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ORCIDBioinformatics, Volume 37
Volume 37, Number 1, April 2021
- M. K. Sobczyk
, Tom R. Gaunt, Lavinia Paternoster:
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. 1-8
- Aditya Gorla, Brandon Jew, Luke Zhang, Jae Hoon Sul:
xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery. 9-16 - Benjamin 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