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ORCIDBMC Bioinformatics, Volume 15
Volume 15, 2014
- Christine B. Trame, Yuanyuan Chang, Herbert L. Axelrod, Ruth Y. Eberhardt
, Penelope Coggill, Marco Punta, Neil D. Rawlings:
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. 1
- Wentian Li, Jan Freudenberg, Pedro Miramontes:
Diminishing Return for Increased Mappability with Longer Sequencing Reads: Implications of the k-mer Distributions in the Human Genome. 2 - Tao Yang, Hong-Wen Deng, Tianhua Niu:
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences. 3 - Xiang Liu, Tao Lu, Yongchao Dou, Bin Yu, Chi Zhang:
Identification of RNA silencing components in soybean and sorghum. 4 - Mingming Liu, Layne T. Watson, Liqing Zhang:
Quantitative prediction of the effect of genetic variation using hidden Markov models. 5 - Predrag Kukic, Claudio Mirabello, Giuseppe Tradigo, Ian Walsh, Pierangelo Veltri, Gianluca Pollastri:
Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks. 6 - Travis J. Wheeler, Jody Clements, Robert D. Finn:
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. 7 - Miron B. Kursa:
Robustness of Random Forest-based gene selection methods. 8 - Jaza Gul-Mohammed, Ignacio Arganda-Carreras, Philippe Andrey, Vincent Galy, Thomas Boudier:
A generic classification-based method for segmentation of nuclei in 3D images of early embryos. 9 - Daniel Taliun, Johann Gamper, Cristian Pattaro:
Efficient haplotype block recognition of very long and dense genetic sequences. 10 - Jianlong Qi, Hassan Asl, Johan Björkegren, Tom Michoel:
kruX: matrix-based non-parametric eQTL discovery. 11 - Kota Kasahara, Kengo Kinoshita:
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. 12 - Hyunjung Kang, Ikjung Choi, Sooyoung Cho, Daeun Ryu, Sanghyuk Lee, Wan Kyu Kim:
gsGator: an integrated web platform for cross-species gene set analysis. 13 - Doulaye Dembélé, Philippe Kastner:
Fold change rank ordering statistics: a new method for detecting differentially expressed genes. 14 - Rimpi Khurana, Vinod Kumar Verma, Abdul Rawoof, Shrish Tiwari, Rekha A. Nair, Ganesh Mahidhara, Mohammed M. Idris, Alan R. Clarke, Lekha Dinesh Kumar:
OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer. 15 - Stefano Teso, Andrea Passerini:
Joint probabilistic-logical refinement of multiple protein feature predictors. 16 - Rong Xu, QuanQiu Wang:
Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection. 17 - Herbert Baier, Jörg Schultz:
ISAAC - InterSpecies Analysing Application using Containers. 18 - Ate van der Burgt, Edouard Severing, Jérôme Collemare, Pierre J. G. M. de Wit:
Automated alignment-based curation of gene models in filamentous fungi. 19 - Jaydeep De, Huiqi Li, Li Cheng:
Tracing retinal vessel trees by transductive inference. 20 - Barrie S. Bradley, Joseph C. Loftus, Clinton J. Mielke, Valentin Dinu:
Differential expression of microRNAs as predictors of glioblastoma phenotypes. 21 - Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront:
BioShell-Threading: versatile Monte Carlo package for protein 3D threading. 22 - Eran Elhaik, Matteo Pellegrini, Tatiana V. Tatarinova:
Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. 23 - Sergii Zakharov, Garrett H. K. Teoh, Agus Salim, Anbupalam Thalamuthu:
A method to incorporate prior information into score test for genetic association studies. 24 - Marianna D'Addario, Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann:
A modular computational framework for automated peak extraction from ion mobility spectra. 25 - Anirban Mukhopadhyay, Sumanta Ray, Ujjwal Maulik:
Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach. 26 - Kyung In Kim, Richard Simon:
Using single cell sequencing data to model the evolutionary history of a tumor. 27 - Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S. Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder:
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. 28 - Peter K. Busk:
A tool for design of primers for microRNA-specific quantitative RT-qPCR. 29 - Jeffrey G. Reid, Andrew Carroll, Narayanan Veeraraghavan, Mahmoud Dahdouli, Andreas Sundquist, Adam C. English, Matthew N. Bainbridge, Simon White, William J. Salerno, Christian Buhay, Fuli Yu, Donna M. Muzny, Richard Daly, Geoff Duyk, Richard A. Gibbs, Eric Boerwinkle:
Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. 30 - Miguel Reboiro-Jato, Joel Arrais, José Luís Oliveira, Florentino Fdez-Riverola:
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. 31 - Hamid Mohamadlou, Joseph C. Shope, Nicholas S. Flann:
Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation. 32 - Ram Shrestha, Baruch Lubinsky, Vijay B. Bansode, Mónica B. J. Moinz, Grace P. McCormack, Simon A. A. Travers:
QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform. 33 - Marius Nicolae, Sanguthevar Rajasekaran:
Efficient Sequential and Parallel Algorithms for Planted Motif Search. 34 - Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris:
Inferring clonal evolution of tumors from single nucleotide somatic mutations. 35 - Adam Skarshewski, Mitchell Stanton-Cook, Thomas Huber, Sumaya Al Mansoori, Ross Smith, Scott A. Beatson, Joseph A. Rothnagel:
uPEPperoni: An online tool for upstream open reading frame location and analysis of transcript conservation. 36 - Yiyi Liu, Quanquan Gu, Jack P. Hou, Jiawei Han, Jian Ma:
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. 37 - Martin Nettling, Nils Thieme, Andreas Both, Ivo Grosse:
DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data. 38 - Evelien Vaes, Mona Khan, Peter Mombaerts:
Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes. 39 - Swetansu Pattnaik, Saurabh Gupta, Arjun A. Rao, Binay Panda:
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data. 40 - Susan M. Huse, David B. Mark Welch, Andy Voorhis, Anna Shipunova, Hilary G. Morrison, A. Murat Eren, Mitchell L. Sogin:
VAMPS: a website for visualization and analysis of microbial population structures. 41 - Jongik Kim, Chen Li, Xiaohui Xie:
Improving read mapping using additional prefix grams. 42 - Chris J. Stubben, Jean F. Challacombe:
Mining locus tags in PubMed Central to improve microbial gene annotation. 43 - Youri Lammers, Tamara Peelen, Rutger A. Vos, Barbara Gravendeel:
The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. 44 - Heather C. Wick, Harold J. Drabkin, Huy Ngu, Michael Sackman, Craig Fournier, Jessica Haggett, Judith A. Blake, Diana W. Bianchi, Donna K. Slonim:
DFLAT: functional annotation for human development. 45 - Suhas Tikole, Victor Jaravine, Vladimir Rogov, Volker Dötsch, Peter Güntert:
Peak picking NMR spectral data using non-negative matrix factorization. 46 - Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger, Alejandro A. Schäffer:
PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. 47 - Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng:
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms. 48 - Kun-Huang Chen, Kung-Jeng Wang, Min-Lung Tsai, Kung-Min Wang, Angelia Melani-Adrian, Wei-Chung Cheng, Tzu-Sen Yang, Nai-Chia Teng, Kuo-Pin Tan, Ku-Shang Chang:
Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm. 49 - Xin Zhang, Renqian Du, Shilin Li, Feng Zhang, Li Jin, Hongyan Wang:
Evaluation of copy number variation detection for a SNP array platform. 50 - Hiroyuki Yamamoto, Tamaki Fujimori, Hajime Sato, Gen Ishikawa, Kenjiro Kami, Yoshiaki Ohashi:
Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis. 51 - Louis-Philippe Lemieux Perreault, Marc-André Legault, Amina Barhdadi, Sylvie Provost, Valérie Normand, Jean-Claude Tardif, Marie-Pierre Dubé:
Comparison of genotype clustering tools with rare variants. 52 - Sagi Abelson:
Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data. 53 - Pawel Gasior, Malgorzata Kotulska:
FISH Amyloid - a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids. 54 - Vladimir Arinkin, Ilya Digel, Dariusz Porst, Aysegül Artmann, Gerhard M. Artmann:
Phenotyping date palm varieties via leaflet cross-sectional imaging and artificial neural network application. 55 - Hongjian Li, Kwong-Sak Leung, Takanori Nakane, Man Hon Wong:
iview: an interactive WebGL visualizer for protein-ligand complex. 56 - Qian Liu, Steven C. H. Hoi, Chee Keong Kwoh, Limsoon Wong, Jinyan Li:
Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots. 57 - Murat Sariyar, Isabell Hoffmann, Harald Binder:
Combining techniques for screening and evaluating interaction terms on high-dimensional time-to-event data. 58 - Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor:
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. 59 - Jiabin Huang, Björn Voß:
Analysing RNA-kinetics based on folding space abstraction. 60 - Bart Hazes:
CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences. 61 - Jianwei Gou, Yang Zhao, Yongyue Wei, Chen Wu, Ruyang Zhang, Yongyong Qiu, Ping Zeng, Wen Tan, Dianke Yu, Tangchun Wu, Zhibin Hu, Dongxin Lin, Hongbing Shen, Feng Chen:
Stability SCAD: a powerful approach to detect interactions in large-scale genomic study. 62 - Micah J. Manary, Suriya S. Singhakul, Erika L. Flannery, Selina E. R. Bopp, Victoria C. Corey, Andrew Bright, Case W. McNamara, John R. Walker, Elizabeth A. Winzeler:
Identification of pathogen genomic variants through an integrated pipeline. 63 - Ning Kang, Bharat Singh, Quoc-Chinh Bui, Zubair Afzal, Erik M. van Mulligen, Jan A. Kors:
Knowledge-based extraction of adverse drug events from biomedical text. 64 - Michal Wozniak, Limsoon Wong, Jerzy Tiuryn:
eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains. 65 - Nicholas J. Hudson, Laercio R. Porto-Neto, James Kijas, Sean McWilliam, Ryan J. Taft, Antonio Reverter:
Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest. 66 - Irene Pala:
Reviewer acknowledgement 2013. 67 - Helge G. Roider, Nadia Pavlova, Ivaylo Kirov, Stoyan Slavov, Todor Slavov, Zlatyo Uzunov, Bertram Weiss:
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. 68 - Zhuohui Gan, Jianwu Wang, Nathan Salomonis, Jennifer C. Stowe, Gabriel G. Haddad, Andrew D. McCulloch, Ilkay Altintas, Alexander C. Zambon:
MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. 69 - Hongmin Cai, Peiying Ruan, Michael Kwok-Po Ng, Tatsuya Akutsu:
Feature weight estimation for gene selection: a local hyperlinear learning approach. 70 - Mariko Nakagome, Elena Solovieva, Akira Takahashi, Hiroshi Yasue, Hirohiko Hirochika, Akio Miyao:
Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. 71 - Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Torres-Mendoza, Mario Flores-Soto, Mildred Vázquez-Torres, Francisco Gálvez-Gastelum, Arturo Viniegra-Osorio, Marcelo Castillero-Manzano, Eduardo Vázquez-Valls:
Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis. 72 - Mehmet Deveci, Ümit V. Çatalyürek, Amanda E. Toland:
mrSNP: Software to detect SNP effects on microRNA binding. 73 - Shengping Yang, Xiangqin Cui, Zhide Fang:
BCRgt: a Bayesian cluster regression-based genotyping algorithm for the samples with copy number alterations. 74 - Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Robert D. Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind:
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. 75 - Simon Roux, Jeremy Tournayre, Antoine Mahul, Didier Debroas, François Enault:
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. 76 - Mark C. Evans, Pham Phung, Agnes C. Paquet, Anvi Parikh, Christos J. Petropoulos, Terri Wrin, Mojgan Haddad:
Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method. 77 - Shaylan K. Govind, Amin Zia, Pablo H. Hennings-Yeomans, John D. Watson, Michael Fraser, Catalina V. Anghel, Alexander Wyatt, Theodorus van der Kwast, Colin C. Collins, John D. McPherson, Robert G. Bristow, Paul C. Boutros:
ShatterProof: operational detection and quantification of chromothripsis. 78 - Neil R. Clark, Kevin S. Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma'ayan:
The characteristic direction: a geometrical approach to identify differentially expressed genes. 79 - Dawit Nigatu, Attiya Mahmood, Werner Henkel:
The Empirical Codon Mutation Matrix as a Communication Channel. 80 - Kristoffer Vitting-Seerup, Bo T. Porse, Albin Sandelin, Johannes Waage:
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. 81 - Calem J. Bendell, Shalon Liu, Tristan Aumentado-Armstrong, Bogdan Istrate, Paul T. Cernek, Samuel Khan, Sergiu Picioreanu, Michael Zhao, Robert A. Murgita:
Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor. 82 - Tung T. Nguyen, John S. A. Mattick, Qian Yang, Mehmet A. Orman, Marianthi G. Ierapetritou, Francois Berthiaume, Ioannis P. Androulakis:
Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver. 83 - Chandrasekhar Ramakrishnan, Andrej Bieri, Nora Sauter, Sophie Roizard, Philippe Ringler, Shirley A. Müller, Kenneth N. Goldie, Kaloyan Enimanev, Henning Stahlberg, Bernd Rinn, Thomas Braun:
openBEB: open biological experiment browser for correlative measurements. 84 - László Kaján, Thomas A. Hopf, Matú Kala, Debora S. Marks, Burkhard Rost:
FreeContact: fast and free software for protein contact prediction from residue co-evolution. 85 - Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis, Hongyu Zhao:
A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. 86 - Brett Hanson, Charles Westin, Mario Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L. MacDonald, Greg Dodge, Paule M. Boli, Cyprian W. Corwin, Haeja Kessler, Talia McKay, Herbert J. Bernstein, Paul A. Craig:
Estimation of protein function using template-based alignment of enzyme active sites. 87 - Koen Van der Borght, Geert Verbeke, Herman van Vlijmen:
Multi-model inference using mixed effects from a linear regression based genetic algorithm. 88 - Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß:
TSSAR: TSS annotation regime for dRNA-seq data. 89 - Koldo Garcia-Etxebarria, Marc Garcia-Garcerà, Francesc Calafell:
Consistency of metagenomic assignment programs in simulated and real data. 90 - Andrea Rau, Guillemette Marot, Florence Jaffrézic:
Differential meta-analysis of RNA-seq data from multiple studies. 91 - Nysia I. George, Ching-Wei Chang:
DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression. 92 - Bastiaan A. van den Berg, Marcel J. T. Reinders, Johannes A. Roubos, Dick de Ridder:
SPiCE: a web-based tool for sequence-based protein classification and exploration. 93 - Helena Andrade, Iván Area, Juan J. Nieto, Angela Torres:
The number of reduced alignments between two DNA sequences. 94 - Hsin-Wei Wang, Chia-Han Chu, Wen-Ching Wang, Tun-Wen Pai:
A local average distance descriptor for flexible protein structure comparison. 95 - Mehmet Gültas, Güncel Düzgün, Sebastian Herzog, Sven Joachim Jäger, Cornelia Meckbach, Edgar Wingender, Stephan Waack:
Quantum Coupled Mutation Finder: Predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming. 96 - Suyan Tian, Howard H. Chang, Chi Wang, Jing Jiang, Xiaomei Wang, Junqi Niu:
Multi-TGDR, a multi-class regularization method, identifies the metabolic profiles of hepatocellular carcinoma and cirrhosis infected with hepatitis B or hepatitis C virus. 97 - Markus K. Muellner, Gerhard Dürnberger, Florian Ganglberger, Claudia Kerzendorfer, Iris Z. Uras, Andreas Schoenegger, Klaudia Bagienski, Jacques Colinge, Sebastian M. B. Nijman:
TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens. 98 - Birte Kehr, Kathrin Trappe, Manuel Holtgrewe, Knut Reinert:
Genome alignment with graph data structures: a comparison. 99 - Peter Kerpedjiev, Jes Frellsen, Stinus Lindgreen, Anders Krogh:
Adaptable probabilistic mapping of short reads using position specific scoring matrices. 100 - Diego H. Milone, Georgina Stegmayer, Mariana G. Lopez, Laura Kamenetzky, Fernando Carrari:
Improving clustering with metabolic pathway data. 101 - Xuan Guo, Meng Yu, Ning Yu, Yi Pan:
Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering. 102 - Claudio Saccà, Stefano Teso, Michelangelo Diligenti, Andrea Passerini:
Improved multi-level protein¿protein interaction prediction with semantic-based regularization. 103 - Brandi L. Cantarel, Daniel Weaver, Nathan McNeill, Jianhua Zhang, Aaron J. Mackey, Justin T. Reese:
BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity. 104 - Rong Xu, Li Li, QuanQiu Wang:
dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text. 105 - Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka Varga, Veronika Ölvedy, Hong Jiang, Jianhua Wang, William E. Smiddy, Anikó Somogyi, Delia Cabrera DeBuc:
Automated classifiers for early detection and diagnosis of retinopathy in diabetic eyes. 106 - Jean-Pierre Flandrois, Gérard Lina, Oana Dumitrescu:
MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis. 107 - Yihan Li, Debashis Ghosh:
A Two-Step Hierarchical Hypothesis Set Testing Framework, with Applications to Gene Expression Data on Ordered Categories. 108 - Heng Wang, Dan Nettleton, Kai Ying:
Copy number variation detection using next generation sequencing read counts. 109 - Yun Zhang, Charles A. Phillips, Gary L. Rogers, Erich J. Baker, Elissa J. Chesler, Michael A. Langston:
On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types. 110 - Carlos Bermejo-Das-Neves, Hoan-Ngoc Nguyen, Olivier Poch, Julie Dawn Thompson:
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). 111 - Anna Sheydina, Ruth Y. Eberhardt, Daniel J. Rigden, Yuanyuan Chang, Zhanwen Li, Christian M. Zmasek, Herbert L. Axelrod, Adam Godzik:
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. 112 - Juuso A. Parkkinen, Samuel Kaski:
Probabilistic drug connectivity mapping. 113 - Christina A. Castellani, Melkaye G. Melka, Andrea E. Wishart, M. Elizabeth Locke, Zain Awamleh, Richard L. O'Reilly, Shiva M. Singh:
Biological relevance of CNV calling methods using familial relatedness including monozygotic twins. 114 - Ståle Nygård, Trond Reitan, Trevor Clancy, Vegard Nygaard, Johannes Bjørnstad, Biljana Skrbic, Theis Tønnessen, Geir Christensen, Eivind Hovig:
Identifying pathogenic processes by integrating microarray data with prior knowledge. 115 - Mark A. van de Wiel, Maarten Neerincx, Tineke E. Buffart, Daoud Sie, Henk M. W. Verheul:
ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs. 116