


default search action
Bioinformatics, 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