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ORCIDBioinformatics, Volume 34
Volume 34, Number 1, January 2018
Genome Analysis
- Karolina Elzbieta Kaczor-Urbanowicz
, Yong Kim, Feng Li, Timur Galeev, Robert R. Kitchen, Mark Gerstein, Kikuye Koyano, Sung-Hee Jeong, Xiaoyan Wang, David Elashoff, So Young Kang, Su Mi Kim, Kyoung Kim, Sung Kim, David Chia, Xinshu Xiao, Joel S. Rozowsky, David T. W. Wong:
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. 1-8
- Sha Joe Zhu, Jacob Almagro-Garcia, Gil McVean:
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. 9-15 - Brian J. Mendoza, Cong T. Trinh:
Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. 16-23
- Ergude Bao, Chang-Jin Song, Lingxiao Lan:
ReMILO: reference assisted misassembly detection algorithm using short and long reads. 24-32 - Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou:
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. 33-40
- Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary:
In silico structural modeling of multiple epigenetic marks on DNA. 41-48 - Brian Jiménez-García, Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González, Juan Fernández-Recio:
LightDock: a new multi-scale approach to protein-protein docking. 49-55
- Xu Shi, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. 56-63
- Andrew Elliott, Elizabeth Leicht, Alan Whitmore, Gesine Reinert, Felix Reed-Tsochas:
A nonparametric significance test for sampled networks. 64-71
- Lewis H. Mervin, Krishna C. Bulusu, Leen Kalash, Avid M. Afzal, Fredrik Svensson, Mike A. Firth, Ian P. Barrett, Ola Engkvist, Andreas Bender:
Orthologue chemical space and its influence on target prediction. 72-79 - Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu:
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. 80-87
- Elco Bakker, Peter S. Swain, Matthew M. Crane:
Morphologically constrained and data informed cell segmentation of budding yeast. 88-96 - Carlo Biffi, Antonio de Marvao, Mark I Attard, Timothy J. W. Dawes, Nicola Whiffin, Wenjia Bai, Wenzhe Shi, Catherine Francis, Hannah Meyer, Rachel J. Buchan, Stuart A. Cook, Daniel Rueckert, Declan P. O'Regan:
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. 97-103
Genome Analysis
- Laura Seaman, Indika Rajapakse:
4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities. 104-106 - Jochen Singer, Hans-Joachim Ruscheweyh, Ariane L. Hofmann, Thomas Thurnherr, Franziska Singer, Nora C. Toussaint, Charlotte K. Y. Ng, Salvatore Piscuoglio, Christian Beisel, Gerhard Christofori, Reinhard Dummer, Michael N. Hall, Wilhelm Krek, Mitchell P. Levesque, Markus G. Manz, Holger Moch, Andreas Papassotiropoulos, Daniel J. Stekhoven, Peter Wild, Thomas Wüst, Bernd Rinn, Niko Beerenwinkel:
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. 107-108 - Kun-Tze Chen, Chia-Liang Liu, Shang-Hao Huang, Hsin-Ting Shen, Yi-Kung Shieh, Hsien-Tai Chiu, Chin Lung Lu:
CSAR: a contig scaffolding tool using algebraic rearrangements. 109-111 - Nils Ternès, Federico Rotolo, Stefan Michiels:
biospear: an R package for biomarker selection in penalized Cox regression. 112-113
- Christopher Wilks, Phani Gaddipati, Abhinav Nellore, Ben Langmead:
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. 114-116 - Houxiang Zhu, Emily Richmond, Chun Liang:
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity. 117-119
- Yuri Binev, Daniela Peixoto, Florbela Pereira, Ian Rodrigues, Sofia Cavaco, Ana M. Lobo, João Aires-de-Sousa:
NavMol 3.0: enabling the representation of metabolic reactions by blind users. 120-121 - Damiano Piovesan, Silvio C. E. Tosatto:
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. 122-123
- Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer:
PySCeSToolbox: a collection of metabolic pathway analysis tools. 124-125 - Sara Brin Rosenthal, Julia Len, Mikayla Webster, Aaron Gary, Amanda Birmingham, Kathleen M. Fisch:
Interactive network visualization in Jupyter notebooks: visJS2jupyter. 126-128
- Oded Rimon, Dana Reichmann:
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements. 129-130
- Oriol López-Massaguer, Ferran Sanz, Manuel Pastor:
An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. 131-133
- Rani Arielly, Yuval Ebenstein:
Irys Extract. 134-136 - Kristoffer Bernhem, Hjalmar Brismar:
SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy. 137-138
Gene expression
- Zhe Sun, Ting Wang, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, Wei Chen:
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. 139-146
- Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir:
Faucet: streaming de novo assembly graph construction. 147-154
- Vikas Bansal:
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. 155-162 - Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David S. Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov:
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. 163-170 - Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F. Elliott, Chen Qian, Jinze Liu:
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. 171-178
Sequence Analysis
- Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, Karthik Ganesan, Tsachy Weissman:
QVZ: lossy compression of quality values. 179
Sequence Analysis
- Zhi-Kai Yang, Feng Gao:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 180
Volume 34, Number 2, January 2018
Genome Analysis
- Gulce Kale, Erman Ayday, Oznur Tastan:
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases. 181-189
- Hsin-Nan Lin, Wen-Lian Hsu:
DART: a fast and accurate RNA-seq mapper with a partitioning strategy. 190-197 - Jun Ding, Xiaoman Li, Haiyan Hu:
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. 198-206
- Matteo Tiberti, Alessandro Pandini, Franca Fraternali, Arianna Fornili:
In silico identification of rescue sites by double force scanning. 207-214 - Dmytro Guzenko, Sergei V. Strelkov:
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments. 215-222 - Thomas C. Northey, Anja Baresic, Andrew C. R. Martin:
IntPred: a structure-based predictor of protein-protein interaction sites. 223-229 - Jing Yang, Hong-Bin Shen:
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain. 230-238
- Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Pingjian Ding:
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations. 239-248 - Yiming Kang, Hien-Haw Liow, Ezekiel J. Maier, Michael R. Brent:
NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. 249-257 - Nan Papili Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan:
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. 258-266
- Yingli Zhong, Ping Xuan, Xiao Wang, Tiangang Zhang, Jianzhong Li, Yong Liu, Weixiong Zhang:
A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network. 267-277
- Lei Du, Kefei Liu, Tuo Zhang, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen:
A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics. 278-285
Genome Analysis
- Chris Chatzinakos, Donghyung Lee, Bradley Todd Webb, Vladimir I. Vladimirov, Kenneth S. Kendler, Silviu-Alin Bacanu:
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts. 286-288 - Roberto Vera Alvarez, Shan Li, David Landsman, Ivan Ovcharenko:
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. 289-291
- James Hadfield, Nicholas J. Croucher, Richard J. Goater, Khalil AbuDahab, David M. Aanensen, Simon R. Harris:
Phandango: an interactive viewer for bacterial population genomics. 292-293
- Guillaume Brysbaert, Kevin Lorgouilloux, Wim F. Vranken, Marc F. Lensink:
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction. 294-296 - Anastasia A. Anashkina, Yuri Kravatsky, Eugene N. Kuznetsov, Alexander A. Makarov, Alexei A. Adzhubei:
Meta-server for automatic analysis, scoring and ranking of docking models. 297-299
- Christopher J. Green, Matthew R. Gazzara, Yoseph Barash:
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. 300-302
- Daniel Boloc, Natalia Rodríguez, Patricia Gassó, Josep F. Abril, Miquel Bernardo, Amalia Lafuente, Sergi Mas:
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling. 303-305 - Lisa A. Ouellette, Robert W. Reid, Steven G. Blanchard, Cory R. Brouwer:
LinkageMapView - rendering high-resolution linkage and QTL maps. 306-307
- Michael Seifert, Andreas Beyer:
regNet: an R package for network-based propagation of gene expression alterations. 308-311 - Maxime Chazalviel, Clément Frainay, Nathalie Poupin, Florence Vinson, Benjamin Merlet, Yoann Gloaguen, Ludovic Cottret, Fabien Jourdan:
MetExploreViz: web component for interactive metabolic network visualization. 312-313 - Huey-Eng Chua, Sourav S. Bhowmick, Jie Zheng:
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. 314-316
- Joe Wandy, Yunfeng Zhu, Justin J. J. van der Hooft, Rónán Daly, Michael P. Barrett, Simon Rogers:
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. 317-318
- Kun-Hsing Yu, Michael R. Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder:
Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction. 319-320 - Jonathan Lo, Deric Zhang, Emily Speranza, Jose A. Negron, John H. Connor:
HoTResDB: host transcriptional response database for viral hemorrhagic fevers. 321-322
Genome Analysis
- Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan W. Sousa da Silva, Adrian M. Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. 323-329
Genome Analysis
- Xiaoqing Huang, Damian Wójtowicz, Teresa M. Przytycka:
Detecting presence of mutational signatures in cancer with confidence. 330-337 - Abhijit Chakraborty, Ferhat Ay:
Identification of copy number variations and translocations in cancer cells from Hi-C data. 338-345
- Layla Oesper, Simone Dantas, Benjamin J. Raphael:
Identifying simultaneous rearrangements in cancer genomes. 346-352 - Rebecca Elyanow, Hsin-Ta Wu, Benjamin J. Raphael:
Identifying structural variants using linked-read sequencing data. 353-360
Volume 34, Number 3, February 2018
Genome Analysis
- Zhi-Kai Yang, Feng Gao:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 361-366
- Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew F. Teich:
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. 367-371
Genome Analysis
- Tarmo Äijö, Christian L. Müller, Richard Bonneau:
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. 372-380 - Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q. Zhang, Xiangfeng Wang, Zhongfu Ni:
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. 381-387 - Sun-Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B. Bull, Yun Joo Yoo:
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs. 388-397 - Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff, Quan Zou:
Tumor origin detection with tissue-specific miRNA and DNA methylation markers. 398-406
- Paul D. Blischak, Laura Salter Kubatko, Andrea D. Wolfe:
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. 407-415 - Haoyu Cheng, Ming Wu, Yun Xu:
FMtree: a fast locating algorithm of FM-indexes for genomic data. 416-424 - Tom Paridaens, Glenn Van Wallendael, Wesley De Neve, Peter Lambert:
AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality. 425-433 - Evgenii I Olekhnovich, Artem T. Vasilyev, Vladimir Ulyantsev, Elena S. Kostryukova, Alexander V. Tyakht:
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. 434-444
- Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto:
A comprehensive assessment of long intrinsic protein disorder from the DisProt database. 445-452 - Yumeng Yan, Sheng-You Huang:
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. 453-458 - Francesca Nadalin, Alessandra Carbone:
Protein-protein interaction specificity is captured by contact preferences and interface composition. 459-468 - Hyun-Ho Kyeong, Yoonjoo Choi, Hak-Sung Kim:
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking. 469-476 - Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
Structure-based prediction of protein- peptide binding regions using Random Forest. 477-484
- Ghislain Durif, Laurent Modolo, Jakob Michaelsson, Jeff E. Mold, Sophie Lambert-Lacroix, Franck Picard:
High dimensional classification with combined adaptive sparse PLS and logistic regression. 485-493
- Claudio Angione:
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism. 494-501 - Zhengwei Xie, Tianyu Zhang, Qi Ouyang:
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm. 502-510
Genome Analysis
- Mark F. Rogers, Hashem A. Shihab, Matthew E. Mort, David N. Cooper, Tom R. Gaunt, Colin Campbell:
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. 511-513 - Fabiano B. Menegidio, Daniela L. Jabes, Regina Costa de Oliveira, Luiz R. Nunes:
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses. 514-515 - Sergii Ivakhno, Eric Roller, Camilla Colombo, Philip Tedder, Anthony J. Cox:
Canvas SPW: calling de novo copy number variants in pedigrees. 516-518 - Ho Jang, Hyunju Lee:
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data. 519-521 - Javier Palarea-Albaladejo, Kevin McLean, Frank Wright, David G. E. Smith:
MALDIrppa: quality control and robust analysis for mass spectrometry data. 522-523
- María José Nueda, Jordi Martorell-Marugan, Cristina Martí, Sonia Tarazona, Ana Conesa:
Identification and visualization of differential isoform expression in RNA-seq time series. 524-526
- Anna Okula Basile, Marta Byrska-Bishop, John R. Wallace, Alex Thomas Frase, Marylyn D. Ritchie:
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants. 527-529
- Mahito Sugiyama, M. Elisabetta Ghisu, Felipe Llinares-López, Karsten M. Borgwardt:
graphkernels: R and Python packages for graph comparison. 530-532
- Sergio Picart-Armada, Wesley K. Thompson, Alfonso Buil, Alexandre Perera-Lluna:
diffuStats: an R package to compute diffusion-based scores on biological networks. 533-534
- Éva Schád, Erzsébet Fichó, Rita Pancsa, István Simon, Zsuzsanna Dosztányi, Bálint Mészáros:
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. 535-537
- Virginie Uhlmann, Carsten Haubold, Fred A. Hamprecht, Michael Unser:
DiversePathsJ: diverse shortest paths for bioimage analysis. 538-540
Volume 34, Number 4, February 2018
Genome Analysis
- Cristian A. Yones, Georgina Stegmayer, Diego H. Milone:
Genome-wide pre-miRNA discovery from few labeled examples. 541-549 - Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger:
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. 550-557 - Shubham Chandak, Kedar Tatwawadi, Tsachy Weissman:
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. 558-567
- Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
Squeakr: an exact and approximate k-mer counting system. 568-575 - Taikai Takeda, Michiaki Hamada:
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. 576-584 - Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet:
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. 585-591
- Manuel Alejandro Marín-López, Joan Planas-Iglesias, Joaquim Aguirre-Plans, Jaume Bonet, Javier García-García, Narcis Fernandez-Fuentes, Baldo Oliva:
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. 592-598 - Stanislav A. Bondarev, Olga V. Bondareva, Galina A. Zhouravleva, Andrey V. Kajava:
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. 599-608 - Jasmin Cevost, Cédric Vaillant, Sam Meyer:
ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. 609-616
- Y. X. Rachel Wang, Ke Liu, Elizabeth Theusch, Jerome I Rotter, Marisa W. Medina, Michael S. Waterman, Haiyan Huang:
Generalized correlation measure using count statistics for gene expression data with ordered samples. 617-624 - Angela Serra, Pietro Coretto, Michele Fratello, Roberto Tagliaferri:
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data. 625-634
- Xiayuan Huang, Robert C. Elston, Guilherme J. Rosa, John Mayer, Zhan Ye, Terrie E. Kitchner, Murray H. Brilliant, David Page, Scott J. Hebbring:
Applying family analyses to electronic health records to facilitate genetic research. 635-642 - Jun Chen, Emily King, Rebecca Deek, Zhi Wei, Yue Yu, Diane E. Grill, Karla V. Ballman:
An omnibus test for differential distribution analysis of microbiome sequencing data. 643-651