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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 - Barbara Mirel, Carsten Görg:
Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support. 117 - Jan-Oliver Janda, Ajmal Popal, Jochen Bauer, Markus Busch, Michael Klocke, Wolfgang Spitzer, Jörg Keller, Rainer Merkl:
H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments. 118 - Thomas Hrabe, Adam Godzik:
ConSole: using modularity of contact maps to locate Solenoid domains in protein structures. 119 - Renzhi Cao, Zheng Wang, Yiheng Wang, Jianlin Cheng:
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. 120 - You Li, Hao Chi, Leihao Xia, Xiaowen Chu:
Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs. 121 - Thorsten Bischler, Matthias Kopf, Björn Voß:
Transcript mapping based on dRNA-seq data. 122 - Carmen Maria Livi, Enrico Blanzieri:
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. 123 - Ivani de Oliveira Negrão Lopes, Alexander Schliep, André Carlos Ponce de Leon Ferreira de Carvalho:
The discriminant power of RNA features for pre-miRNA recognition. 124 - Andrew R. Carson, Erin N. Smith, Hiroko Matsui, Sigrid K. Brækkan, Kristen Jepsen, John-Bjarne Hansen, Kelly A. Frazer:
Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. 125 - Sergey Koren, Todd J. Treangen, Christopher Michael Hill, Mihai Pop, Adam M. Phillippy:
Automated ensemble assembly and validation of microbial genomes. 126 - Leo van Iersel, Steven Kelk, Nela Lekic, Céline Scornavacca:
A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. 127 - Ralf Stefan Neumann, Surendra Kumar, Thomas Hendricus Haverkamp, Kamran Shalchian-Tabrizi:
BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data. 128 - Gustavo A. Salazar, Ayton Meintjes, Gaston K. Mazandu, Holifidy A. Rapanoël, Richard O. Akinola, Nicola J. Mulder:
A web-based protein interaction network visualizer. 129 - Rui Henriques, Sara C. Madeira:
BicSPAM: flexible biclustering using sequential patterns. 130 - Adrianto Wirawan, Robert S. Harris, Yongchao Liu, Bertil Schmidt, Jan Schröder:
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. 131 - Daniele Pepe, Mario Grassi:
Investigating perturbed pathway modules from gene expression data via structural equation models. 132 - Filip Bielejec, Philippe Lemey, Luiz Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard:
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. 133 - Narjeskhatoon Habibi, Siti Zaiton Mohd Hashim, Alireza Norouzi, Mohammed Samian:
A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli. 134 - Claudia Angelini, Daniela De Canditiis, Italia De Feis:
Computational approaches for isoform detection and estimation: good and bad news. 135 - Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez:
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. 136 - Minta Thomas, Kris De Brabanter, Bart De Moor:
New Bandwidth Selection Criterion for Kernel PCA: Approach to Dimensionality Reduction and Classification Problems. 137 - Zhifa Liu, Stan Pounds:
An R Package that Automatically Collects and Archives Details for Reproducible Computing. 138 - Susanne Bornelöv, Simon Marillet, Jan Komorowski:
Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers. 139 - Maurice H. T. Ling, Chueh-Loo Poh:
A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations. 140 - Martin A. Rijlaarsdam, Yvonne G. van der Zwan, Lambert C. J. Dorssers, Leendert H. J. Looijenga:
DMR2+: identifying Differentially Methylated Regions between unique samples using array based methylation profiles. 141 - Zhongxue Chen, Hanwen Huang, Qingzhong Liu:
Detecting differentially methylated loci for multiple treatments based on high-throughput methylation data. 142 - Joshua D. Kangas, Armaghan W. Naik, Robert F. Murphy:
Efficient discovery of responses of proteins to compounds using active learning. 143 - Timo Lassmann, Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki:
MOIRAI: A Compact Workflow System for CAGE Analysis. 144 - Vittorio Fortino, Olli-Pekka Smolander, Petri Auvinen, Roberto Tagliaferri, Dario Greco:
Transcriptome dynamics-based operon prediction in prokaryotes. 145 - Justin Andrew Powell:
GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. 146 - Hosna Jabbari, Anne Condon:
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures. 147 - Hirokazu Chiba, Ikuo Uchiyama:
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. 148 - Sarah A. Killcoyne, Antonio del Sol:
FIGG: Simulating populations of whole genome sequences for heterogeneous data analyses. 149 - Luna De Ferrari, John B. O. Mitchell:
From sequence to enzyme mechanism using multi-label machine learning. 150 - Anna Hristoskova, Veselka Boeva, Elena Tsiporkova:
A Formal Concept Analysis Approach to Consensus Clustering of Multi-Experiment Expression Data. 151 - Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang, Xia Li:
LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. 152 - Zixing Wang, F. Anthony San Lucas, Peng Qiu, Yin Liu:
Improving the sensitivity of sample clustering by leveraging gene co-expression networks in variable selection. 153 - Su Yeon Kim, Laurent Jacob, Terence P. Speed:
Combining calls from multiple somatic mutation-callers. 154 - Rachael P. Huntley, Midori A. Harris, Yasmin Alam-Faruque, Judith A. Blake, Seth Carbon, Heiko Dietze, Emily C. Dimmer, Rebecca E. Foulger, David P. Hill, Varsha K. Khodiyar, Antonia Lock, Jane Lomax, Ruth C. Lovering, Prudence Mutowo-Meullenet, Tony Sawford, Kimberly Van Auken, Valerie Wood, Christopher J. Mungall:
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. 155 - Dominique Tessier, Sami Laroum, Béatrice Duval, Emma M. Rath, W. Bret Church, Jin-Kao Hao:
In silico evaluation of the influence of the translocon on partitioning of membrane segments. 156 - Greg W. Clark, Sharon H. Ackerman, Elisabeth R. Tillier, Domenico L. Gatti:
Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments. 157 - Ruijie Liu, Zhiyin Dai, Meredith Yeager, Rafael A. Irizarry, Matthew E. Ritchie:
KRLMM: an adaptive genotype calling method for common and low frequency variants. 158 - Jacob D. Durrant, Rommie E. Amaro:
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. 159 - Richard Tzong-Han Tsai, Po-Ting Lai:
A resource-saving collective approach to biomedical semantic role labeling. 160 - Refat Sharmin, Abul Bashar Mir Md Khademul Islam:
A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. 161 - Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami:
A multivariate approach to the integration of multi-omics datasets. 162 - José Ignacio Lucas-Lledó, David Vicente-Salvador, Cristina Aguado, Mario Cáceres:
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm. 163 - Weihua Pan, Yanan Zhao, Yun Xu, Fengfeng Zhou:
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences. 164 - Miguel Ferreira, Nuno Roma, Luís M. S. Russo:
Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER. 165 - Wing-Cheong Wong, Sebastian Maurer-Stroh, Birgit Eisenhaber, Frank Eisenhaber:
On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation. 166 - Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh:
PVT: an efficient computational procedure to speed up next-generation sequence analysis. 167 - Steffen Falgreen, Maria Bach Laursen, Julie Støve Bødker, Malene Krag Kjeldsen, Alexander Schmitz, Mette Nyegaard, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted:
Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition. 168 - Mukhtar Bizrah, Steve C. Dakin, Li Guo, Farzana Rahman, Miles Parnell, Eduardo Normando, Shereen Nizari, Benjamin Davis, Ahmed Younis, M. Francesca Cordeiro:
A semi-automated technique for labeling and counting of apoptosing retinal cells. 169 - Natalie S. Fox, Maud H. W. Starmans, Syed Haider, Philippe Lambin, Paul C. Boutros:
Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences. 170 - Reyhaneh Esmaielbeiki, Jean-Christophe Nebel:
Scoring docking conformations using predicted protein interfaces. 171 - Mohammad H. Ferdosi, Brian P. Kinghorn, Julius H. J. Van der Werf, Seung Hwan Lee, Cedric Gondro:
hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. 172 - Chun-Pei Cheng, Christopher M. DeBoever, Kelly A. Frazer, Yu-Cheng Liu, Vincent S. Tseng:
MiningABs: mining associated biomarkers across multi-connected gene expression datasets. 173 - Ambarish Biswas, Chris M. Brown:
Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3[prime] untranslated regions (3[prime] UTRs) of mRNAs. 174 - Elsa G. Guillot, Murray P. Cox:
SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations. 175 - Sean R. Wilkinson, Jonas S. Almeida:
QMachine: commodity supercomputing in web browsers. 176 - Thilakam Murali, Svetlana Pacifico, Russell L. Finley Jr.:
Integrating the interactome and the transcriptome of Drosophila. 177 - Marianna Budnikova, Jeffrey W. Habig, Daniel Lobo, Nicolas Cornia, Michael Levin, Timothy L. Andersen:
Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search. 178 - Toshihide Ono, Satoru Kuhara:
A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH(R) terms. 179 - Adam C. English, William J. Salerno, Jeffrey G. Reid:
PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping. 180 - Jan M. Brauner, Teja W. Groemer, Armin Stroebel, Simon Grosse-Holz, Timo Oberstein, Jens Wiltfang, Johannes Kornhuber, Juan Manuel Maler:
Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm. 181 - Hongshan Jiang, Rong Lei, Shou-Wei Ding, Shuifang Zhu:
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. 182 - Wasiu A. Akanni, Christopher J. Creevey, Mark D. Wilkinson, Davide Pisani:
L.U.St: a tool for approximated maximum likelihood supertree reconstruction. 183 - Mikel Diez, Víctor Petuya, Luis Alfonso Martínez-Cruz, Alfonso Hernández:
Insights into mechanism kinematics for protein motion simulation. 184 - Wei Luo, Marcus Gallagher, Bill Loveday, Susan Ballantyne, Jason P. Connor, Janet Wiles:
Detecting contaminated birthdates using generalized additive models. 185 - Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Hong Yan:
Detecting overlapping protein complexes based on a generative model with functional and topological properties. 186 - Alex Rudniy, Min Song, James Geller:
Mapping biological entities using the Longest Approximately Common Prefix method. 187 - Cyril Filloux, Cédric Meersseman, Romain Philippe, Lionel Forestier, Christophe Klopp, Dominique Rocha, Abderrahman Maftah, Daniel Petit:
An integrative method to normalize RNA-Seq data. 188 - Osamu Gotoh, Mariko Morita, David R. Nelson:
Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment. 189 - Xinyu Liu, Yupeng Wang, T. N. Sriram:
Determination of sample size for a multi-class classifier based on single-nucleotide polymorphisms: a volume under the surface approach. 190 - Mikhail Zaslavskiy, Claudia Bertonati, Philippe Duchateau, Aymeric Duclert, George H. Silva:
Efficient design of meganucleases using a machine learning approach. 191 - Bahar Yilmazel, Yanhui Hu, Frederic Sigoillot, Jennifer A. Smith, Caroline E. Shamu, Norbert Perrimon, Stephanie E. Mohr:
Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. 192 - Thomas Wilhelm:
Phenotype prediction based on genome-wide DNA methylation data. 193 - Xiaohan Sun, Junying Zhang:
Identification of putative pathogenic SNPs implied in schizophrenia-associated miRNAs. 194 - Chang-Chang Cao, Cheng Li, Xiao Sun:
Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers. 195 - Daniel J. Rigden, Ruth Y. Eberhardt, Harry J. Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik:
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. 196 - Saulo Henrique Pires de Oliveira, Felipe A. N. Ferraz, Rodrigo V. Honorato, José Xavier-Neto, Tiago José P. Sobreira, Paulo S. L. de Oliveira:
KVFinder: steered identification of protein cavities as a PyMOL plugin. 197 - Delphine Naquin, Yves d'Aubenton-Carafa, Claude Thermes, Maud Silvain:
CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data. 198 - Xinhui Wang, Peter W. Laird, Toshinori Hinoue, Susan Groshen, Kimberly D. Siegmund:
Non-specific filtering of beta-distributed data. 199 - Günter Jäger, Alexander Peltzer, Kay Nieselt:
inPHAP: Interactive visualization of genotype and phased haplotype data. 200 - Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau:
eXamine: Exploring annotated modules in networks. 201 - William C. Ray, Samuel L. Wolock, Nicholas W. Callahan, Min Dong, Qingshun Quinn Li, Chun Liang, Thomas J. Magliery, Christopher W. Bartlett:
Addressing the unmet need for visualizing conditional random fields in biological data. 202 - Hao Ding, Chao Wang, Kun Huang, Raghu Machiraju:
iGPSe: A visual analytic system for integrative genomic based cancer patient stratification. 203 - Eileen Marie Hanna, Nazar M. Zaki:
Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. 204 - Ingo Bulla, Anne-Kathrin Schultz, Christophe Chesneau, Tanya Mark, Florin Serea:
A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. 205 - Benedict Paten, Daniel R. Zerbino, Glenn Hickey, David Haussler:
A unifying model of genome evolution under parsimony. 206 - Pavankumar Videm, Deepika Gunasekaran, Bernd Schröder, Bettina Mayer, Martin L. Biniossek, Oliver Schilling:
Automated peptide mapping and protein-topographical annotation of proteomics data. 207 - Tommi Suvitaival, Simon Rogers, Samuel Kaski:
Stronger findings from mass spectral data through multi-peak modeling. 208 - Rongjian Li, Wenlu Zhang, Shuiwang Ji:
Automated identification of cell-type-specific genes in the mouse brain by image computing of expression patterns. 209 - Ruifeng Liu, Narender Singh, Gregory J. Tawa, Anders Wallqvist, Jaques Reifman:
Exploiting large-scale drug-protein interaction information for computational drug repurposing. 210 - Marten Boetzer, Walter Pirovano:
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. 211 - Dadakhalandar Doddamani, A. V. S. K. Mohan Katta, Aamir W. Khan, Gaurav Agarwal, Trushar M. Shah, Rajeev K. Varshney:
CicArMiSatDB: the chickpea microsatellite database. 212 - Yoichi Murakami, Kenji Mizuguchi:
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. 213 - Daniel Arend, Matthias Lange, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht, Uwe Scholz:
e!DAL - a framework to store, share and publish research data. 214 - Egor Dolzhenko, Andrew D. Smith:
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. 215 - Davor Sluga, Tomaz Curk, Blaz Zupan, Uros Lotric:
Heterogeneous computing architecture for fast detection of SNP-SNP interactions. 216 - Anthony Santella, Zhuo Du, Zhirong Bao:
A Semi-Local Neighborhood-based Framework for Probabilistic Cell Lineage Tracing. 217 - Michael Kloster, Gerhard Kauer, Bánk Beszteri:
SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects. 218 - Arnd Gross, Sibylle Schirm, Markus Scholz:
Ycasd - a tool for capturing and scaling data from graphical representations. 219 - Pratha Sah, Lisa Singh, Aaron Clauset, Shweta Bansal:
Exploring community structure in biological networks with random graphs. 220 - Alan Veliz-Cuba, Boris Aguilar, Franziska Hinkelmann, Reinhard C. Laubenbacher:
Steady state analysis of Boolean molecular network models via model reduction and computational algebra. 221 - Mehdi Khafif, Ludovic Cottret, Claudine Balagué, Sylvain Raffaele:
Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes. 222 - Rajkumar Palaniappan, Kenneth Sundaraj, Sebastian Sundaraj:
A comparative study of the svm and k-nn machine learning algorithms for the diagnosis of respiratory pathologies using pulmonary acoustic signals. 223 - Krishna R. Kalari, Asha A. Nair, Jaysheel D. Bhavsar, Daniel R. O'Brien, Jaime I. Dávila, Matthew A. Bockol, Jinfu J. Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher:
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. 224 - Mario Latendresse:
Efficiently Gap-Filling Reaction Networks. 225 - Yihan Li, Debashis Ghosh:
Meta-Analysis Based on Weighted Ordered P-values for Genomic Data with Heterogeneity. 226 - Neda Zamani, Görel Sundström, Jennifer R. S. Meadows, Marc P. Höppner, Jacques Dainat, Henrik Lantz, Brian J. Haas, Manfred G. Grabherr:
A universal genomic coordinate translator for comparative genomics. 227 - Reiji Teramoto, Chiaki Saito, Shin-ichi Funahashi:
Estimating causal effects with a non-paranormal method for the design of efficient intervention experiments. 228 - Ian Reid, Nicholas O'Toole, Omar Zabaneh, Reza Nourzadeh, Mahmoud Dahdouli, Mostafa Abdellateef, Paul M. K. Gordon, Jung Soh, Gregory Butler, Christoph W. Sensen, Adrian Tsang:
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models. 229 - Todd H. Oakley, Markos A. Alexandrou, Roger Ngo, M. Sabrina Pankey, Celia K. Churchill, William Chen, Karl B. Lopker:
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. 230 - Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Robert D. Bjornson, Daniel Zelterman, Yorgo Modis, Hongyu Zhao:
A spatial simulation approach to account for protein structure when identifying non-random somatic mutations. 231 - Simone Wahl, Nora Fenske, Sonja Zeilinger, Karsten Suhre, Christian Gieger, Melanie Waldenberger, Harald Grallert, Matthias Schmid:
On the potential of models for location and scale for genome-wide DNA methylation data. 232 - Lia Di, Pedro E. Pagan, Daniel Packer, Che L. Martin, Saymon Akther, Girish Ramrattan, Emmanuel F. Mongodin, Claire M. Fraser, Steven E. Schutzer, Benjamin J. Luft, Sherwood R. Casjens, Wei-Gang Qiu:
BorreliaBase: a phylogeny-centered browser of Borrelia genomes. 233 - Kalai Vanii Jayaseelan, Christoph Steinbeck:
Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking. 234 - Solon P. Pissis:
MoTeX-II: structured MoTif eXtraction from large-scale datasets. 235 - Nimisha Chaturvedi, Jelle J. Goeman, Judith M. Boer, Wessel N. van Wieringen, Renée X. de Menezes:
A test for comparing two groups of samples when analyzing multiple omics profiles. 236 - Shea N. Gardner, Tom Slezak:
Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes. 237 - Florian Martin, Alain Sewer, Marja Talikka, Yang Xiang, Julia Hoeng, Manuel C. Peitsch:
Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models. 238 - Evrim Acar, Evangelos E. Papalexakis, Gozde Gürdeniz, Morten A. Rasmussen, Anders J. Lawaetz, Mathias Nilsson, Rasmus Bro:
Structure-Revealing Data Fusion. 239 - Justin Feigelman, Fabian J. Theis, Carsten Marr:
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. 240 - Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters:
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. 241 - Michael B. Sohn, Lingling An, Naruekamol Pookhao, Qike Li:
Accurate genome relative abundance estimation for closely related species in a metagenomic sample. 242 - Raffael A. C. Oliveira, Ricardo V. M. Almeida, Márcia D. A. Dantas, Felipe N. Castro, João Paulo M. S. Lima, Daniel C. F. Lanza:
In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae. 243 - Vesna Memievi, Kamal Kumar, Li Cheng, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman:
DBSecSys: a database of Burkholderia mallei secretion systems. 244 - Suyu Mei, Hao Zhu:
Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens. 245 - Jose L. Gualdrón Duarte, Rodolfo J. C. Cantet, Ronald O. Bates, Catherine W. Ernst, Nancy E. Raney, Juan P. Steibel:
Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. 246 - Alison M. Meynert, Morad Ansari, David R. FitzPatrick, Martin S. Taylor:
Variant detection sensitivity and biases in whole genome and exome sequencing. 247 - Aaron J. Masino, Elizabeth T. Dechene, Matthew C. Dulik, Alisha Wilkens, Nancy B. Spinner, Ian D. Krantz, Jeffrey W. Pennington, Peter N. Robinson, Peter S. White:
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. 248 - Adam Spiro, Luca Cardelli, Ehud Shapiro:
Lineage grammars: describing, simulating and analyzing population dynamics. 249 - Narsis Aftab Kiani, Lars Kaderali:
Dynamic Probabilistic Threshold Networks to Infer Signaling Pathways from Time-Course Perturbation Data. 250 - Igor Mekterovic, Darko Mekterovic, Zeljka Maglica:
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies. 251 - Xin Deng, Jianlin Cheng:
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. 252 - Andrei Kramer, Ben Calderhead, Nicole Radde:
Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems. 253 - Keisuke Ueno, Akihiro Ishii, Kimihito Ito:
ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset. 254 - Ting Wang, Jin Gu, Yanda Li:
Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. 255 - Zhimin Deng, Tianhai Tian:
A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. 256 - Brian J. Stucky, John Deck, Tom Conlin, Lukasz Ziemba, Nico Cellinese, Robert P. Guralnick:
The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web. 257 - Dany Morisset, Petra Kralj Novak, Darko Zupanic, Kristina Gruden, Nada Lavrac, Jana Zel:
GMOseek: a user friendly tool for optimized GMO testing. 258 - Paul D. Shaw, Martin Graham, Jessie B. Kennedy, Iain Milne, David F. Marshall:
Helium: visualization of large scale plant pedigrees. 259 - Xiaoming Wang, Saumyadipta Pyne, Irina Dinu:
Gene set enrichment analysis for multiple continuous phenotypes. 260 - Wannarat Yim-im, Orathai Sawatdichaikul, Suwanna Semsri, Natharinee Horata, Wanwimon Mokmak, Sissades Tongsima, Apichart Suksamrarn, Kiattawee Choowongkomon:
Computational analyses of curcuminoid analogs against kinase domain of HER2. 261 - Allyson L. Byrd, Joseph F. Perez-Rogers, Solaiappan Manimaran, Eduardo Castro-Nallar, Ian Toma, Tim McCaffrey, Marc Siegel, Gary Benson, Keith A. Crandall, William Johnson:
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. 262 - Ines Wagner, Michael Volkmer, Malvika Sharan, Jose M. Villaveces, Felix Oswald, Vineeth Surendranath, Bianca Habermann:
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. 263 - Tilo Buschmann, Rong Zhang, Douglas E. Brash, Leonid V. Bystrykh:
Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate. 264 - Dimitrios P. Lyras, Dirk Metzler:
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach. 265 - Anne-Dominique Pham, Aurélie Névéol, Thomas Lavergne, Daisuke Yasunaga, Olivier Clément, Guy Meyer, Rémy Morello, Anita Burgun:
Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings. 266 - Halil Bisgin, Zhichao Liu, Hong Fang, Reagan Kelly, Xiaowei Xu, Weida Tong:
A phenome-guided drug repositioning through a latent variable model. 267 - Joseph M. E. X. Lucas, Matthieu Muffato, Hugues Roest Crollius:
PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees. 268 - Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret:
Study of cell differentiation by phylogenetic analysis using histone modification data. 269 - Chunkao Wang, Dzianis Prakapenka, Shengwen Wang, Sujata Pulugurta, Hakizumwami Runesha, Yang Da:
GVCBLUP: a computer package for genomic prediction and variance component estimation of additive and dominance effects. 270 - Junhua Zhang, Ling-Yun Wu, Xiang-Sun Zhang, Shihua Zhang:
Discovery of co-occurring driver pathways in cancer. 271 - Siamak Tafavogh, Daniel R. Catchpoole, Paul J. Kennedy:
Cellular quantitative analysis of neuroblastoma tumor and splitting overlapping cells. 272 - Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhiming Ma, Shuhua Xu:
A New Method for Modeling Coalescent Processes with Recombination. 273 - Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Metodi V. Metodiev, Berthold Lausen:
A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. 274 - Jiyuan An, John Lai, Atul Sajjanhar, Melanie L. Lehman, Colleen C. Nelson:
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. 275 - Michael J. Kane, Natalie Price, Matthew Scotch, Peter Rabinowitz:
Comparison of ARIMA and Random Forest time series models for prediction of avian influenza H5N1 outbreaks. 276 - Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke, Stephan Waack:
CRF-based models of protein surfaces improve protein-protein interaction site predictions. 277 - Jeffrey R. Long, Vanessa Pittet, Brett Trost, Qingxiang Yan, David Vickers, Monique Haakensen, Anthony J. Kusalik:
Equivalent input produces different output in the UniFrac significance test. 278 - Dominik Schweiger, Zlatko Trajanoski, Stephan Pabinger:
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. 279 - Huihuang Yan, Jared Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Li, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher:
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. 280 - Kristoffer Sahlin, Francesco Vezzi, Björn Nystedt, Joakim Lundeberg, Lars Arvestad:
BESST - Efficient scaffolding of large fragmented assemblies. 281 - Arun Sharma, Deepak Singla, Mamoon Rashid, Gajendra Pal Singh Raghava:
Designing of peptides with desired half-life in intestine-like environment. 282 - Bart K. M. Jacobs, Els Goetghebeur, Lieven Clement:
Impact of variance components on reliability of absolute quantification using digital PCR. 283 - Scott M. Yourstone, Derek S. Lundberg, Jeffery L. Dangl, Corbin D. Jones:
MT-Toolbox: improved amplicon sequencing using molecule tags. 284 - Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. 285 - Rey-Long Liu, Chia Chun Shih:
Identification of highly related references about gene-disease association. 286 - Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz Montes, Rebekah H. Gensure, Fuyong Xing, Hua Zhong, Lauri A. Goodell, Manish Parashar, David J. Foran, Lin Yang:
Content-based histopathology image retrieval using CometCloud. 287 - David C. Whitley, Valeria Runfola, Peter Cary, Liliya Nazlamova, Matt Guille, Garry Scarlett:
APTE: identification of indirect read-out A-DNA promoter elements in genomes. 288 - Junbai Wang:
Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence. 289 - Susan M. Grimes, Hanlee P. Ji:
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing. 290 - Hongjian Li, Kwong-Sak Leung, Man Hon Wong, Pedro J. Ballester:
Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study. 291 - Benjamin Lutz, Claude Sinner, Stefan Bozic, Ivan Kondov, Alexander Schug:
Native structure-based modeling and simulation of biomolecular systems per mouse click. 292 - Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel, Christophe Klopp:
jvenn: an interactive Venn diagram viewer. 293 - Patrick Kück, Sandra A. Meid, Christian Groß, Johann-Wolfgang Wägele, Bernhard Misof:
AliGROOVE - visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support. 294 - Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka Varga, Vera Ölvedy, William E. Smiddy, Robert Tchitnga, Anikó Somogyi, Delia Cabrera DeBuc:
Fractal-based analysis of optical coherence tomography data to quantify retinal tissue damage. 295 - Chia-Jung Chang, Pei-Lung Chen, Wei-Shiung Yang, Kun-Mao Chao:
A fault-tolerant method for HLA typing with PacBio data. 296 - Dong-Jun Yu, Jun Hu, Hui Yan, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen:
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble. 297 - Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo, Quan Zou:
nDNA-prot: identification of DNA-binding proteins based on unbalanced classification. 298 - Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh, Ken Chen:
Towards accurate characterization of clonal heterogeneity based on structural variation. 299 - Tuan Hue Thi, Li Wang, Ning Ye, Jian Zhang, Sebastian Maurer-Stroh, Li Cheng:
Recognizing flu-like symptoms from videos. 300 - Adriano N. Raposo, Abel João Padrão Gomes:
Efficient deformation algorithm for plasmid DNA simulations. 301 - Lucian Ilie, Bahlul Haider, Michael Molnar, Roberto Solis-Oba:
SAGE: String-overlap Assembly of GEnomes. 302 - Prashant Shingate, Malini Manoharan, Anshul Sukhwal, Ramanathan Sowdhamini:
ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. 303 - Kai Sun, Joana P. Gonçalves, Chris Larminie, Natasa Przulj:
Predicting disease associations via biological network analysis. 304 - Fergal J. Duffy, Marc Devocelle, David R. Croucher, Denis C. Shields:
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. 305 - Andreas Dander, Matthias Baldauf, Michael Sperk, Stephan Pabinger, Benjamin Hiltpolt, Zlatko Trajanoski:
Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages. 306 - Jungkap Park, Kazuhiro Saitou:
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures. 307 - Simon Kebede Merid, Daria Goranskaya, Andrey Alexeyenko:
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. 308 - Elisa Cilia, Stefano Teso, Sergio Ammendola, Tom Lenaerts, Andrea Passerini:
Predicting virus mutations through statistical relational learning. 309 - Hongyuan Wang, Fuyong Xing, Hai Su, Arnold J. Stromberg, Lin Yang:
Novel image markers for non-small cell lung cancer classification and survival prediction. 310 - Aimin Li, Junying Zhang, Zhongyin Zhou:
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. 311 - Maitreyee Bose, Chong Wu, James S. Pankow, Ellen W. Demerath, Jan Bressler, Myriam Fornage, Megan L. Grove, Thomas H. Mosley Jr., Chindo Hicks, Kari E. North, Wen Kao, Yu Zhang, Eric Boerwinkle, Weihua Guan:
Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk In Communities (ARIC) Study. 312 - Feng Cui, Linlin Chen, Peter R. LoVerso, Victor B. Zhurkin:
Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy. 313 - Murat Dundar, Ferit Akova, Halid Ziya Yerebakan, Bartek Rajwa:
A Non-parametric Bayesian Model for Joint Cell Clustering and Cluster Matching: Identification of Anomalous Sample Phenotypes with Random Effects. 314 - Li Jiang, Stefan M. Edwards, Bo Thomsen, Christopher T. Workman, Bernt Guldbrandtsen, Peter Sørensen:
A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records. 315 - John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai:
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. 316 - Yu-Ting Huang, Jiue-in Yang, Marek Chrobak, James Borneman:
PRISE2: Software for designing sequence-selective PCR primers and probes. 317 - Abiel Roche-Lima, Michael Domaratzki, Brian Fristensky:
Metabolic Network Prediction Through Pairwise Rational Kernels. 318 - Brian G. Pierce, Thom Vreven, Zhiping Weng:
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. 319 - Tane Kim, Weilong Hao:
DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. 320 - Junpeng Bao, Ruiyu Yuan, Zhe Bao:
An improved alignment-free model for dna sequence similarity metric. 321 - Basel Abu-Jamous, Rui Fa, David Roberts, Asoke K. Nandi:
Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis. 322 - Quanhu Sheng, Yu Shyr, Xi Chen:
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. 323 - William R. Pitt, Rinaldo W. Montalvão, Tom L. Blundell:
Polyphony: superposition independent methods for ensemble-based drug discovery. 324 - Junzhong Ji, Lang Jiao, Cuicui Yang, Jia Wei Lv, Aidong Zhang:
MAE-FMD: Multi-agent evolutionary method for functional module detection in protein-protein interaction networks. 325 - Bharat Panwar, Gajendra P. S. Raghava:
Prediction of uridine modifications in tRNA sequences. 326 - Viktorian Miok, Saskia M. Wilting, Mark A. van de Wiel, Annelieke Jaspers, Paula I. van Noort, Ruud H. Brakenhoff, Peter J. F. Snijders, Renske D. M. Steenbergen, Wessel N. van Wieringen:
tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities. 327 - Eric Wait, Mark R. Winter, Christopher Björnsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple, Andrew R. Cohen:
Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences. 328 - Gabriel Renaud, Matthew C. LaFave, Jin Liang, Tyra G. Wolfsberg, Shawn M. Burgess:
trieFinder: an efficient program for annotating digital gene expression (DGE) tags. 329 - Anna C. T. Abelin, Georgi K. Marinov, Brian A. Williams, Kenneth McCue, Barbara J. Wold:
A ratiometric-based measure of gene co-expression. 331 - Yan Guo, Shilin Zhao, Brian D. Lehmann, Quanhu Sheng, Timothy M. Shaver, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr:
Detection of internal exon deletion with exon Del. 332 - Mohammad Ali Moni, Pietro Liò:
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. 333 - Shawn M. Waldon, Peter M. Thompson, Patrick J. Hahn, Russell M. Taylor II:
SketchBio: a scientist's 3D interface for molecular modeling and animation. 334 - Le Ou-Yang, Dao-Qing Dai, Xiaoli Li, Min Wu, Xiao-Fei Zhang, Peng Yang:
Detecting temporal protein complexes from dynamic protein-protein interaction networks. 335 - Zhi-Ping Liu, Hulin Wu, Jian Zhu, Hongyu Miao:
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. 336 - Devon Patrick Ryan, Dan Ehninger:
Bison: bisulfite alignment on nodes of a cluster. 337 - Fabian Sievers, Graham M. Hughes, Desmond G. Higgins:
Systematic exploration of guide-tree topology effects for small protein alignments. 338 - Hsiao Ping Lee, Tzu-Fang Sheu:
An algorithm of discovering signatures from DNA databases on a computer cluster. 339 - Liqi Li, Sanjiu Yu, Weidong Xiao, Yongsheng Li, Lan Huang, Xiaoqi Zheng, Shiwen Zhou, Hua Yang:
Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM. 340 - Cuong Cao Dang, Le Sy Vinh, Olivier Gascuel, Bart Hazes, Si Quang Le:
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets. 341 - Syed Abbas, Tjeerd Dijkstra, Tom Heskes:
A comparative study of cell classifiers for image-based high-throughput screening. 342 - Mutharasu Gnanavel, Prachi Mehrotra, Ramaswamy Rakshambikai, Juliette Martin, Narayanaswamy Srinivasan, Ramachandra M. Bhaskara:
CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins. 343 - Christopher K. Hobbs, Michelle Leung, Herbert H. Tsang, H. Ebhardt:
CIG-P: Circular Interaction Graph for Proteomics. 344 - Ivan Kolesár, Július Parulek, Ivan Viola, Stefan Bruckner, Anne-Kristin Stavrum, Helwig Hauser:
Interactively Illustrating Polymerization using Three-level Model Fusion. 345 - Serena G. Liao, Yan Lin, Dongwan D. Kang, Divay Chandra, Jessica Bon, Naftali Kaminski, Frank C. Sciurba, George C. Tseng:
Missing value imputation in high-dimensional phenomic data: imputable or not, and how? 346 - Alexandre Kuhn:
Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14: 89. 347 - Joshua P. Katz, James M. Pipas:
SummonChimera infers integrated viral genomes with nucleotide precision from NGS data. 348 - Garrett Saunders, John R. Stevens, S. Isom:
A shortcut for multiple testing on the directed acyclic graph of gene ontology. 349 - Daniel I. Speiser, M. Sabrina Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley:
Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. 350 - Shicai Wang, Ioannis Pandis, David Johnson, Ibrahim Emam, Florian Guitton, Axel Oehmichen, Yike Guo:
Optimising parallel R correlation matrix calculations on gene expression data using MapReduce. 351 - Wencke Walter, Bernd Striberny, Emmanuel Gaquerel, Ian T. Baldwin, Sang-Gyu Kim, Ines Heiland:
Improving the accuracy of expression data analysis in time course experiments using resampling. 352 - Elisabetta Fersini, Enza Messina, Francesco Archetti:
A p-Median approach for predicting drug response in tumour cells. 353 - Fei Hu, Yu Lin, Jijun Tang:
MLGO: phylogeny reconstruction and ancestral inference from gene-order data. 354 - Edward W. J. Curry:
A framework for generalized subspace pattern mining in high-dimensional datasets. 355 - Thorfinn Korneliussen, Anders Albrechtsen, Rasmus Nielsen:
ANGSD: Analysis of Next Generation Sequencing Data. 356 - Jamison M. McCorrison, Pratap Venepally, Indresh Singh, Derrick E. Fouts, Roger S. Lasken, Barbara A. Methé:
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. 357 - Maysson Al-Haj Ibrahim, Sabah Jassim, Michael Anthony Cawthorne, Kenneth Langlands:
A MATLAB tool for pathway enrichment using a topology-based pathway regulation score. 358 - Zhiyi Li, Xiaowei Wu, Bin He, Liqing Zhang:
Vindel: a simple pipeline for checking indel redundancy. 359 - Nils Fredriksson, Malte Hermansson, Britt-Marie Wilén:
Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics. 360 - Nils Fredriksson, Malte Hermansson, Britt-Marie Wilén:
Tools for T-RFLP data analysis using Excel. 361 - Prabina Kumar Meher, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao, Sant Wahi:
A statistical approach for 5′ splice site prediction using short sequence motifs and without encoding sequence data. 362 - Irene Righetto, Adelaide Milani, Giovanni Cattoli, Francesco Filippini:
Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features. 363 - Ruolin Liu, Ann E. Loraine, Julie A. Dickerson:
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. 364 - Chien-Chi Lo, Patrick S. G. Chain:
Rapid evaluation and quality control of next generation sequencing data with FaQCs. 366 - Tom Heskes, Rob Eisinga, Rainer Breitling:
A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments. 367 - Andrew L. Beam, Alison A. Motsinger-Reif, Jon Doyle:
Bayesian neural networks for detecting epistasis in genetic association studies. 368 - Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. 369 - Andreas Warnecke, Tatyana Sandalova, Adnane Achour, Robert A. Harris:
PyTMs: a useful PyMOL plugin for modeling common post-translational modifications. 370 - Tina Gunderson, Yen-Yi Ho:
An efficient algorithm to explore liquid association on a genome-wide scale. 371 - Michael E. Jones, George C. Mayne, Tingting Wang, David I. Watson, Damian J. Hussey:
A fixed-point algorithm for estimating amplification efficiency from a polymerase chain reaction dilution series. 372 - Zubair Afzal, Ewoud Pons, Ning Kang, Miriam C. J. M. Sturkenboom, Martijn J. Schuemie, Jan A. Kors:
ContextD: an algorithm to identify contextual properties of medical terms in a Dutch clinical corpus. 373 - Raphael B. M. Aggio, Arno Mayor, Sophie Reade, Chris Probert, Katya Ruggiero:
Identifying and quantifying metabolites by scoring peaks of GC-MS data. 374 - Rocío Rodríguez-López, Armando Reyes-Palomares, Francisca Sánchez-Jiménez, Miguel Angel Medina:
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. 375 - Ken Aoshima, Kentaro Takahashi, Masayuki Ikawa, Takayuki Kimura, Mitsuru Fukuda, Satoshi Tanaka, Howell E. Parry, Yuichiro Fujita, Akiyasu C. Yoshizawa, Shin-ichi Utsunomiya, Shigeki Kajihara, Koichi Tanaka, Yoshiya Oda:
A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry. 376 - Arthur Gilly, Mathilde Etcheverry, Mohammed-Amin Madoui, Julie Guy, Leandro Quadrana, Adriana Alberti, Antoine Martin, Tony Heitkam, Stefan Engelen, Karine Labadie, Jeremie Le Pen, Patrick Wincker, Vincent Colot, Jean-Marc Aury:
TE-Tracker: systematic identification of transposition events through whole-genome resequencing. 377 - Yuh-Jyh Hu, Shun-Chien Lin, Yu-Lung Lin, Kuan-Hui Lin, Shun-Ning You:
A meta-learning approach for B-cell conformational epitope prediction. 378 - Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka:
Anatomy of enzyme channels. 379 - Audrey M. Michel, Dmitry E. Andreev, Pavel V. Baranov:
Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning. 380 - Chin Lung Lu, Kun-Tze Chen, Shih-Yuan Huang, Hsien-Tai Chiu:
CAR: contig assembly of prokaryotic draft genomes using rearrangements. 381 - Sajung Yun, Sijung Yun:
Masking as an effective quality control method for next-generation sequencing data analysis. 382 - Andrew Schoenrock, Bahram Samanfar, Sylvain Pitre, Mohsen Hooshyar, Ke Jin, Charles A. Phillips, Hui Wang, Sadhna Phanse, Katayoun Omidi, Yuan Gui, Md Alamgir, Alex Wong, Fredrik Barrenäs, Mohan Babu, Mikael Benson, Michael A. Langston, James R. Green, Frank K. H. A. Dehne, Ashkan Golshani:
Efficient prediction of human protein-protein interactions at a global scale. 383 - Daniel Langenkämper, Alexander Goesmann, Tim W. Nattkemper:
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization. 384 - Caroline Truntzer, Elise Mostacci, Aline Jeannin, Jean-Michel Petit, Patrick Ducoroy, Hervé Cardot:
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data. 385 - Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper:
Finding gene regulatory network candidates using the gene expression knowledge base. 386 - Enzo Acerbi, Teresa Zelante, Vipin Narang, Fabio Stella:
Gene network inference using continuous time Bayesian networks: a comparative study and application to Th17 cell differentiation. 387 - Carl Barton, Alice Héliou, Laurent Mouchard, Solon P. Pissis:
Linear-time computation of minimal absent words using suffix array. 388 - John P. Archer, Gareth Whiteley, Nicholas R. Casewell, Robert A. Harrison, Simon C. Wagstaff:
VTBuilder: a tool for the assembly of multi isoform transcriptomes. 389 - Lingjian Yang, Chrysanthi Ainali, Sophia Tsoka, Lazaros G. Papageorgiou:
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework. 390 - Raphaël Champeimont, Alessandra Carbone:
SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis. 391 - Antonio Di Narzo, Haoxiang Cheng, Jianwei Lu, Ke Hao:
Meta-eQTL: a tool set for flexible eQTL meta-analysis. 392 - Xuewu Liu, Yuxiao Huang, Jiao Liang, Shuai Zhang, Yinghui Li, Jun Wang, Yan Shen, Zhikai Xu, Ya Zhao:
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites. 393 - Quentin Grimonprez, Alain Celisse, Samuel Blanck, Meyling Cheok, Martin Figeac, Guillemette Marot:
MPAgenomics: an R package for multi-patient analysis of genomic markers. 394 - Zeeshan Gillani, Muhammad Akash, Md. Matiur Rahaman, Ming Chen:
CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks. 395 - Martin A. Fitzpatrick, Catherine M. McGrath, Stephen P. Young:
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. 396 - Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko:
Comparative evaluation of gene set analysis approaches for RNA-Seq data. 397 - Isaak Y. Tecle, Jeremy D. Edwards, Naama Menda, Chiedozie Egesi, Ismail Y. Rabbi, Peter Kulakow, Robert Kawuki, Jean-Luc Jannink, Lukas A. Mueller:
solGS: a web-based tool for genomic selection. 398 - Lars Skjærven, Xin-Qiu Yao, Guido Scarabelli, Barry J. Grant:
Integrating protein structural dynamics and evolutionary analysis with Bio3D. 399 - Young Hwan Chang, Joe W. Gray, Claire J. Tomlin:
Exact reconstruction of gene regulatory networks using compressive sensing. 400 - Jason M. Knight, Ivan Ivanov, Edward R. Dougherty:
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. 401 - Joseph P. Salisbury, Qian Liu, Jeffrey N. Agar:
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure. 403 - Joao A. Ascensao, Mary E. Dolan, David P. Hill, Judith A. Blake:
Methodology for the inference of gene function from phenotype data. 405 - Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa:
CLAST: CUDA implemented large-scale alignment search tool. 406 - Lars Gerdes, Ulrich Busch, Sven Pecoraro:
A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions. 407 - Leif Väremo, Francesco Gatto, Jens Nielsen:
Kiwi: a tool for integration and visualization of network topology and gene-set analysis. 408 - Tommy Öman, May-Britt Tessem, Tone F. Bathen, Helena Bertilsson, Anders Angelsen, Mattias Hedenström, Trygve Andreassen:
Identification of metabolites from 2D 1H-13C HSQC NMR using peak correlation plots. 413 - Jose A. Gomez, Kai Höffner, Paul I. Barton:
DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis. 409 - Yao Lian, Meng Ge, Xian-Ming Pan:
EPMLR: Sequence-based linear B-cell epitope prediction method using multiple linear regression. 414 - Megumi Nakao, Shintaro Takemoto, Tadao Sugiura, Kazuaki Sawada, Ryosuke Kawakami, Tomomi Nemoto, Tetsuya Matsuda:
Interactive visual exploration of overlapping similar structures for three-dimensional microscope images. 415 - Soshichiro Nagano, Ting-Yu Lin, Jyotheeswara Edula, Jonathan Heddle:
Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. 416 - Frauke Kracke, Jens O. Krömer:
Identifying target processes for microbial electrosynthesis by elementary mode analysis. 6590 - Anagha Joshi:
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. 6591 - Alexandre Angers-Loustau, Mauro Petrillo, Laura Bonfini, Francesco Gatto, Sabrina Rosa, Alexandre Patak, Joachim Kreysa:
JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies. 6592 - Kai Wang, Chun Liang, Jinding Liu, Huamei Xiao, Shuiqing Huang, Jianhua Xu, Fei Li:
Prediction of piRNAs using transposon interaction and a support vector machine. 6593 - Alberto Noronha, Paulo Vilaça, Miguel Rocha:
An integrated network visualization framework towards metabolic engineering applications. 6594 - Jun Meng, Dong Liu, Chao Sun, Yushi Luan:
Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine. 6595 - Truyen Tran, Wei Luo, Dinh Q. Phung, Sunil Gupta, Santu Rana, Richard Kennedy, Ann Larkins, Svetha Venkatesh:
A framework for feature extraction from hospital medical data with applications in risk prediction. 6596 - Sandhya P. Tiwari, Edvin Fuglebakk, Siv Midtun Hollup, Lars Skjærven, Tristan Cragnolini, Svenn Helge Grindhaug, Kidane M. Tekle, Nathalie Reuter:
WEBnm@ v2.0: Web server and services for comparing protein flexibility. 6597 - Joe Chalfoun, Michael Majurski, Alden Dima, Christina H. Stuelten, Adele P. Peskin, Mary Brady:
FogBank: a single cell segmentation across multiple cell lines and image modalities. 6598 - Broto Chakrabarty, Nita Parekh:
Identifying tandem Ankyrin repeats in protein structures. 6599 - Erik K. Malm, Vaibhav Srivastava, Gustav Sundqvist, Vincent Bulone:
APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools. 6600 - Preston V. Lee, Valentin Dinu:
BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions. 6601 - Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, Sebastian Will:
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. 6602 - Minta Thomas, Kris De Brabanter, Johan A. K. Suykens, Bart De Moor:
Predicting breast cancer using an expression values weighted clinical classifier. 6603
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