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ORCIDBioinformatics, Volume 35
Volume 35, Number 1, January 2019
Genome Analysis
- Nilotpal Sanyal
, Min-Tzu Lo, Karolina Kauppi, Srdjan Djurovic, Ole A. Andreassen, Valen E. Johnson, Chi-Hua Chen:
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies. 1-11
- Nelson Gil, András Fiser:
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. 12-19 - Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach:
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. 20-27
- Kieran R. Campbell, Christopher Yau:
A descriptive marker gene approach to single-cell pseudotime inference. 28-35 - Eleonora Lusito, Barbara Felice, Giovanni D'Ario, Alessandro Ogier, Francesca Montani, Pier Paolo Di Fiore, Fabrizio Bianchi:
Unraveling the role of low-frequency mutated genes in breast cancer. 36-46 - Sumon Ahmed, Magnus Rattray, Alexis Boukouvalas:
GrandPrix: scaling up the Bayesian GPLVM for single-cell data. 47-54 - Marjan Farahbod, Paul Pavlidis:
Differential coexpression in human tissues and the confounding effect of mean expression levels. 55-61 - Andrea Rau, Michael Flister, Hallgeir Rui, Paul L. Auer:
Exploring drivers of gene expression in the Cancer Genome Atlas. 62-68
- Christian X. Weichenberger, Johannes Rainer, Cristian Pattaro, Peter P. Pramstaller, Francisco S. Domingues:
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. 69-76
- Lei Han, Lei Li, Feng Wen, Lei Zhong, Tong Zhang, Xiu-Feng Wan:
Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus. 77-87 - Barnali Das, Abhijeet Rajendra Patil, Pralay Mitra:
A network-based zoning for parallel whole-cell simulation. 88-94 - Mohammad Sajjad Ghaemi, Daniel B. DiGiulio, Kévin Contrepois, Benjamin J. Callahan, Thuy T. M. Ngo, Brittany Lee-McMullen, Benoit Lehallier, Anna Robaczewska, David Mcilwain, Yael Rosenberg-Hasson, Ronald J. Wong, Cecele Quaintance, Anthony Culos, Natalie Stanley, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul H. Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D. Winn, Maurice L. Druzin, Ronald Gibbs, Gary L. Darmstadt, David B. Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry P. Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour:
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. 95-103 - Fangping Wan, Lixiang Hong, An Xiao, Tao Jiang, Jianyang Zeng:
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. 104-111
- Jianwen Fang:
Tightly integrated genomic and epigenomic data mining using tensor decomposition. 112-118
Genome Analysis
- Jerome Kelleher, Mike Lin, Carl H. Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y. González, David K. Jackson, Aaron Kemp, John Marshall, Andrew Nowak, Alexander Senf, Jaime M. Tovar-Corona, Alexander Vikhorev, Thomas M. Keane, GA4GH Streaming Task Team:
htsget: a protocol for securely streaming genomic data. 119-121 - Velimir Gayevskiy, Tony Roscioli, Marcel E. Dinger, Mark J. Cowley:
Seave: a comprehensive web platform for storing and interrogating human genomic variation. 122-125 - Zhaohui Gu, Charles Mullighan:
ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations. 126-129 - André Gohr, Manuel Irimia:
Matt: Unix tools for alternative splicing analysis. 130-132 - Sebastian Deorowicz, Adam Gudys, Maciej Dlugosz, Marek Kokot, Agnieszka Danek:
Kmer-db: instant evolutionary distance estimation. 133-136 - Patrick K. Kimes, Alejandro Reyes:
Reproducible and replicable comparisons using SummarizedBenchmark. 137-139 - Marc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort:
WAVES: a web application for versatile enhanced bioinformatic services. 140-142
- Levent Albayrak, Kamil Khanipov, George Golovko, Yuriy Fofanov:
Broom: application for non-redundant storage of high throughput sequencing data. 143-145 - Seyed Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
Cryfa: a secure encryption tool for genomic data. 146-148
- Salvatore Cosentino, Wataru Iwasaki:
SonicParanoid: fast, accurate and easy orthology inference. 149-151
- Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk:
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. 152-155
- Jamil Najafov, Ayaz Najafov:
GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution. 156-159
- Shijia Zhu, Tongqi Qian, Yujin Hoshida, Yuan Shen, Jing Yu, Ke Hao:
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data. 160-163 - Corbin Quick, Christian Fuchsberger, Daniel Taliun, Gonçalo R. Abecasis, Michael Boehnke, Hyun Min Kang:
emeraLD: rapid linkage disequilibrium estimation with massive datasets. 164-166
- Pierre Salvy, Georgios Fengos, Meriç Ataman, Thomas Pathier, Keng C. Soh, Vassily Hatzimanikatis:
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. 167-169
- Jean-Michel Claverie, Thi Ngan Ta:
ACDtool: a web-server for the generic analysis of large data sets of counts. 170-171
- Chuan Jiao, Pengpeng Yan, Cuihua Xia, Zhaoming Shen, Zexi Tan, Yanyan Tan, Kangli Wang, Yi Jiang, Lingling Huang, Rujia Dai, Yu Wei, Yan Xia, Qingtuan Meng, Yanmei Ouyang, Liu Yi, Fangyuan Duan, Jiacheng Dai, Shunan Zhao, Chunyu Liu, Chao Chen:
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. 172-174 - Zeyu Wen, Jiahua He, Huanyu Tao, Sheng-You Huang:
PepBDB: a comprehensive structural database of biological peptide-protein interactions. 175-177
- Paolo Inglese, Gonçalo D. S. Correia, Zoltan Takats, Jeremy K. Nicholson, Robert C. Glen:
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data. 178-180
Volume 35, Number 2, January 2019
Genome Analysis
- Joeri J. Meijsen, Alexandros Rammos, Archie Campbell, Caroline Hayward, David J. Porteous, Ian J. Deary, Riccardo E. Marioni, Kristin K. Nicodemus:
Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study. 181-188 - Malene Juul, Tobias Madsen, Qianyun Guo, Johanna Bertl, Asger Hobolth, Manolis Kellis, Jakob Skou Pedersen:
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. 189-199 - Bianca Dumitrascu, Gregory Darnell, Julien Ayroles, Barbara E. Engelhardt:
Statistical tests for detecting variance effects in quantitative trait studies. 200-210 - Chris-André Leimeister, Thomas Dencker, Burkhard Morgenstern:
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. 211-218 - Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng:
Metagenomic binning through low-density hashing. 219-226
- Sebastian Deorowicz, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz:
CoMSA: compression of protein multiple sequence alignment files. 227-234
- Yu-Chen Lo, Tianyun Liu, Kari M. Morrissey, Satoko Kakiuchi-Kiyota, Adam R. Johnson, Fabio Broccatelli, Yu Zhong, Amita Joshi, Russ B. Altman:
Computational analysis of kinase inhibitor selectivity using structural knowledge. 235-242 - Miha Skalic, Alejandro Varela-Rial, José Jiménez, Gerard Martínez-Rosell, Gianni De Fabritiis:
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks. 243-250
- Jiaan Dai, Wei Jiang, Fengchao Yu, Weichuan Yu:
Xolik: finding cross-linked peptides with maximum paired scores in linear time. 251-257 - Emmanuel Curis, Cindie Courtin, Pierre Alexis Geoffroy, Jean-Louis Laplanche, Bruno Saubaméa, Cynthia Marie-Claire:
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios. 258-265
- Matthias P. Gerstl, Stefan Müller, Georg Regensburger, Jürgen Zanghellini:
Flux tope analysis: studying the coordination of reaction directions in metabolic networks. 266-273 - Clément Frainay, Sandrine Aros, Maxime Chazalviel, Thomas Garcia, Florence Vinson, Nicolas Weiss, Benoit Colsch, Frédéric Sedel, Dominique Thabut, Christophe Junot, Fabien Jourdan:
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. 274-283 - Olivia Eriksson, Alexandra Jauhiainen, Sara Maad Sasane, Andrei Kramer, Anu G. Nair, Carolina Sartorius, Jeanette Hellgren Kotaleski:
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models. 284-292
- Piotr Klukowski, Mario Schubert:
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. 293-300 - Etienne Becht, Yannick Simoni, Elaine Coustan-Smith, Maximilien Evrard, Yang Cheng, Lai Guan Ng, Dario Campana, Evan W. Newell:
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting. 301-308 - Masashi Tsubaki, Kentaro Tomii, Jun Sese:
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences. 309-318
- Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang:
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. 319-328
Genome Analysis
- Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet:
GeneSpy, a user-friendly and flexible genomic context visualizer. 329-331
- David Jakubec, Jirí Vondrásek, Robert D. Finn:
3DPatch: fast 3D structure visualization with residue conservation. 332-334 - Sebastian Uhrig, Holger Klein:
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data. 335-336 - James K. Bonfield, Shane A. McCarthy, Richard Durbin:
Crumble: reference free lossy compression of sequence quality values. 337-339
- Dana Wyman, Ali Mortazavi:
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts. 340-342 - Sara B. Linker, Jonathan Y. Hsu, Adela Pfaff, Debha Amatya, Shu-Meng Ko, Sarah Voter, Quinn Wong, Fred H. Gage:
BrainImageR: spatiotemporal gene set analysis referencing the human brain. 343-345
- Soumita Ghosh, Abhik Datta, Kaisen Tan, Hyungwon Choi:
SLIDE - a web-based tool for interactive visualization of large-scale - omics data. 346-348
- David R. Damerell, Claire Strain-Damerell, Sefa Garsot, Stephen P. Joyce, Paul Barrett, Brian D. Marsden:
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications. 349-351
Databases and Ontologies
- Hojjat Naderi-Meshkin, Xin Lai, Raheleh Amirkhah, Julio Vera, John E. J. Rasko, Ulf Schmitz:
Exosomal lncRNAs and cancer: connecting the missing links. 352-360
Volume 35, Number 3, February 2019
Systems Biology
- Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang:
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. 361-364
Genome Analysis
- Nora von Thenen, Erman Ayday, A. Ercüment Çiçek:
Re-identification of individuals in genomic data-sharing beacons via allele inference. 365-371
- Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich:
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. 372-379 - Wei Zheng, Qi Mao, Robert J. Genco, Jean Wactawski-Wende, Michael Buck, Yunpeng Cai, Yijun Sun:
A parallel computational framework for ultra-large-scale sequence clustering analysis. 380-388 - Xinguo Lu, Xin Qian, Xing Li, Qiumai Miao, Shaoliang Peng:
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters. 389-397 - Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC. 398-406 - Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles:
Dynamic compression schemes for graph coloring. 407-414 - Chen Sun, Paul Medvedev:
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. 415-420 - Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles:
Scaling read aligners to hundreds of threads on general-purpose processors. 421-432 - Avdesh Mishra, Pujan Pokhrel, Md. Tamjidul Hoque:
StackDPPred: a stacking based prediction of DNA-binding protein from sequence. 433-441 - Jeffrey M. Yunes, Patricia C. Babbitt:
Effusion: prediction of protein function from sequence similarity networks. 442-451
- Marcin Kowiel, Dariusz Brzezinski, Przemyslaw J. Porebski, Ivan G. Shabalin, Mariusz Jaskolski, Wladek Minor:
Automatic recognition of ligands in electron density by machine learning. 452-461 - Justina Jankauskaite, Brian Jiménez-García, Justas Dapkunas, Juan Fernández-Recio, Iain H. Moal:
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. 462-469 - Rubén Sánchez García, Carlos Oscar Sánchez Sorzano, José María Carazo, Joan Segura:
BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. 470-477
- Rasmus Henningsson, Magnus Fontes:
SMSSVD: SubMatrix Selection Singular Value Decomposition. 478-486 - Shiquan Sun, Jiaqiang Zhu, Sahar Mozaffari, Carole Ober, Mengjie Chen, Xiang Zhou:
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. 487-496
- Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot:
Random walk with restart on multiplex and heterogeneous biological networks. 497-505
- Bruce A. Corliss, H. Clifton Ray, James T. Patrie, Jennifer Mansour, Sam Kesting, Janice H. Park, Gustavo K. Rohde, Paul A. Yates, Kevin A. Janes, Shayn M. Peirce:
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. 506-514
Genome Analysis
- Caralyn Reisle, Karen L. Mungall, Caleb Choo, Daniel Paulino, Dustin W. Bleile, Amir Muhammadzadeh, Andrew J. Mungall, Richard A. Moore, Inna Shlafman, Robin Coope, Stephen Pleasance, Yussanne Ma, Steven J. M. Jones:
MAVIS: merging, annotation, validation, and illustration of structural variants. 515-517 - Haiming Tang, Robert D. Finn, Paul D. Thomas:
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. 518-520
- Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer, Erik Bongcam-Rudloff:
Simulating Illumina metagenomic data with InSilicoSeq. 521-522 - Robert Lanfear, Miriam Schalamun, David Kainer, Weiwen Wang, Benjamin Schwessinger:
MinIONQC: fast and simple quality control for MinION sequencing data. 523-525
- Emmanuel Paradis, Klaus Schliep:
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. 526-528
- Zongxiao He, Lu Wang, Andrew Thomas DeWan, Suzanne M. Leal:
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data. 529-531
- Kieu Trinh Do, David J. N. P. Rasp, Gabi Kastenmüller, Karsten Suhre, Jan Krumsiek:
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. 532-534 - Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes:
gMCS: fast computation of genetic minimal cut sets in large networks. 535-537
- Zainab Noor, Jemma X. Wu, Dana Pascovici, Abidali Mohamedali, Mark P. Molloy, Mark S. Baker, Shoba Ranganathan:
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries. 538-539
Data and Text Mining
- Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard:
polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. 540
Volume 35, Number 4, February 2019
Sequence Analysis
- Reuben J. Pengelly, Andrew Collins:
Linkage disequilibrium maps to guide contig ordering for genome assembly. 541-545
Genome Analysis
- Justin Miller, Brandon D. Pickett, Perry G. Ridge:
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. 546-552 - Zi Yang, George Michailidis:
Quantifying heterogeneity of expression data based on principal components. 553-559 - Timothy J. Peters, Hugh J. French, Stephen T. Bradford, Ruth Pidsley, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A. Giles, Aaron L. Statham, Helen Speirs, Terence P. Speed, Susan J. Clark:
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. 560-570 - Jack M. Fu, Elizabeth J. Leslie, Alan F. Scott, Jeffrey C. Murray, Mary L. Marazita, Terri H. Beaty, Robert B. Scharpf, Ingo Ruczinski:
Detection of de novo copy number deletions from targeted sequencing of trios. 571-578 - Markus Fricke, Ruman Gerst, Bashar Ibrahim, Michael Niepmann, Manja Marz:
Global importance of RNA secondary structures in protein-coding sequences. 579-583
- Bansho Masutani, Shinichi Morishita:
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer. 584-592 - Wenying He, Cangzhi Jia, Quan Zou:
4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction. 593-601
- Jiazhou Chen, Hong Peng, Guoqiang Han, Hongmin Cai, Jiulun Cai:
HOGMMNC: a higher order graph matching with multiple network constraints model for gene-drug regulatory modules identification. 602-610 - Magdalena E. Strauß, John E. Reid, Lorenz Wernisch:
GPseudoRank: a permutation sampler for single cell orderings. 611-618 - Sungwon Jung:
KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein-protein interactions. 619-627
- Miao-Xin Li, Lin Jiang, Timothy Shin Heng Mak, Johnny S. H. Kwan, Chao Xue, Peikai Chen, Henry Chi-Ming Leung, Liqian Cui, Tao Li, Pak Chung Sham:
A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia. 628-635
- Beibei Ru, Yin Tong, Jiangwen Zhang:
MR4Cancer: a web server prioritizing master regulators for cancer. 636-642 - Eunji Kim, Ivan Ivanov, Edward R. Dougherty:
Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. 643-649
- Tatiana Radchenko, Fabien Fontaine, Luca Morettoni, Ismael Zamora:
WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source. 650-655
- Magnus Palmblad, Anna-Lena Lamprecht, Jon C. Ison, Veit Schwämmle:
Automated workflow composition in mass spectrometry-based proteomics. 656-664 - Richard Wilton, Sarah J. Wheelan, Alexander S. Szalay, Steven L. Salzberg:
The Terabase Search Engine: a large-scale relational database of short-read sequences. 665-670
Genome Analysis