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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 J. M. 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