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ORCIDBMC Bioinformatics, Volume 18
Volume 18, Number 1, December 2017
- Dongmei Li
, Zidian Xie, Martin S. Zand, Thomas Fogg, Timothy D. Dye:
Bon-EV: an improved multiple testing procedure for controlling false discovery rates. 1:1-1:10 - Annika Röhl, Alexander Bockmayr:
A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks. 2:1-2:10 - Johannes W. R. Martini, Ning Gao, Diercles F. Cardoso, Valentin Wimmer, Malena Erbe, Rodolfo J. C. Cantet, Henner Simianer:
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE). 3:1-3:16 - Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K. Benson, Nengjun Yi:
Negative binomial mixed models for analyzing microbiome count data. 4:1-4:10 - Davoud Torkamaneh, Jérôme Laroche, Maxime Bastien, Amina Abed, François Belzile:
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. 5:1-5:7 - Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek:
TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas. 6:1-6:9 - Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich:
JACUSA: site-specific identification of RNA editing events from replicate sequencing data. 7:1-7:15 - Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel:
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. 8:1-8:15 - Milos D. Radovic, Mohamed F. Ghalwash, Nenad Filipovic, Zoran Obradovic:
Minimum redundancy maximum relevance feature selection approach for temporal gene expression data. 9:1-9:14 - Shirin Taghipour, Peyman Zarrineh, Mohammad Ganjtabesh, Abbas Nowzari-Dalini:
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. 10:1-10:9 - Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt:
Accelerating metagenomic read classification on CUDA-enabled GPUs. 11:1-11:10 - Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R. de Haan, Dirk Metzler:
PERGOLA: fast and deterministic linkage mapping of polyploids. 12:1-12:9 - Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias:
T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. 13:1-13:8 - Thomas S. Wingo, Alex Kotlar, David J. Cutler:
MPD: multiplex primer design for next-generation targeted sequencing. 14:1-14:5 - Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti, Bernhard Lüscher:
Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant. 15:1-15:9 - Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann, Simone Fulle:
KinMap: a web-based tool for interactive navigation through human kinome data. 16:1-16:6 - Nicolas Bosc, Christophe Meyer, Pascal Bonnet:
The use of novel selectivity metrics in kinase research. 17:1-17:12 - Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian, Xiaohong Li:
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data. 18:1-18:12 - Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann:
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. 19:1-19:8 - Hashem A. Shihab, Mark F. Rogers, Michael Ferlaino, Colin Campbell, Tom R. Gaunt:
GTB - an online genome tolerance browser. 20:1-20:6 - Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko, Andrew P. Morris:
SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes. 25:1-25:8 - Roberto A. Barrero, Kathryn R. Napier, James Cunnington, Lia Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás O. Szabó, Simon Bulman, Adam Hunter, Lisa Ward, Mark Whattam, Matthew I. Bellgard:
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. 26:1-26:12 - Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu:
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. 27:1-27:13 - Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi:
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. 30:1-30:11 - Wei-Sheng Wu, Meng-Jhun Jhou:
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. 31:1-31:10 - Nikhil Cheerla, Olivier Gevaert:
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. 32:1-32:11 - Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus:
TTCA: an R package for the identification of differentially expressed genes in time course microarray data. 33:1-33:11 - Sylvester Olubolu Orimaye, Jojo Sze-Meng Wong, Karen Jennifer Golden, Chee Piau Wong, Ireneous N. Soyiri:
Predicting probable Alzheimer's disease using linguistic deficits and biomarkers. 34:1-34:13 - Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang:
iGC - an integrated analysis package of gene expression and copy number alteration. 35:1-35:9 - Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González:
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. 36:1-36:7 - Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue, Vera van Noort:
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. 37:1-37:9 - Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim:
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. 38:1-38:12 - Yiding Lu, Yufan Guo, Anna Korhonen:
Link prediction in drug-target interactions network using similarity indices. 39:1-39:9 - Noah Eyal-Altman, Mark Last, Eitan Rubin:
PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine. 40:1-40:7 - N. Ari Wijetunga, Andrew D. Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M. Greally:
SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. 41:1-41:13 - Fan Zhang, Patrick Flaherty:
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. 45:1-45:10 - Tsukasa Fukunaga, Wataru Iwasaki:
Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants. 46:1-46:9 - Jiaoyun Yang, Haipeng Wang, Huitong Ding, Ning An, Gil Alterovitz:
Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization. 47:1-47:10 - Hatem Elshazly, Yassine Souilmi, Peter J. Tonellato, Dennis P. Wall, Mohamed Abouelhoda:
MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants. 49:1-49:14 - Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma:
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation. 51:1-51:11 - David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga:
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. 52:1-52:24 - Virginie Stanislas, Cyril Dalmasso, Christophe Ambroise:
Eigen-Epistasis for detecting gene-gene interactions. 54:1-54:14 - Victor Alexandre Padilha, Ricardo J. G. B. Campello:
A systematic comparative evaluation of biclustering techniques. 55:1-55:25 - Michal Jablonski, Jana Starcuková, Zenon Starcuk Jr.:
Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. 56:1-56:11 - Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau, Trent R. Northen:
Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. 57:1-57:12 - Giulia Paciello, Elisa Ficarra:
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. 58:1-58:12 - Yasir Rahmatallah, Boris L. Zybailov, Frank Emmert-Streib, Galina V. Glazko:
GSAR: Bioconductor package for Gene Set analysis in R. 61:1-61:12 - Fereshteh Chitsazian, Mehdi Sadeghi, Elahe Elahi:
Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines. 67:1-67:14 - Rob Eisinga, Tom Heskes, Ben Pelzer, Manfred te Grotenhuis:
Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers. 68:1-68:18 - Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiao-Tai Huang, Wanxin Tang:
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. 72:1-72:13 - Orsolya Pipek, Dezso Ribli, János Molnár, Ádam Póti, Marcin Krzystanek, András Bodor, Gábor E. Tusnády, Zoltan Szallasi, István Csabai, David Szüts:
Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. 73:1-73:11 - Shupeng Gui, Andrew P. Rice, Rui Chen, Liang Wu, Ji Liu, Hongyu Miao:
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. 74:1-74:13 - Wutao Lin, Donghong Ji, Yanan Lu:
Disorder recognition in clinical texts using multi-label structured SVM. 75:1-75:11 - Zohar Zafrir, Tamir Tuller:
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. 77:1-77:10 - Govind Nair, Christian Jungreuthmayer, Jürgen Zanghellini:
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization. 78:1-78:9 - Sinjini Sikdar, Susmita Datta:
A novel statistical approach for identification of the master regulator transcription factor. 79:1-79:11 - Cristiano Lacerda Nunes Pinto, Cristiane Neri Nobre, Luis Enrique Zárate:
Transductive learning as an alternative to translation initiation site identification. 81:1-81:15 - Rui Henriques, Francisco L. Ferreira, Sara C. Madeira:
BicPAMS: software for biological data analysis with pattern-based biclustering. 82:1-82:16 - Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke, J. Hendrik Venter:
Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp. 83:1-83:13 - Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe Jr., Denise M. Scholtens:
Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data. 84:1-84:17 - James C. Wilgenbusch, Wen Huang, Kyle A. Gallivan:
Visualizing phylogenetic tree landscapes. 85:1-85:12 - Daniel Ian McSkimming, Khaled Rasheed, Natarajan Kannan:
Classifying kinase conformations using a machine learning approach. 86:1-86:15 - Jiapeng Zhou, Jing Xin, Yayun Niu, Shiwen Wu:
DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD. 87:1-87:10 - Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W.-N. Lee, Silvia Marin, Marta Cascante:
MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. 88:1-88:9 - Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin:
Erratum to: Integrating mean and variance heterogeneities to identify differentially expressed genes. 89:1 - Yanhui Fan, You-Qiang Song:
PyHLA: tests for the association between HLA alleles and diseases. 90:1-90:5 - Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano:
Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis. 91:1-91:13 - Quan Zhang, Yuzhen Ye:
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. 92:1-92:12 - Hirokazu Chiba, Ikuo Uchiyama:
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. 93:1-93:6 - W. Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A. Shelburne, Marina Vannucci:
An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. 94:1-94:12 - Georgios A. Dalkas, Marianne Rooman:
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. 95:1-95:12 - Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché, Juan A. G. Ranea:
How can functional annotations be derived from profiles of phenotypic annotations? 96:1-96:12 - Raja Ali, Mikael Bark, Jorge Miró, Sayyed Muhammad, Joel Sjöstrand, Syed M. Zubair, Raja M. Abbas, Lars Arvestad:
VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces. 97:1-97:8 - Yanhui Hu, Aram Comjean, Norbert Perrimon, Stephanie E. Mohr:
The Drosophila Gene Expression Tool (DGET) for expression analyses. 98:1-98:9 - Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W. Ressom:
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. 99:1-99:14 - Tran Tuan Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao:
Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. 100:1-100:10 - Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou:
iHMS: a database integrating human histone modification data across developmental stages and tissues. 103:1-103:9 - Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes, Daniella C. Bartholomeu:
TipMT: Identification of PCR-based taxon-specific markers. 104:1-104:8 - Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng, Stephan Beck:
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. 105:1-105:14 - Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali:
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. 106:1-106:7 - Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. 107:1-107:11 - Kosuke Yoshida, Junichiro Yoshimoto, Kenji Doya:
Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data. 108:1-108:11 - Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu:
Improvement of peptide identification with considering the abundance of mRNA and peptide. 109:1-109:8 - Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris, Inga Prokopenko:
MARV: a tool for genome-wide multi-phenotype analysis of rare variants. 110:1-110:8 - Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis:
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. 111:1-111:10 - Francesco Napolitano:
repo: an R package for data-centered management of bioinformatic pipelines. 112:1-112:9 - Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro de Vasconcelos, Fabio Ribeiro Cerqueira:
Erratum to: Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction. 113:1 - Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar, Guy N. Brock:
Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies. 114:1-114:13 - Julia Koehler Leman, Sergey Lyskov, Richard Bonneau:
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. 115:1-115:9 - Matthias Barann, Ralf Zimmer, Fabian Birzele:
Manananggal - a novel viewer for alternative splicing events. 120:1-120:13 - Sergio Gonzalez, Bernardo J. Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego:
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. 121:1-121:9 - Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee:
Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing. 122:1-122:11 - Diego Pasqualin, Marcos Barbeitos, Fabiano Silva:
SFREEMAP - A simulation-free tool for stochastic mapping. 123:1-123:8 - Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Massimo Fato, Francesco Cardinale:
SEEG assistant: a 3DSlicer extension to support epilepsy surgery. 124:1-124:13 - Ilya Zhbannikov, Konstantin G. Arbeev, Igor Akushevich, Eric Stallard, Anatoliy I. Yashin:
stpm: an R package for stochastic process model. 125:1-125:12 - Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Abolfazl Seyed Motahari, Babak Hossein Khalaj:
Meta-aligner: long-read alignment based on genome statistics. 126:1-126:9 - Joshua L. Cherry:
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history. 127:1-127:12 - Florian Rohart, Aida Eslami, Nicholas Matigian, Stéphanie Bougeard, Kim-Anh Lê Cao:
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. 128:1-128:13 - Li Zhang, Jason Cham, Alan Paciorek, James Trager, Nadeem Sheikh, Lawrence Fong:
3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data. 129:1-129:14 - Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park, Youngmi Yoon:
Drug voyager: a computational platform for exploring unintended drug action. 131:1-131:13 - Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu, Tzu-Hung Hsiao, Eric Y. Chuang, Yidong Chen:
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. 132:1-132:11 - Sarah Sandmann, Aniek O. de Graaf, Martin Dugas:
BBCAnalyzer: a visual approach to facilitate variant calling. 133:1-133:6 - Xiaoyong Pan, Hong-Bin Shen:
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. 136:1-136:14 - Saghi Nojoomi, Patrice Koehl:
String kernels for protein sequence comparisons: improved fold recognition. 137:1-137:15 - Philip L. Tzou, Xiaoqiu Huang, Robert W. Shafer:
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. 138:1-138:6 - M.-H. Elsensohn, N. Leblay, Sarra Dimassi, Amandine Campan-Fournier, A. Labalme, Florence Roucher Boulez, D. Sanlaville, Gaetan Lesca, C. Bardel, Pascal Roy:
Statistical method to compare massive parallel sequencing pipelines. 139:1-139:11 - Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman K. Halgamuge:
Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes. 140:1-140:15 - Martin Nettling, Hendrik Treutler, Jesús Cerquides, Ivo Grosse:
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. 141:1-141:10 - Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner-Martinez, Pablo Marín-García, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob:
Reactome pathway analysis: a high-performance in-memory approach. 142:1-142:9