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ORCIDBMC Bioinformatics, Volume 17
Volume 17, 2016
- Ákos Tényi, Pedro de Atauri
, David Gomez-Cabrero, Isaac Cano, Kim Clarke, Francesco Falciani, Marta Cascante, Josep Roca, Dieter Maier:
ChainRank, a chain prioritisation method for contextualisation of biological networks. 17 - Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé, Yves Van de Peer:
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. 18 - James J. Yang, Jia Li, L. Keoki Williams, Anne Buu:
An efficient genome-wide association test for multivariate phenotypes based on the Fisher combination function. 19 - Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos, Francisco Melo:
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. 20 - Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer:
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. 21 - Van-Vinh Le, Tran Van Lang, Tran Van Hoai:
A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads. 22 - Manuel Binet, Olivier Gascuel, Céline Scornavacca, Emmanuel J. P. Douzery, Fabio Pardi:
Fast and accurate branch lengths estimation for phylogenomic trees. 23 - Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V. Uzilov, Rong Chen:
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. 24 - Kerstin Johnsson, Jonas Wallin, Magnus Fontes:
BayesFlow: latent modeling of flow cytometry cell populations. 25 - Nithin Shivashankar, Sonali Patil, Amrisha Bhosle, Nagasuma Chandra, Vijay Natarajan:
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. 26 - Roman Hornung, Anne-Laure Boulesteix, David Causeur:
Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. 27 - Yubo Zhang, Yi Ding:
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.). 28 - Arthur T. O. Melo, Radhika Bartaula, Iago Hale:
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. 29 - Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister M. Swenson:
Aligning the unalignable: bacteriophage whole genome alignments. 30 - Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro F. Santibanez-Koref, David J. Elliott, Michael S. Jackson:
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. 31 - Eugene Tseytlin, Kevin J. Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan, Rebecca S. Jacobson:
NOBLE - Flexible concept recognition for large-scale biomedical natural language processing. 32 - Mari van Reenen, Carolus J. Reinecke, Johan A. Westerhuis, J. Hendrik Venter:
Variable selection for binary classification using error rate p-values applied to metabolomics data. 33 - Kamal Taha, Paul D. Yoo:
Predicting the functions of a protein from its ability to associate with other molecules. 34 - Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass:
Deciphering transcriptional regulations coordinating the response to environmental changes. 35 - Shuai Li, Michael Woodfin, S. Seth Long, Peter G. Fuerst:
IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination. 36 - Lun-Ching Chang, Bingshan Li, Zhou Fang, Scott Vrieze, Matthew McGue, William G. Iacono, George C. Tseng, Wei Chen:
A computational method for genotype calling in family-based sequencing data. 37 - Veronika B. Dubinkina, Dmitry S. Ischenko, Vladimir Ulyantsev, Alexander V. Tyakht, Dmitry G. Alexeev:
Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. 38 - Sandeep K. Kushwaha, Lokeshwaran Manoharan, Tejashwari Meerupati, Katarina Hedlund, Dag G. Ahrén:
Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics. 39 - Vassily A. Lyubetsky, Roman Gershgorin, Alexander V. Seliverstov, Konstantin Yu. Gorbunov:
Algorithms for reconstruction of chromosomal structures. 40 - Francisco Pina-Martins, Bruno M. Vieira, Sofia G. Seabra, Dora Batista, Octávio S. Paulo:
4Pipe4 - A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. 41 - Daniele Muraro, Alison Simmons:
An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease. 42 - Elo Leung, Amy Huang, Eithon Cadag, Aldrin Montana, Jan Lorenz Soliman, Carol L. Ecale Zhou:
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations. 43 - Yuan Chen, Lifeng Wang, Lanzhi Li, Hongyan Zhang, Zheming Yuan:
Informative gene selection and the direct classification of tumors based on relative simplicity. 44 - Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer:
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. 45 - André C. A. Nascimento, Ricardo B. C. Prudêncio, Ivan G. Costa:
A multiple kernel learning algorithm for drug-target interaction prediction. 46 - Tzu-Yu Liu, Thomas Burke, Lawrence P. Park, Christopher W. Woods, Aimee K. Zaas, Geoffrey S. Ginsburg, Alfred O. Hero III:
An individualized predictor of health and disease using paired reference and target samples. 47 - Daniel A. Janies, Zachary L. Witter, Gregorio V. Linchangco, David W. Foltz, Allison K. Miller, Alexander M. Kerr, Jeremy J. Jay, Robert W. Reid, Gregory A. Wray:
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. 48 - David Rio Deiros, Richard A. Gibbs, Jeffrey Rogers:
DNAism: exploring genomic datasets on the web with Horizon Charts. 49 - Giovanni Mele:
Arabidopsis Motif Scanner. 50 - Virginie Uhlmann, Shantanu Singh, Anne E. Carpenter:
CP-CHARM: segmentation-free image classification made accessible. 51 - Wei Zhang, Huiyun Li, Zhaohai Li, Qizhai Li:
A two-phase procedure for non-normal quantitative trait genetic association study. 52 - Patrick Schorderet:
NEAT: a framework for building fully automated NGS pipelines and analyses. 53 - Alencar Xavier, William M. Muir, Katy Martin Rainey:
Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans. 55 - Ram Vinay Pandey, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel:
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research. 56 - Liguo Wang, Jinfu J. Nie, Hugues Sicotte, Ying Li, Jeanette E. Eckel-Passow, Surendra Dasari, Peter T. Vedell, Poulami Barman, Liewei Wang, Richard Weinshiboum, Jin Jen, Haojie Huang, Manish Kohli, Jean-Pierre A. Kocher:
Measure transcript integrity using RNA-seq data. 58 - Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos, Raquel M. Silva:
The exceptional genomic word symmetry along DNA sequences. 59 - Hua-zhen Wang, Fan Yang, Zhiyuan Luo:
An experimental study of the intrinsic stability of random forest variable importance measures. 60 - Christos Kozanitis, David A. Patterson:
GenAp: a distributed SQL interface for genomic data. 63 - Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti:
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. 64 - Anthony O'Hare, Samantha Lycett, Thomas Doherty, Liliana C. M. Salvador, Rowland R. Kao:
Broadwick: a framework for computational epidemiology. 65 - Benjamin K. Johnson, Matthew B. Scholz, Tracy K. Teal, Robert B. Abramovitch:
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. 66 - Katharina Imkeller, Peter F. Arndt, Hedda Wardemann, Christian E. Busse:
sciReptor: analysis of single-cell level immunoglobulin repertoires. 67 - Ludmil B. Alexandrov, Alan R. Bishop, Kim Ø. Rasmussen, Boian S. Alexandrov:
The role of structural parameters in DNA cyclization. 68 - Jincheol Park, Shili Lin:
Impact of data resolution on three-dimensional structure inference methods. 70 - Shabnam Shamriz, Hamideh Ofoghi:
Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant. 71 - Mario Deng, Johannes Brägelmann, Joachim L. Schultze, Sven Perner:
Web-TCGA: an online platform for integrated analysis of molecular cancer data sets. 72 - Xiaochun Sun, Rita H. Mumm:
Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation. 73 - Huey-miin Hsueh, Chen-An Tsai:
Gene set analysis using sufficient dimension reduction. 74 - Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf-Dieter Schubert, Alan Christoffels:
Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis. 75 - Joeri Ruyssinck, Piet Demeester, Tom Dhaene, Yvan Saeys:
Netter: re-ranking gene network inference predictions using structural network properties. 76 - Renée X. de Menezes, Leila Mohammadi, Jelle J. Goeman, Judith M. Boer:
Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. 77 - Adam S. Brown, Sek Won Kong, Isaac S. Kohane, Chirag J. Patel:
ksRepo: a generalized platform for computational drug repositioning. 78 - Dirk Krüger:
BMC Bioinformatics reviewer acknowledgement 2015. 79 - Giorgio E. M. Melloni, Stefano de Pretis, Laura Riva, Mattia Pelizzola, Arnaud Céol, Jole Costanza, Heiko Müller, Luca Zammataro:
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. 80 - Jeff Daily:
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. 81 - Simon Dellicour, Rebecca Rose, Oliver G. Pybus:
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. 82 - Suvir Jain, Kashyap R. Tumkur, Tsung-Ting Kuo, Shitij Bhargava, Gordon Lin, Chun-Nan Hsu:
Erratum to: Weakly supervised learning of biomedical information extraction from curated data. 84 - Marcin Piechota, Michal Korostynski, Joanna Ficek, Andrzej Tomski, Ryszard Przewlocki:
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators. 85 - Jiadong Ji, Zhongshang Yuan, Xiaoshuai Zhang, Fuzhong Xue:
A powerful score-based statistical test for group difference in weighted biological networks. 86 - Klaus Hahn, Peter R. Massopust, Sergei Prigarin:
A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain. 87 - Diana L. Delibaltov, Utkarsh Gaur, Jennifer Kim, Matthew Kourakis, Erin Newman-Smith, William Smith, Samuel A. Belteton, Daniel Szymanski, B. S. Manjunath:
CellECT: cell evolution capturing tool. 88 - Kahn Rhrissorrakrai, Kristin C. Gunsalus:
Erratum to: MINE: Module Identification in Networks. 89 - Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie:
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. 90 - Ivan Vujaklija, Ana Bielen, Tina Paradzik, Sinisa Bidin, Pavle Goldstein, Dusica Vujaklija:
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. 91 - Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro F. Santibanez-Koref, David J. Elliott, Michael S. Jackson:
Erratum to: PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. 92 - Jared S. Fowles, Kristen C. Brown, Ann M. Hess, Dawn L. Duval, Daniel L. Gustafson:
Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma. 93 - Minji Kim, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli, Olgica Milenkovic:
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. 94 - Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Keles:
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. 96 - Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung:
Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins. 97 - Nicholas C. Wong, Bernard J. Pope, Ida L. Candiloro, Darren Korbie, Matt Trau, Stephen Q. Wong, Thomas Mikeska, Xinmin Zhang, Mark Pitman, Stefanie Eggers, Stephen R. Doyle, Alexander Dobrovic:
MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. 98 - Chan-seok Jeong, Dongsup Kim:
Structure-based Markov random field model for representing evolutionary constraints on functional sites. 99 - Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai, Xiaoli Li, Hong Yan:
A two-layer integration framework for protein complex detection. 100 - M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Seth M. Bybee:
Detecting false positive sequence homology: a machine learning approach. 101 - Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty:
GEMINI: a computationally-efficient search engine for large gene expression datasets. 102 - Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim:
Trimming of sequence reads alters RNA-Seq gene expression estimates. 103 - Anjana Grandhi, Wenge Guo, Shyamal D. Peddada:
A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies. 104 - Kamal Taha, Paul D. Yoo:
Erratum to: Predicting the functions of a protein from its ability to associate with other molecules. 105 - Hanyu Jiang, Narayan Ganesan:
CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU. 106 - Joaquín Tárraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquín Dopazo:
HPG pore: an efficient and scalable framework for nanopore sequencing data. 107 - Meng-Yun Wu, Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Yuan Zhu, Hong Yan:
Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer. 108 - Shihai Feng, Chien-Chi Lo, Po-E Li, Patrick S. G. Chain:
ADEPT, a dynamic next generation sequencing data error-detection program with trimming. 109 - Mihails Delmans, Martin Hemberg:
Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data. 110 - Mingon Kang, Liping Tang, Jean Gao:
Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice. 111 - Biao Liu, Jessica L. Childs-Disney, Brent M. Znosko, Dan Wang, Mohammad Fallahi, Steven M. Gallo, Matthew D. Disney:
Analysis of secondary structural elements in human microRNA hairpin precursors. 112 - Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao, Tatsuya Akutsu:
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order. 113 - Youzhong Liu, Kirill Smirnov, Marianna Lucio, Régis D. Gougeon, Hervé Alexandre, Philippe Schmitt-Kopplin:
MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics. 114 - Mohammed-Amin Madoui, Carole Dossat, Léo d'Agata, Jan van Oeveren, Edwin van der Vossen, Jean-Marc Aury:
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. 115 - Binghuang Cai, Xia Jiang:
Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences. 116 - Javier Pérez-Rodríguez, Nicolás García-Pedrajas:
Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences. 117 - Armin Rauschenberger, Marianne A. Jonker, Mark A. van de Wiel, Renée X. de Menezes:
Testing for association between RNA-Seq and high-dimensional data. 118 - Frazier N. Baker, Aleksey A. Porollo:
CoeViz: a web-based tool for coevolution analysis of protein residues. 119 - Devin C. Koestler, Meaghan J. Jones, Joseph Usset, Brock C. Christensen, Rondi A. Butler, Michael S. Kobor, John K. Wiencke, Karl T. Kelsey:
Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). 120 - Sumanta Ray, Sanghamitra Bandyopadhyay:
A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs. 121 - Yafang Li, Jinyoung Byun, Guoshuai Cai, Xiangjun Xiao, Younghun Han, Olivier Cornelis, James E. Dinulos, Joe Dennis, Douglas F. Easton, Ivan P. Gorlov, Michael F. Seldin, Christopher I. Amos:
FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data. 122 - Aristeidis G. Telonis, Phillipe Loher, Yohei Kirino, Isidore Rigoutsos:
Consequential considerations when mapping tRNA fragments. 123 - Mirela Domijan, Paul E. Brown, Boris V. Shulgin, David A. Rand:
PeTTSy: a computational tool for perturbation analysis of complex systems biology models. 124 - Melanie Schirmer, Rosalinda D'Amore, Umer Zeeshan Ijaz, Neil Hall, Christopher Quince:
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. 125 - Kevin C. Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew C. Parnell, Stephen V. Gordon, David E. MacHugh:
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. 126 - Luis de la Garza, Johannes Veit, András Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert, Oliver Kohlbacher:
From the desktop to the grid: scalable bioinformatics via workflow conversion. 127 - Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. 128 - Shailesh Tripathi, Salissou Moutari, Matthias Dehmer, Frank Emmert-Streib:
Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules. 129 - Matteo Comin, Morris Antonello:
On the comparison of regulatory sequences with multiple resolution Entropic Profiles. 130 - Bo Yao, Zhong Li, Meng Ding, Minhong Chen:
Three-dimensional protein model similarity analysis based on salient shape index. 131 - Sapna Kumari, Wenping Deng, Chathura Gunasekara, Vincent Chiang, Huann-Sheng Chen, Hao Ma, Xin Davis, Hairong Wei:
Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. 132 - Kiyoshi Ezawa:
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. 133 - Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp:
Modeling the integration of bacterial rRNA fragments into the human cancer genome. 134