivity interaction features: improving binding affinity prediction through chemical description. 1376-1382 - Tiago Olivoto, Maicon Nardino:
MGIDI: toward an effective multivariate selection in biological experiments. 1383-1389 - Xiaofeng Zhu, Xiaoyin Li, Rong Xu, Tao Wang:
An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics. 1390-1400 - Hyun-Myung Woo, Byung-Jun Yoon:
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes. 1401-1410 - Francesco Bardozzo, Pietro Lió, Roberto Tagliaferri:
Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks. 1411-1419 - Antonio de Falco, Zoltán Dezsö, Francesco Ceccarelli, Luigi Cerulo, Angelo Ciaramella, Michele Ceccarelli:
Adaptive one-class Gaussian processes allow accurate prioritization of oncology drug targets. 1420-1427 - Robert W. Gregg, Fathima Shabnam, Jason E. Shoemaker:
Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production. 1428-1434 - Alexia Giannoula, Emilio Centeno, Miguel Angel Mayer, Ferran Sanz, Laura I. Furlong:
A system-level analysis of patient disease trajectories based on clinical, phenotypic and molecular similarities. 1435-1443 - Beatriz García Jiménez, Jorge Muñoz, Sara Cabello, Joaquín Medina, Mark D. Wilkinson:
Predicting microbiomes through a deep latent space. 1444-1451 - Inna Chervoneva, Amy R. Peck, Misung Yi, Boris Freydin, Hallgeir Rui:
Quantification of spatial tumor heterogeneity in immunohistochemistry staining images. 1452-1460 - Krzysztof J. Szkop, David S. Moss, Irene Nobeli:
flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. 1461-1464 - Yoshiaki Yasumizu, Atsushi Hara, Shimon Sakaguchi, Naganari Ohkura:
VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data. 1465-1467 - Mujtahid Akon, Muntashir Akon, Mohimenul Kabir, Mohammad Saifur Rahman, M. Sohel Rahman:
ADACT: a tool for analysing (dis)similarity among nucleotide and protein sequences using minimal and relative absent words. 1468-1470 - Giacomo Janson, Alessandro Paiardini:
PyMod 3: a complete suite for structural bioinformatics in PyMOL. 1471-1472 - David J. Wooten, Réka Albert:
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy. 1473-1474 - Hasan Balci, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein, Charles Auffray, Özgün Babur, Emek Demir, Ugur Dogrusoz:
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. 1475-1477 - Jorge Álvarez-Jarreta, Patricia Rodrigues, Eoin Fahy, Anne O'connor, Anna Price, Caroline Gaud, Simon Andrews, H. Paul Benton, Gary Siuzdak, Jade I Hawksworth, Maria Valdivia-Garcia, Stuart M. Allen, Valerie B. O'Donnell:
LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. 1478-1479 - Juan Saez Hidalgo, Karen Y. Oróstica, Anamaria Sanchez-Daza, Alvaro Olivera-Nappa:
BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA. 1480-1481 - Romain Fernandez, Cédric Moisy:
Fijiyama: a registration tool for 3D multimodal time-lapse imaging. 1482-1484 - Gabriel Landini, Giovanni Martinelli, Filippo Piccinini:
Colour deconvolution: stain unmixing in histological imaging. 1485-1487
Volume 37, Number 11, July 2021
- Ron Zeira, Ron Shamir:
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. 1489-1496 - Ramesh Rajaby, Wing-Kin Sung:
SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing. 1497-1505 - Jia-Ming Chang, Evan W. Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cédric Notredame:
Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. 1506-1514 - Baldomero Imbernón, Antonio Serrano, Andrés Bueno-Crespo, José L. Abellán, Horacio Pérez Sánchez, José M. Cecilia:
METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking. 1515-1520 - Yuqing Zhang, Prasad Patil, W. Evan Johnson, Giovanni Parmigiani:
Robustifying genomic classifiers to batch effects via ensemble learning. 1521-1527 - Andrew E. Teschendorff, Alok K. Maity, Xue Hu, Weiyan Chen, Matthias Lechner:
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data. 1528-1534 - Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya:
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. 1535-1543 - Hyejin Kang, Hongryul Ahn, Kyuri Jo, Minsik Oh, Sun Kim:
mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. 1544-1553 - Le Zhang, Guangdi Liu, Meijing Kong, Tingting Li, Dan Wu, Xiaobo Zhou, Chuanwei Yang, Lei Xia, Zhenzhou Yang, Luonan Chen:
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model. 1554-1561 - Byunghan Lee, Hyeyoung Min, Sungroh Yoon:
MUGAN: multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. 1562-1570 - Ignacio Díaz Blanco, José M. Enguita, Ana González, Diego García-Pérez, Abel A. Cuadrado, María D. Chiara, Nuria Valdés:
Morphing projections: a new visual technique for fast and interactive large-scale analysis of biomedical datasets. 1571-1580 - Hao Fei, Yue Zhang, Yafeng Ren, Donghong Ji:
A span-graph neural model for overlapping entity relation extraction in biomedical texts. 1581-1589 - Shixiang Wang, Ziyu Tao, Tao Wu, Xue-Song Liu:
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis. 1590-1592 - Etienne Routhier, Ayman Bin Kamruddin, Julien Mozziconacci:
keras_dna: a wrapper for fast implementation of deep learning models in genomics. 1593-1594 - Nehemiah Wilson, Ni Zhao, Xiang Zhan, Hyunwook Koh, Weijia Fu, Jun Chen, Hongzhe Li, Michael C. Wu, Anna M. Plantinga:
MiRKAT: kernel machine regression-based global association tests for the microbiome. 1595-1597 - Ting Wei, Jinfu J. Nie, Nicholas B. Larson, Zhenqing Ye, Jeanette E. Eckel-Passow, Keith D. Robertson, Jean-Pierre A. Kocher, Liguo Wang:
CpGtools: a python package for DNA methylation analysis. 1598-1599 - Héctor Rodríguez-Pérez, Laura Ciuffreda, Carlos Flores:
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data. 1600-1601 - Carlos Pintado, Jaime Santos, Valentín Iglesias, Salvador Ventura:
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins. 1602-1603 - Yuansheng Liu, Xiaocai Zhang, Quan Zou, Xiangxiang Zeng:
Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers. 1604-1606 - Aziz Khan, Rafael Riudavets Puig, Paul Boddie, Anthony Mathelier:
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. 1607-1609 - Ahmed Ibrahem Hafez, Ricardo Futami, Amir Arastehfar, Farnaz Daneshnia, Ana Miguel, Francisco J. Roig, Beatriz Soriano, Jaume Pérez-Sánchez, Teun Boekhout, Toni Gabaldón, Carlos Lloréns:
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. 1610-1612 - Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski:
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. 1613-1615 - Renmin Han, Lun Li, Peng Yang, Fa Zhang, Xin Gao:
A novel constrained reconstruction model towards high-resolution subtomogram averaging. 1616-1626 - Anhui Huang, Dianting Liu:
EBglmnet: a comprehensive R package for sparse generalized linear regression models. 1627-1629 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB Overton Prize: Jian Peng. 1630-1631 - Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura:
CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data. 1632-1634 - Michael G. Leeming, Sean O'Callaghan, Luana Licata, Marta Iannuccelli, Prisca Lo Surdo, Elisa Micarelli, Ching-Seng Ang, Shuai Nie, Swati Varshney, Sadia Ameen, Heung-Chin Cheng, Nicholas A. Williamson:
Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets. 1635-1636 - Sage Hahn, Dekang Yuan, Wesley K. Thompson, Max M. Owens, Nicholas A. Allgaier, Hugh Garavan:
Brain Predictability toolbox: a Python library for neuroimaging-based machine learning. 1637-1638
Volume 37, Number 12, July 2021
- Alaina Shumate, Steven L. Salzberg:
Liftoff: accurate mapping of gene annotations. 1639-1643 - Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz:
Genome-scale de novo assembly using ALGA. 1644-1651 - Yi-Juan Hu, Andrea Lane, Glen A. Satten:
A rarefaction-based extension of the LDM for testing presence-absence associations in the microbiome. 1652-1657 - Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo:
Alignment-free Genomic Analysis via a Big Data Spark Platform. 1658-1665 - Vladimir Smirnov, Tandy J. Warnow:
MAGUS: Multiple sequence Alignment using Graph clUStering. 1666-1672 - Susana Posada-Céspedes, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J. Metzner, Niko Beerenwinkel:
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. 1673-1680 - Stelios K. Mylonas, Apostolos Axenopoulos, Petros Daras:
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins. 1681-1690 - Olga I. Zolotareva, Sahand Khakabimamaghani, Olga I Isaeva, Zoe Chervontseva, Alexey Savchik, Martin Ester:
Identification of differentially expressed gene modules in heterogeneous diseases. 1691-1698 - Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love:
Compression of quantification uncertainty for scRNA-seq counts. 1699-1707 - Zahra Razaghi-Moghadam, Zoran Nikoloski:
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. 1717-1723 - Eric Bach, Simon Rogers, John Williamson, Juho Rousu:
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification. 1724-1731 - Alexey Ovchinnikov, Isabel Cristina Pérez-Verona, Gleb Pogudin, Mirco Tribastone:
CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations. 1732-1738 - Masaki Asada, Makoto Miwa, Yutaka Sasaki:
Using drug descriptions and molecular structures for drug-drug interaction extraction from literature. 1739-1746 - Lianne Abrahams:
Single-cell systems analysis: decision geometry in outliers. 1747-1755 - Dolors Pelegí-Sisó, Paula de Prado, Justiina Ronkainen, Mariona Bustamante, Juan R. González:
methylclock: a Bioconductor package to estimate DNA methylation age. 1759-1760 - Frédéric Lemoine, Luc Blassel, Jakub Voznica, Olivier Gascuel:
COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM. 1761-1762 - Nuwan Goonasekera, Alexandru Mahmoud, John Chilton, Enis Afgan:
GalaxyCloudRunner: enhancing scalable computing for Galaxy. 1763-1765 - John A. Rhodes, Hector Baños, Jonathan D. Mitchell, Elizabeth S. Allman:
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. 1766-1768 - Anku Gupta, Mohit Choudhary, Sanjay Kumar Mohanty, Aayushi Mittal, Krishan Gupta, Aditya Arya, Suvendu Kumar, Nikhil Katyayan, Nilesh Kumar Dixit, Siddhant Kalra, Manshi Goel, Megha Sahni, Vrinda Singhal, Tripti Mishra, Debarka Sengupta, Gaurav Ahuja:
Machine-OlF-Action: a unified framework for developing and interpreting machine-learning models for chemosensory research. 1769-1771 - Nam D. Nguyen, Ting Jin, Daifeng Wang:
Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. 1772-1775 - Johann F. Jadebeck, Axel Theorell, Samuel Leweke, Katharina Nöh:
HOPS: high-performance library for (non-)uniform sampling of convex-constrained models. 1776-1777 - Nick Strayer, Jana K. Shirey-Rice, Yu Shyr, Joshua C. Denny, Jill M. Pulley, Yaomin Xu:
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. 1778-1780 - Manuel Bernal Llinares, Javier Ferrer-Gómez, Nick S. Juty, Carole A. Goble, Sarala M. Wimalaratne, Henning Hermjakob:
Identifiers.org: Compact Identifier services in the cloud. 1781-1782 - Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz:
Corrigendum to: ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays. 1783 - Maximilian Collatz, Florian Mock, Emanuel Barth, Martin Hölzer, Konrad Sachse, Manja Marz:
EpiDope: a deep neural network for linear B-cell epitope prediction. 1784
Volume 37, Number 13, July 2021
- Tony Robinson, Jim Harkin, Priyank Shukla:
Hardware acceleration of genomics data analysis: challenges and opportunities. 1785-1795 - Michaela Areti Zervou, Effrosyni Doutsi, Pavlos Pavlidis, Panagiotis Tsakalides:
Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs. 1796-1804 - Joan Carles Pons, David Páez-Espino, Gabriel Riera, Natalia Ivanova, Nikos Kyrpides, Mercè Llabrés:
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. 1805-1813 - Jianxiong Tang, Jianxiao Zou, Mei Fan, Qi Tian, Jiyang Zhang, Shicai Fan:
CaMelia: imputation in single-cell methylomes based on local similarities between cells. 1814-1820 - Xi Zeng, Linghao Zhao, Chenhang Shen, Yi Zhou, Guoliang Li, Wing-Kin Sung:
HIVID2: an accurate tool to detect virus integrations in the host genome. 1821-1827 - Phillipe Loher, Nestoras Karathanasis, Eric Londin, Paul F. Bray, Venetia Pliatsika, Aristeidis G. Telonis, Isidore Rigoutsos:
IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets. 1828-1838 - Nidhi Shah, Erin K. Molloy, Mihai Pop, Tandy J. Warnow:
TIPP2: metagenomic taxonomic profiling using phylogenetic markers. 1839-1845 - Ting-Hsuan Wang, Cheng-Ching Huang, Jui-Hung Hung:
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences. 1846-1852 - Daniel A. Nissley, Anna Carbery, Mark Chonofsky, Charlotte M. Deane:
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. 1853-1859 - Juho Timonen, Henrik Mannerström, Aki Vehtari, Harri Lähdesmäki:
lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data. 1860-1867 - Jonas Meisner, Siyang Liu, Mingxi Huang, Anders Albrechtsen:
Large-scale inference of population structure in presence of missingness using PCA. 1868-1875 - Ksenia Lavrichenko, Øyvind Helgeland, Pål R. Njølstad, Inge Jonassen, Stefan Johansson:
SeeCiTe: a method to assess CNV calls from SNP arrays using trio data. 1876-1883 - Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. 1884-1890 - Weizhong Zhao, Yao Zhao, Xingpeng Jiang, Tingting He, Fan Liu, Ning Li:
Efficient multiple biomedical events extraction via reinforcement learning. 1891-1899 - Yassene Mohammed, Pallab Bhowmick, Sarah A. Michaud, Albert Sickmann, Christoph H. Borchers:
Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. 1900-1908 - Edith M. Ross, Kerstin Haase, Peter Van Loo, Florian Markowetz:
Allele-specific multi-sample copy number segmentation in ASCAT. 1909-1911 - Gonzalo López, Laura E. Egolf, Federico M. Giorgi, Sharon J. Diskin, Adam A. Margolin:
svpluscnv: analysis and visualization of complex structural variation data. 1912-1914 - Dandan Huang, Zhao Wang, Yao Zhou, Qian Liang, Pak Chung Sham, Hongcheng Yao, Mulin Jun Li:
vSampler: fast and annotation-based matched variant sampling tool. 1915-1917 - Rajeeva Musunuri, Kanika Arora, André Corvelo, Minita Shah, Jennifer Shelton, Michael C. Zody, Giuseppe Narzisi:
Somatic variant analysis of linked-reads sequencing data with Lancet. 1918-1919 - Esaie Kuitche, Yanchun Qi, Nadia Tahiri, Jack Parmer, Aïda Ouangraoua:
DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation. 1920-1922 - Richard H. Adams, Todd A. Castoe, Michael Degiorgio:
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. 1923-1925 - Naifu Zhang, Xiaohe Yu, Xinchao Zhang, Sheena D'arcy:
HD-eXplosion: visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering. 1926-1927 - Lyuba V. Bozhilova, Javier Pardo-Diaz, Gesine Reinert, Charlotte M. Deane:
COGENT: evaluating the consistency of gene co-expression networks. 1928-1929 - R. Pinto-Cámara, Alejandro Linares, D. S. Moreno-Gutiérrez, Haydee O. Hernández, Jose Damian Martinez Reyes, J. M. Rendón-Mancha, Christopher D. Wood, Adán Guerrero:
FCSlib: an open-source tool for fluorescence fluctuation spectroscopy analysis for mobility, number and molecular brightness in R. 1930-1931
Volume 37, Number 14, August 2021
- Javier Pardo-Diaz, Lyuba V. Bozhilova, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert:
Robust gene coexpression networks using signed distance correlation. 1982-1989 - Armin Rauschenberger, Enrico Glaab, Mark A. van de Wiel:
Predictive and interpretable models via the stacked elastic net. 2012-2016 - Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher:
Succinct dynamic de Bruijn graphs. 1946-1952 - Yang Zhang, Tianyuan Liu, Jing Wang, Bohao Zou, Le Li, Linhui Yao, Kechen Chen, Lin Ning, Bingyi Wu, Xiaoyang Zhao, Dong Wang:
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. 2025-2032 - Martin R. Smith:
Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees. 2077-2078 - Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data. 2079
- Jennifer L. Harrow, Rachel Drysdale, Andrew Smith, Susanna Repo, Jerry Lanfear, Niklas Blomberg:
ELIXIR: providing a sustainable infrastructure for life science data at European scale. 2506-2511 - Dimitris V. Manatakis, Aaron Vandevender, Elias S. Manolakos:
Erratum to: An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures. 2512
Volume 37, Number 15, August 2021
- Bernhard Haubold, Fabian Klötzl, Lars Hellberg, Daniel Thompson, Markus Cavalar:
Fur: Find unique genomic regions for diagnostic PCR. 2081-2087 - Stefano Franzini, Marco Di Stefano, Cristian Micheletti:
essHi-C: essential component analysis of Hi-C matrices. 2088-2094 - Mengyang Xu, Lidong Guo, Xiao Du, Lei Li, Brock A. Peters, Li Deng, Ou Wang, Fang Chen, Jun Wang, Zhesheng Jiang, Jinglin Han, Ming Ni, Huanming Yang, Xun Xu, Xin Liu, Jie Huang, Guangyi Fan:
Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios. 2095-2102 - Yanrong Ji, Zhihan Zhou, Han Liu, Ramana V. Davuluri:
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. 2112-2120 - Emmanuel Sapin, Matthew C. Keller:
Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data. 2121-2125 - Gregor Entzian, Ivo L. Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer:
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. 2126-2133 - Fergus Imrie, Anthony R. Bradley, Charlotte M. Deane:
Generating property-matched decoy molecules using deep learning. 2134-2141 - Peter Hettegger, Klemens Vierlinger, Andreas Weinhäusel:
Random rotation for identifying differentially expressed genes with linear models following batch effect correction. 2142-2149 - Jie-Huei Wang, Yi-Hau Chen:
Network-adjusted Kendall's Tau Measure for Feature Screening with Application to High-dimensional Survival Genomic Data. 2150-2156 - Hao Wang, Pengfei Liang, Lei Zheng, Chunshen Long, Hanshuang Li, Yongchun Zuo:
eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition. 2157-2164 - Jean-Michel Nguyen, Pascal Jézéquel, Pierre Gillois, Luisa Silva, Faouda Ben Azzouz, Sophie Lambert-Lacroix, Philippe P. Juin, Mario Campone, Aurélie Gaultier, Alexandre Moreau-Gaudry, Daniel Antonioli:
Random forest of perfect trees: concept, performance, applications and perspectives. 2165-2174 - Luca Cardelli, Isabel Cristina Pérez-Verona, Mirco Tribastone, Max Tschaikowski, Andrea Vandin, Tabea Waizmann:
Exact maximal reduction of stochastic reaction networks by species lumping. 2175-2182 - Yuanyuan Han, Lan Huang, Fengfeng Zhou:
A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers. 2183-2189 - Kishlay Jha, Guangxu Xun, Aidong Zhang:
Continual representation learning for evolving biomedical bipartite networks. 2190-2197 - Phuc-Loi Luu, Phuc-Thinh Ong, Tran Thai Huu Loc, Dilys Lam, Ruth Pidsley, Clare Stirzaker, Susan J. Clark:
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection. 2198-2200 - Jiannan Liu, Chuanpeng Dong, Yunlong Liu, Huanmei Wu:
CGPE: an integrated online server for Cancer Gene and Pathway Exploration. 2201-2202 - Markus Hiltunen, Martin Ryberg, Hanna Johannesson:
ARBitR: an overlap-aware genome assembly scaffolder for linked reads. 2203-2205 - Diogo B. Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke:
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. 2206-2208 - Yan Gao, Yongzhuang Liu, Yanmei Ma, Bo Liu, Yadong Wang, Yi Xing:
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. 2209-2211 - Ming Tang, Yasin Kaymaz, Brandon L. Logeman, Stephen Eichhorn, Zhengzheng S. Liang, Catherine Dulac, Timothy B. Sackton:
Evaluating single-cell cluster stability using the Jaccard similarity index. 2212-2214 - Hannes P. Eggertsson, Bjarni V. Halldórsson:
read_haps: using read haplotypes to detect same species contamination in DNA sequences. 2215-2217 - Carl Beuchel, Holger Kirsten, Uta Ceglarek, Markus Scholz:
Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis. 2218-2220 - Zhuohang Yu, Zengrui Wu, Weihua Li, Guixia Liu, Yun Tang:
MetaADEDB 2.0: a comprehensive database on adverse drug events. 2221-2222 - A. Sina Booeshaghi, Lior Pachter:
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x). 2223-2224
Volume 37, Number 16, August 2021
- Divon Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas:
Genozip: a universal extensible genomic data compressor. 2225-2230 - Hai Yang, Rui Chen, Dongdong Li, Zhe Wang:
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data. 2231-2237 - Wencan Zhu, Céline Lévy-Leduc, Nils Ternès:
A variable selection approach for highly correlated predictors in high-dimensional genomic data. 2238-2244 - Zachary F. Gerring, Angela Mina-Vargas, Eric R. Gamazon, Eske M. Derks:
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics. 2245-2249 - Balaram Bhattacharyya, Uddalak Mitra, Ramkishore Bhattacharyya:
Tandem repeat interval pattern identifies animal taxa. 2250-2258 - Sheng-Mao Chang, Meng Yang, Wenbin Lu, Yu-Jyun Huang, Yueyang Huang, Hung Hung, Jeffrey C. Miecznikowski, Tzu-Pin Lu, Jung-Ying Tzeng:
Gene-set integrative analysis of multi-omics data using tensor-based association test. 2259-2265 - Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye:
Detecting high-scoring local alignments in pangenome graphs. 2266-2274 - Daniele Raimondi, Jaak Simm, Adam Arany, Yves Moreau:
A novel method for data fusion over entity-relation graphs and its application to protein-protein interaction prediction. 2275-2281 - Denisa Bojkova, Jake E. McGreig, Katie-May McLaughlin, Stuart G. Masterson, Magdalena Antczak, Marek Widera, Verena Krähling, Sandra Ciesek, Mark N. Wass, Martin Michaelis, Jindrich Cinatl:
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour. 2282-2288 - Bennett J. Kapili, Anne E. Dekas:
PPIT: an R package for inferring microbial taxonomy from nifH sequences. 2289-2298 - Jérémy Charlier, Robert Nadon, Vladimir Makarenkov:
Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing. 2299-2307 - Yang Lin, Xiaoyong Pan, Hong-Bin Shen:
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. 2308-2316 - Payam Dibaeinia, Shayan Tabe-Bordbar, Tandy J. Warnow:
FASTRAL: improving scalability of phylogenomic analysis. 2317-2324 - Jacob L. Steenwyk, Thomas J. Buida, Abigail L. Labella, Yuanning Li, Xing-Xing Shen, Antonis Rokas:
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. 2325-2331 - Ilia Igashov, Kliment Olechnovic, Maria Kadukova, Ceslovas Venclovas, Sergei Grudinin:
VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures. 2332-2339 - Xuefeng Du, Haohan Wang, Zhenxi Zhu, Xiangrui Zeng, Yi-Wei Chang, Jing Zhang, Eric P. Xing, Min Xu:
Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography. 2340-2346 - Ashleigh C. Myall, Simon Perkins, David Rushton, Jonathan David, Phillippa Spencer, Andrew R. Jones, Philipp Antczak:
An OMICs-based meta-analysis to support infection state stratification. 2347-2355 - Davide Risso, Stefano Maria Pagnotta:
Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles. 2356-2364 - Valentin Junet, Judith Farrés, José M. Mas, Xavier Daura:
CuBlock: a cross-platform normalization method for gene-expression microarrays. 2365-2373 - Jinjin Tian, Jiebiao Wang, Kathryn Roeder:
ESCO: single cell expression simulation incorporating gene co-expression. 2374-2381 - Darawan Rinchai, Jessica Roelands, Mohammed Toufiq, Wouter Hendrickx, Matthew C. Altman, Davide Bedognetti, Damien Chaussabel:
BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R. 2382-2389 - Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
d-PBWT: dynamic positional Burrows-Wheeler transform. 2390-2397 - Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List:
BiCoN: network-constrained biclustering of patients and omics data. 2398-2404 - So Yeon Kim, Eun Kyung Choe, Manu K. Shivakumar, Dokyoon Kim, Kyung-Ah Sohn:
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. 2405-2413 - Meet Barot, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau:
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. 2414-2422 - Yahui Long, Min Wu, Yong Liu, Jie Zheng, Chee Keong Kwoh, Jiawei Luo, Xiaoli Li:
Graph contextualized attention network for predicting synthetic lethality in human cancers. 2432-2440 - Martin Pirkl, Niko Beerenwinkel:
Inferring perturbation profiles of cancer samples. 2441-2449 - Sachin Heerah, Roberto Molinari, Stéphane Guerrier, Amy Marshall-Colon:
Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis. 2450-2460 - Liam F. Spurr, Mehdi Touat, Alison M. Taylor, Adrian M. Dubuc, Juliann Shih, David M. Meredith, William V. Pisano, Matthew Meyerson, Keith L. Ligon, Andrew D. Cherniack, Yvonne Y. Li, Rameen Beroukhim:
Quantification of aneuploidy in targeted sequencing data using ASCETS. 2461-2463 - Travis N. Mavrich, Christian Gauthier, Lawrence Abad, Charles A. Bowman, Steven G. Cresawn, Graham F. Hatfull:
pdm_utils: a SEA-PHAGES MySQL phage database management toolkit. 2464-2466 - Hue V. Reardon, Anney Che, Brian T. Luke, Sarangan Ravichandran, Jack R. Collins, Uma S. Mudunuri:
AVIA 3.0: interactive portal for genomic variant and sample level analysis. 2467-2469 - Wenbin Ye, Tao Liu, Hongjuan Fu, Congting Ye, Guoli Ji, Xiaohui Wu:
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples. 2470-2472 - Cameron L. M. Gilchrist, Yit-Heng Chooi:
clinker & clustermap.js: automatic generation of gene cluster comparison figures. 2473-2475 - Mikko Rautiainen, Tobias Marschall:
MBG: Minimizer-based sparse de Bruijn Graph construction. 2476-2478 - Benjamin Crysup, Bruce Budowle, August E. Woerner:
ProDerAl: reference position dependent alignment. 2479-2480 - Santi Santichaivekin, Qing Yang, Jingyi Liu, Ross Mawhorter, Justin Jiang, Trenton Wesley, Yi-Chieh Wu, Ran Libeskind-Hadas:
eMPRess: a systematic cophylogeny reconciliation tool. 2481-2482 - Bruck Taddese, Antoine Garnier, Madeline Deniaud, Daniel Henrion, Marie Chabbert:
Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins. 2483-2484 - José Alquicira-Hernández, Joseph E. Powell:
Nebulosa recovers single-cell gene expression signals by kernel density estimation. 2485-2487 - Julia Yan, Nick Patterson, Vagheesh Narasimhan:
miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization. 2488-2490 - Xudong Han, Qingfei Kong, Chonghui Liu, Liang Cheng, Junwei Han:
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs. 2491-2493 - Vitor Pereira, Fernando Cruz, Miguel Rocha:
MEWpy: a computational strain optimization workbench in Python. 2494-2496 - Xiaoyu Liang, Ying Hu, Chunhua Yan, Ke Xu:
i2d: an R package for simulating data from images and the implications in biomedical research. 2497-2498 - Abeed Sarker:
LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts. 2499-2501 - Haizi Zheng, Michelle S. Zhu, Yaping Liu:
FinaleDB: a browser and database of cell-free DNA fragmentation patterns. 2502-2503 - Gubbi Vani HarshaRani, S. Moza, Naren Ramakrishnan, Upinder S. Bhalla:
SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches. 2504-2505
Volume 37, Number Supplement 1, August 2021
- Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood. 1-6 - Christophe Dessimoz, Teresa M. Przytycka:
ISMB/ECCB 2021 proceedings. 7-8 - Sanna Abrahamsson, Marcela Dávila López:
Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education. 9-15 - Shion Hosoda, Tsukasa Fukunaga, Michiaki Hamada:
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. 16-24 - Jiayu Shang, Jingzhe Jiang, Yanni Sun:
Bacteriophage classification for assembled contigs using graph convolutional network. 25-33 - Yancong Zhang, Kelsey N. Thompson, Curtis Huttenhower, Eric A. Franzosa:
Statistical approaches for differential expression analysis in metatranscriptomics. 34-41 - Omid Bazgir, Souparno Ghosh, Ranadip Pal:
Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction. 42-50 - Ziyang Wei, Shuqin Zhang:
CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data. 51-66 - Dillon Aberasturi, Nima Pouladi, Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Walter W. Piegorsch, Yves A. Lussier:
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. 67-75 - Rafael Peres da Silva, Chayaporn Suphavilai, Niranjan Nagarajan:
TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings. 76-83 - Tiago Pereira, Maryam Abbasi, José Luís Oliveira, Bernardete Ribeiro, Joel Arrais:
Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design. 84-92 - Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu:
Modeling drug combination effects via latent tensor reconstruction. 93-101 - Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar:
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. 102-110 - Wei Wang, Ahmad Hejasebazzi, Julia Zheng, Kevin J. Liu:
Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited. 111-119 - Yoann Anselmetti, Nadia El-Mabrouk, Manuel Lafond, Aïda Ouangraoua:
Gene tree and species tree reconciliation with endosymbiotic gene transfer. 120-132 - Chaitanya Aluru, Mona Singh:
Improved inference of tandem domain duplications. 133-141 - Erin K. Molloy, Arun Durvasula, Sriram Sankararaman:
Advancing admixture graph estimation via maximum likelihood network orientation. 142-150 - Ziye Tao, Griffin M. Weber, Yun William Yu:
Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories. 151-160 - Diyue Bu, XiaoFeng Wang, Haixu Tang:
Haplotype-based membership inference from summary genomic data. 161-168 - Daniel Danciu, Mikhail Karasikov, Harun Mustafa, André Kahles, Gunnar Rätsch:
Topology-based sparsification of graph annotations. 169-176 - Jamshed Khan, Rob Patro:
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. 177-186 - Hongyu Zheng, Carl Kingsford, Guillaume Marçais:
Sequence-specific minimizers via polar sets. 187-195 - Tatiana Dvorkina, Olga Kunyavskaya, Andrey V. Bzikadze, Ivan V. Alexandrov, Pavel A. Pevzner:
CentromereArchitect: inference and analysis of the architecture of centromeres. 196-204 - Yutong Qiu, Carl Kingsford:
Constructing small genome graphs via string compression. 205-213 - Leah L. Weber, Palash Sashittal, Mohammed El-Kebir:
doubletD: detecting doublets in single-cell DNA sequencing data. 214-221 - Daiyun Huang, Bowen Song, Jingjue Wei, Jionglong Su, Frans Coenen, Jia Meng:
Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. 222-230 - Zeyuan Zuo, Liu Cao, Louis-Félix Nothias, Hosein Mohimani:
MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition. 231-236 - Anna Weber, Jannis Born, María Rodríguez Martínez:
TITAN: T-cell receptor specificity prediction with bimodal attention networks. 237-244 - Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez:
On the feasibility of deep learning applications using raw mass spectrometry data. 245-253 - Peiyuan Feng, Jianyang Zeng, Jianzhu Ma:
Predicting MHC-peptide binding affinity by differential boundary tree. 254-261 - Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu:
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. 262-271 - Yangyang Hu, Wenxiu Ma:
EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework. 272-279 - Zhanlin Chen, Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min, Min Xu, Mark Gerstein:
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. 280-288 - Jyun-Yu Jiang, Chelsea J.-T. Ju, Junheng Hao, Muhao Chen, Wei Wang:
JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites. 289-298 - Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang:
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. 299-307 - Salma Sohrabi-Jahromi, Johannes Söding:
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. 308-316 - Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie:
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. 317-326 - Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein:
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. 327-333 - Laura H. Tung, Carl Kingsford:
Practical selection of representative sets of RNA-seq samples using a hierarchical approach. 334-341 - Victoria R. Li, Zijun Zhang, Olga G. Troyanskaya:
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. 342-348 - Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho:
Bayesian information sharing enhances detection of regulatory associations in rare cell types. 349-357 - Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li:
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. 358-366 - Anushua Biswas, Leelavati Narlikar:
Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments. 367-375 - Gwanghoon Jang, Sungjoon Park, Sanghoon Lee, Sunkyu Kim, Se-Jeong Park, Jaewoo Kang:
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. 376-382 - Hung-Cuong Trinh, Yung-Keun Kwon:
A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data. 383-391 - Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Graph transformation for enzymatic mechanisms. 392-400 - Julien Martinelli, Sandrine Dulong, Xiao-Mei Li, Michèle Teboul, Sylvain Soliman, Francis Lévi, François Fages, Annabelle Ballesta:
Model learning to identify systemic regulators of the peripheral circadian clock. 401-409 - Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma:
Disease gene prediction with privileged information and heteroscedastic dropout. 410-417 - Shike Wang, Fan Xu, Yunyang Li, Jie Wang, Ke Zhang, Yong Liu, Min Wu, Jie Zheng:
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers. 418-425 - Marwan Abdellah, Alessandro Foni, Eleftherios Zisis, Nadir Román Guerrero, Samuel Lapere, Jay S. Coggan, Daniel X. Keller, Henry Markram, Felix Schürmann:
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics. 426-433 - Yang Young Lu, Jeff A. Bilmes, Ricard A. Rodriguez-Mias, Judit Villén, William Stafford Noble:
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. 434-432 - Jung Hun Oh, Wookjin Choi, Euiseong Ko, Mingon Kang, Allen R. Tannenbaum, Joseph O. Deasy:
PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma. 443-450 - Trevor S. Frisby, Zhiyun Gong, Christopher James Langmead:
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories. 451-459 - Chirag Jain, Neda Tavakoli, Srinivas Aluru:
A variant selection framework for genome graphs. 460-467 - Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia L. Smith, Martin Ringwald, G. Elisabeta Marai, Cecilia N. Arighi, Hagit Shatkay:
Utilizing image and caption information for biomedical document classification. 468-476 - Haowen Zhang, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Heng Li, Srinivas Aluru:
Real-time mapping of nanopore raw signals. 477-483
Volume 37, Number 17, September 2021
- Fan Yang, Kevin J. Gleason, Jiebiao Wang, Jubao Duan, Xin He, Brandon L. Pierce, Lin S. Chen:
CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression. 2513-2520 - Mandar S. Chaudhary, Vu Viet Hoang Pham, Thuc Duy Le:
NIBNA: a network-based node importance approach for identifying breast cancer drivers. 2521-2528 - Manisha Panta, Avdesh Mishra, Md. Tamjidul Hoque, Joel Atallah:
ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements. 2529-2536 - Amir Bahmani, Ziye Xing, Vandhana Krishnan, Utsab Ray, Frank Mueller, Amir Alavi, Philip S. Tsao, Michael P. Snyder, Cuiping Pan:
Hummingbird: efficient performance prediction for executing genomic applications in the cloud. 2537-2543 - Raghvendra Mall, Abdurrahman Elbasir, Hossam Almeer, Zeyaul Islam, Prasanna R. Kolatkar, Sanjay Chawla, Ehsan Ullah:
A modeling framework for embedding-based predictions for compound-viral protein activity. 2544-2555 - Phasit Charoenkwan, Chanin Nantasenamat, Md. Mehedi Hasan, Balachandran Manavalan, Watshara Shoombuatong:
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides. 2556-2562 - Johan Nyström-Persson, Gabriel Keeble-Gagnère, Niamat Zawad:
Compact and evenly distributed k-mer binning for genomic sequences. 2563-2569 - Debby Dan Wang, Haoran Xie, Hong Yan:
Proteo-chemometrics interaction fingerprints of protein-ligand complexes predict binding affinity. 2570-2579 - Bowen Dai, Chris Bailey-Kellogg:
Protein interaction interface region prediction by geometric deep learning. 2580-2588 - Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou:
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. 2589-2600 - Isabelle Bichindaritz, Guanghui Liu, Christopher L. Bartlett:
Integrative survival analysis of breast cancer with gene expression and DNA methylation data. 2601-2608 - Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz:
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays. 2609-2616 - Calvin Chi, Yuting Ye, Bin Chen, Haiyan Huang:
Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations. 2617-2626 - Zihan Cui, Yuhang Liu, Jinfeng Zhang, Xing Qiu:
Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data. 2627-2636 - Zihao Zheng, Aisha M. Mergaert, Irene M. Ong, Miriam A. Shelef, Michael A. Newton:
MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing. 2637-2643 - Alma Andersson, Joakim Lundeberg:
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling. 2644-2650 - Yujie Chen, Tengfei Ma, Xixi Yang, Jianmin Wang, Bosheng Song, Xiangxiang Zeng:
MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. 2651-2658 - Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J. Faller:
Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq. 2659-2667 - Abdullah Çaglar Öksüz, Erman Ayday, Ugur Güdükbay:
Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy. 2668-2674 - Chih-Hsu Lin, Olivier Lichtarge:
Using interpretable deep learning to model cancer dependencies. 2675-2681 - Wen Liu, Xiang Li, Hong Qi, Yuning Wu, Jing Qu, Zhiyong Yin, Xuejuan Gao, Aidong Han, Jianwei Shuai:
Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system. 2682-2690 - Sorin Draghici, Tuan-Minh Nguyen, Larry A. Sonna, Cordelia Ziraldo, Radu Vanciu, Raef Fadel, Austin Morrison, Rachel M. Kenney, George Alangaden, Mayur Ramesh, Gil Mor:
COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases. 2691-2698 - Yufei Li, Xiaoyong Ma, Xiangyu Zhou, Pengzhen Cheng, Kai He, Chen Li:
Knowledge enhanced LSTM for coreference resolution on biomedical texts. 2699-2705 - Régis Ongaro-Carcy, Marie-Pier Scott-Boyer, Adrien Dessemond, François Belleau, Mickaël Leclercq, Olivier Périn, Arnaud Droit:
KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology. 2706-2713 - Cansu Alakus, Denis Larocque, Sébastien Jacquemont, Fanny Barlaam, Charles-Olivier Martin, Kristian Agbogba, Sarah Lippé, Aurélie Labbe:
Conditional canonical correlation estimation based on covariates with random forests. 2714-2721 - Wang Liu-Wei, Senay Kafkas, Jun Chen, Nicholas J. Dimonaco, Jesper Tegnér, Robert Hoehndorf:
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. 2722-2729 - Lekha Patel, David J. Williamson, Dylan M. Owen, Edward A. K. Cohen:
Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM). 2730-2737 - Alexis Hardy, Mélody Matelot, Amandine Touzeau, Christophe Klopp, Céline Lopez-Roques, Sandra Duharcourt, Matthieu Defrance:
DNAModAnnot: a R toolbox for DNA modification filtering and annotation. 2738-2740 - Yixin Guo, Ziwei Xue, Ruihong Yuan, Jingyi Jessica Li, William A. Pastor, Wanlu Liu:
RAD: a web application to identify region associated differentially expressed genes. 2741-2743 - Chen Cao, Matthew Greenberg, Quan Long:
WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization. 2744-2746 - Sandra Dérozier, Pierre Nicolas, Ulrike Mäder, Cyprien Guérin:
Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations. 2747-2749 - Benjamin Hepp, Violette Da Cunha, Florence Lorieux, Jacques Oberto:
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence. 2750-2752 - Alexander Senf, Robert Davies, Frédéric Haziza, John Marshall, Juan Ramón Troncoso-Pastoriza, Oliver Hofmann, Thomas M. Keane:
Crypt4GH: a file format standard enabling native access to encrypted data. 2753-2754 - Marek Schwarz, Jirí Vohradský, Josef Pánek:
rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output. 2755-2756 - Kang Hu, Neng Huang, You Zou, Xingyu Liao, Jianxin Wang:
MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish. 2757-2760 - David Roura Padrosa, Valentina Marchini, Francesca Paradisi:
CapiPy: python-based GUI-application to assist in protein immobilization. 2761-2762 - Filomeno Sánchez Rodríguez, Shahram Mesdaghi, Adam J. Simpkin, J. Javier Burgos-Mármol, David L. Murphy, Ville Uski, Ronan M. Keegan, Daniel J. Rigden:
ConPlot: web-based application for the visualization of protein contact maps integrated with other data. 2763-2765 - Tomasz Zok:
BioCommons: a robust java library for RNA structural bioinformatics. 2766-2767 - Rob Marissen, Magnus Palmblad:
mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants. 2768-2769 - Hélène Borges, Anne-Marie Hesse, Alexandra Kraut, Yohann Couté, Virginie Brun, Thomas Burger:
Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies. 2770-2771 - Di Wang, Zheng Jing, Kevin He, Lana X. Garmire:
Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data. 2772-2774 - Michael A. Skinnider, Charley Cai, R. Greg Stacey, Leonard J. Foster:
PrInCE: an R/Bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. 2775-2777 - Jonas Förster, Frank T. Bergmann, Jürgen Pahle:
CoRC: the COPASI R Connector. 2778-2779 - Zachary B. Abrams, Caitlin E. Coombes, Suli Li, Kevin R. Coombes:
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation. 2780-2781 - Tobias Pietzsch, Lorenzo Duso, Christoph Zechner:
Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations. 2782-2784 - Ewelina Weglarz-Tomczak, Jakub M. Tomczak, Stanley Brul:
M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models. 2785-2786 - Richard M. Jiang, Bruno Jacob, Matthew Geiger, Sean Matthew, Bryan Rumsey, Prashant Singh, Fredrik Wrede, Tau-Mu Yi, Brian Drawert, Andreas Hellander, Linda R. Petzold:
Epidemiological modeling in StochSS Live! 2787-2788 - Raphael Sonabend, Franz J. Király, Andreas Bender, Bernd Bischl, Michel Lang:
mlr3proba: an R package for machine learning in survival analysis. 2789-2791 - Leon Weber, Mario Sänger, Jannes Münchmeyer, Maryam Habibi, Ulf Leser, Alan Akbik:
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition. 2792-2794 - Shih-Chi Su, James E. Galvin, Shun-Fa Yang, Wen-Hung Chung, Lun-Ching Chang:
wiSDOM: a visual and statistical analytics for interrogating microbiome. 2795-2797 - Quentin Lamy-Besnier, Bryan Brancotte, Hervé Ménager, Laurent Debarbieux:
Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions. 2798-2801
Volume 37, Number 18, September 2021
- Cédric Arisdakessian, Olivia D. Nigro, Grieg F. Steward, Guylaine Poisson, Mahdi Belcaid:
CoCoNet: an efficient deep learning tool for viral metagenome binning. 2803-2810 - Mihai Lefter, Jonathan K. Vis, Martijn Vermaat, Johan T. den Dunnen, Peter E. M. Taschner, Jeroen F. J. Laros:
Mutalyzer 2: next generation HGVS nomenclature checker. 2811-2817 - Zhenxing Guo, Andrew M. Shafik, Peng Jin, Zhijin Wu, Hao Wu:
Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing. 2818-2824 - Yue Cao, Yang Shen:
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. 2825-2833 - Timothy L. Bailey:
STREME: accurate and versatile sequence motif discovery. 2834-2840 - Haochen Zhao, Yaohang Li, Jianxin Wang:
A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals. 2841-2847 - Seth Commichaux, Nidhi Shah, Jay Ghurye, Alexander Stoppel, Jessica A. Goodheart, Guillermo G. Luque, Michael P. Cummings, Mihai Pop:
A critical assessment of gene catalogs for metagenomic analysis. 2848-2857 - Camille Marchet, Maël Kerbiriou, Antoine Limasset:
BLight: efficient exact associative structure for k-mers. 2858-2865 - Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz:
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. 2866-2873 - Filip Ljung, Ingemar André:
ZEAL: protein structure alignment based on shape similarity. 2874-2881 - Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdogan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi:
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples. 2882-2888 - Andrea Blasco, Ted Natoli, Michael G. Endres, Rinat A. Sergeev, Steven Randazzo, Jin H. Paik, N. J. Maximilian Macaluso, Rajiv Narayan, Xiaodong Lu, David Peck, Karim R. Lakhani, Aravind Subramanian:
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map. 2889-2895 - Alain J. Mbebi, Hao Tong, Zoran Nikoloski:
L2, 1-norm regularized multivariate regression model with applications to genomic prediction. 2896-2904 - Juan A. Sánchez, Ana L. Gil-Martinez, Alejandro Cisterna, Sonia García-Ruíz, Alicia Gómez-Pascual, Regina H. Reynolds, Mike A. Nalls, John Hardy, Mina Ryten, Juan A. Botía:
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. 2905-2911 - Sylwester Kloska, Krzysztof Palczynski, Tomasz Marciniak, Tomasz Talaska, Marissa Nitz, Beata J. Wysocki, Paul H. Davis, Tadeusz A. Wysocki:
Queueing theory model of Krebs cycle. 2912-2919 - Junliang Shang, Jing Wang, Yan Sun, Feng Li, Jin-Xing Liu, Honghai Zhang:
Multiscale part mutual information for quantifying nonlinear direct associations in networks. 2920-2929 - Chen Cui, Xiaoyu Ding, Dingyan Wang, Lifan Chen, Fu Xiao, Tingyang Xu, Mingyue Zheng, Xiaomin Luo, Hualiang Jiang, Kaixian Chen:
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network. 2930-2937 - Mattia G. Gollub, Hans-Michael Kaltenbach, Jörg Stelling:
Probabilistic thermodynamic analysis of metabolic networks. 2938-2945 - Joel Dokmegang, Hanh Nguyen, Elena Kardash, Thierry Savy, Matteo Cavaliere, Nadine Peyriéras, René Doursat:
Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis. 2946-2954 - Sunjoo Bang, Jong Ho Jhee, Hyunjung Shin:
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network. 2955-2962 - Zhiqin Wang, Ruiqing Li, Minghui Wang, Ao Li:
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction. 2963-2970 - Jaesik Kim, Dokyoon Kim, Kyung-Ah Sohn:
HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball. 2971-2980 - Ziqiao Zhang, Jihong Guan, Shuigeng Zhou:
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction. 2981-2987 - Yue Yu, Kexin Huang, Chao Zhang, Lucas M. Glass, Jimeng Sun, Cao Xiao:
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization. 2988-2995 - Dejun Lin, Justin Sanders, William Stafford Noble:
HiCRep.py: fast comparison of Hi-C contact matrices in Python. 2996-2997 - Shaoke Lou, Tianxiao Li, Jason Liu, Mark Gerstein:
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. 2998-3000 - Jun-Yu Li, Wei-Xuan Li, An-Tai Wang, Yu Zhang:
MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization. 3001-3003 - Kimberly E. Taylor, K. Mark Ansel, Alexander Marson, Lindsey A. Criswell, Kyle Kai-How Farh:
PICS2: next-generation fine mapping via probabilistic identification of causal SNPs. 3004-3007 - Quirin Manz, Olga Tsoy, Amit Fenn, Jan Baumbach, Uwe Völker, Markus List, Tim Kacprowski:
ASimulatoR: splice-aware RNA-Seq data simulation. 3008-3010 - Guanjue Xiang, Belinda Giardine, Shaun Mahony, Yu Zhang, Ross C. Hardison:
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. 3011-3013 - Christopher Wilks, Omar Y. Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead:
Megadepth: efficient coverage quantification for BigWigs and BAMs. 3014-3016 - Andrew P. Boughton, Ryan P. Welch, Matthew Flickinger, Peter VandeHaar, Daniel Taliun, Gonçalo R. Abecasis, Michael Boehnke:
LocusZoom.js: interactive and embeddable visualization of genetic association study results. 3017-3018 - Urminder Singh, Eve Syrkin Wurtele:
orfipy: a fast and flexible tool for extracting ORFs. 3019-3020 - Sung-Joon Park, Kenta Nakai:
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. 3021-3022 - Xavier Bofill-De Ros, Brian T. Luke, Robert Guthridge, Uma Mudunuri, Michael A. Loss, Shuo Gu:
Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms. 3023-3025 - Chi Song, Shih-Chi Su, Zhiguang Huo, Suleyman Vural, James E. Galvin, Lun-Ching Chang:
HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology. 3026-3028 - Milot Mirdita, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin:
Fast and sensitive taxonomic assignment to metagenomic contigs. 3029-3031 - Benjamin D. Redelings:
Bali-Phy version 3: model-based co-estimation of alignment and phylogeny. 3032-3034 - Louise U. Kurt, Milan A. Clasen, Marlon D. M. Santos, Eduardo S. B. Lyra, Luana O. Santos, Carlos H. I. Ramos, Diogo B. Lima, Fábio C. Gozzo, Paulo C. Carvalho:
Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. 3035-3037 - Atilio O. Rausch, Maria I Freiberger, Cesar O. Leonetti, Diego M. Luna, Leandro G. Radusky, Peter G. Wolynes, Diego U. Ferreiro, R. Gonzalo Parra:
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. 3038-3040 - Woonghee Lee, Mehdi Rahimi, Yeongjoon Lee, Abigail Chiu:
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. 3041-3042 - Nour-al-dain Marzouka, Pontus Eriksson:
multiclassPairs: an R package to train multiclass pair-based classifier. 3043-3044 - Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang, Zihai Li, Qin Ma:
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis. 3045-3047 - Aaron Graubert, François Aguet, Arvind Ravi, Kristin G. Ardlie, Gad Getz:
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts. 3048-3050 - Lucy Sinke, Davy Cats, Bastiaan T. Heijmans:
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies. 3051-3052 - William Goh, Marek Mutwil:
LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. 3053-3055 - Christopher Jürges, Lars Dölken, Florian Erhard:
Integrative transcription start site identification with iTiSS. 3056-3057 - Irzam Sarfraz, Muhammad Asif, Joshua D. Campbell:
ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. 3058-3060 - Nora Scherer, Peggy Sekula, Peter Pfaffelhuber, Pascal Schlosser:
pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS. 3061-3063 - Vishnuvardhan Mahamkali, Tim McCubbin, Moritz Emanuel Beber, Elad Noor, Esteban Marcellin, Lars Keld Nielsen:
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. 3064-3066 - Anastasiya Belyaeva, Chandler Squires, Caroline Uhler:
DCI: learning causal differences between gene regulatory networks. 3067-3069 - Siddharth Annaldasula, Martyna Gajos, Andreas Mayer:
IsoTV: processing and visualizing functional features of translated transcript isoforms. 3070-3072 - Mingyang Ren, Sanguo Zhang, Qingzhao Zhang, Shuangge Ma:
HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis. 3073-3074 - Zhenjia Wang, Yifan Zhang, Chongzhi Zang:
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data. 3075-3078 - Christian Tischer, Ashis Ravindran, Sabine Reither, Nicolas Chiaruttini, Rainer Pepperkok, Nils Norlin:
BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data. 3079-3081 - Callum Arthurs, Aamir Ahmed:
QuArray: an application for tissue array whole slide image export and signal analysis. 3082-3083 - Garrett Winkelmaier, Bahram Parvin:
An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models. 3084-3085 - Qingjie Zhu, Yi Shao, Zhicheng Wang, Xingjun Chen, Chunqiong Li, Zihan Liang, Mingyue Jia, Qingchun Guo, Hu Zhao, Lei Kong, Li Zhang:
DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework. 3086-3087 - Friedrich Preusser, Natália dos Santos, Jörg Contzen, Harald Stachelscheid, Érico Tosoni Costa, Philipp Mergenthaler, Stephan Preibisch:
FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids. 3088-3090
Volume 37, Number 19, October 2021
- Ciara Frances Loughrey, Padraig Fitzpatrick, Nick Orr, Anna Jurek-Loughrey:
The topology of data: opportunities for cancer research. 3091-3098 - Linjing Liu, Xingjian Chen, Ka-Chun Wong:
Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine. 3099-3105 - Shenghua He, Chunfeng Lian, Wade Thorstad, Hiram Gay, Yujie Zhao, Su Ruan, Xiaowei Wang, Hua Li:
A novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers. 3106-3114 - Daniel Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T. Papenfuss:
VIRUSBreakend: Viral Integration Recognition Using Single Breakends. 3115-3119 - Neng Huang, Fan Nie, Peng Ni, Feng Luo, Xin Gao, Jianxin Wang:
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks. 3120-3127 - Julia Markowski, Rieke Kempfer, Alexander Kukalev, Ibai Irastorza-Azcarate, Gesa Loof, Birte Kehr, Ana Pombo, Sven Rahmann, Roland F. Schwarz:
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. 3128-3135 - Jaeho Jeong, Seong-Joon Park, Jae-Won Kim, Jong-Seon No, Ha Hyeon Jeon, Jeong Wook Lee, Albert No, Sunghwan Kim, Hosung Park:
Cooperative sequence clustering and decoding for DNA storage system with fountain codes. 3136-3143 - Michael Apostolides, Yue Jiang, Mia Husic, Robert Siddaway, Cynthia Hawkins, Andrei L. Turinsky, Michael Brudno, Arun K. Ramani:
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. 3144-3151 - Fengyuan Hu, Jia Lu, Louise S. Matheson, Manuel D. Díaz-Muñoz, Alexander Saveliev, Jinbo Xu, Martin Turner:
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes. 3152-3159 - Zheng Dai, Brooke D. Huisman, Haoyang Zeng, Brandon Carter, Siddhartha Jain, Michael E. Birnbaum, David K. Gifford:
Machine learning optimization of peptides for presentation by class II MHCs. 3160-3167 - Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara:
Protein contact map refinement for improving structure prediction using generative adversarial networks. 3168-3174 - Chloé Quignot, Pierre Granger, Pablo Chacón, Raphaël Guérois, Jessica Andreani:
Atomic-level evolutionary information improves protein-protein interface scoring. 3175-3181 - Noelia Ferruz, Jakob Noske, Birte Höcker:
Protlego: a Python package for the analysis and design of chimeric proteins. 3182-3189 - Zhiye Guo, Tianqi Wu, Jian Liu, Jie Hou, Jianlin Cheng:
Improving deep learning-based protein distance prediction in CASP14. 3190-3196 - Jin Li, Jinbo Xu:
Study of real-valued distance prediction for protein structure prediction with deep learning. 3197-3203