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ORCIDBMC Bioinformatics, Volume 14
Volume 14, 2013
- Kevin L. Neff, David P. Argue, Alvin C. Ma, Han B. Lee
, Karl J. Clark, Stephen C. Ekker:
Mojo hand, a TALEN design tool for genome editing applications. 1 - Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou:
BioCause: Annotating and analysing causality in the biomedical domain. 2 - Gabriel Cardona, Arnau Mir, Francesc Rosselló Llompart, Lucia Rotger, David Sanchez:
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf. 3 - Jacques Oberto:
SyntTax: a web server linking synteny to prokaryotic taxonomy. 4 - Lin Song, Peter Langfelder, Steve Horvath:
Random generalized linear model: a highly accurate and interpretable ensemble predictor. 5 - Shuang Wu, Hulin Wu:
More powerful significant testing for time course gene expression data using functional principal component analysis approaches. 6 - Sonja Hänzelmann, Robert Castelo, Justin Guinney:
GSVA: gene set variation analysis for microarray and RNA-Seq data. 7 - Christopher D. Tomlinson, Geraint Barton, Mark Woodbridge, Sarah A. Butcher:
XperimentR: painless annotation of a biological experiment for the laboratory scientist. 8 - Kjetil Klepper, Finn Drabløs:
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. 9 - Raphael Cohen, Michael Elhadad, Noemie Elhadad:
Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies. 10 - Jianjun Zhou, David S. Wishart:
An improved method to detect correct protein folds using partial clustering. 11 - Domonkos Tikk, Illés Solt, Philippe Thomas, Ulf Leser:
A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. 12 - Andrew E. Bruno, Jeffrey C. Miecznikowski, Maochun Qin, Jianmin Wang, Song Liu:
FUSIM: a software tool for simulating fusion transcripts. 13 - Raheel Nawaz, Paul Thompson, Sophia Ananiadou:
Negated bio-events: analysis and identification. 14 - Karan Uppal, Quinlyn A. Soltow, Frederick H. Strobel, W. Stephen Pittard, Kim M. Gernert, Tianwei Yu, Dean P. Jones:
xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data. 15 - Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L. Narro, William H. Piel, Sheldon J. McKay, Sonya J. Lowry, Chris Freeland, Robert K. Peet, Brian J. Enquist:
The taxonomic name resolution service: an online tool for automated standardization of plant names. 16 - Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez:
CySBGN: A Cytoscape plug-in to integrate SBGN maps. 17 - Phillip Seitzer, Tu Anh Huynh, Marc T. Facciotti:
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. 18 - Yuelin Zhu, Robert M. Stephens, Paul S. Meltzer, Sean R. Davis:
SRAdb: query and use public next-generation sequencing data from within R. 19 - Yasin Bakis, Hasan H. Otu, Nivart Taçi, Cem Meydan, Nee Bilgin, Sirri Yüzbaiolu, Osman Ugur Sezerman:
Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. 20 - Jerzy Stanislawski, Malgorzata Kotulska, Olgierd Unold:
Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides. 21 - Robert Aboukhalil, Bernard Fendler, Gurinder S. Atwal:
Kerfuffle: a web tool for multi-species gene colocalization analysis. 22 - Andrew Gallant, Mark D. M. Leiserson, Maxim Kachalov, Lenore J. Cowen, Benjamin J. Hescott:
Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data. 23 - Shintaro Minami, Kengo Sawada, George Chikenji:
MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments. 24 - Zheming Jin, Jason D. Bakos:
Extending the BEAGLE library to a multi-FPGA platform. 25 - Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira, Daron M. Standley:
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. 26 - Shirley Hui, Xiang Xing, Gary D. Bader:
Predicting PDZ domain mediated protein interactions from structure. 27 - R. Mitchell Parry, May D. Wang:
A fast least-squares algorithm for population inference. 28 - Sepideh Babaei, Marc Hulsman, Marcel J. T. Reinders, Jeroen de Ridder:
Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion. 29 - Wenlin Li, Qian Cong, Lisa N. Kinch, Nick V. Grishin:
Seq2Ref: a web server to facilitate functional interpretation. 30 - Ellis Patrick, Michael J. Buckley, Yee Hwa Yang:
Estimation of data-specific constitutive exons with RNA-Seq data. 31 - Cameron Cotten, Jennifer L. Reed:
Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. 32 - Xi Yang, Di Liu, Fei Liu, Jun Wu, Jing Zou, Xue Xiao, Fangqing Zhao, Baoli Zhu:
HTQC: a fast quality control toolkit for Illumina sequencing data. 33 - Takeshi Hayashi, Hiroyoshi Iwata:
A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits. 34 - Heng-Yi Wu, Shreyas D. Karnik, Abhinita Subhadarshini, Zhiping Wang, Santosh Philips, Xu Han, Chienwei Chiang, Lei Liu, Malaz Boustani, Luis M. Rocha, Sara K. Quinney, David A. Flockhart, Lang Li:
An integrated pharmacokinetics ontology and corpus for text mining. 35 - Arkadiusz Gladki, Szymon Kaczanowski, Pawel Szczesny, Piotr Zielenkiewicz:
The evolutionary rate of antibacterial drug targets. 36 - Oliver Tills, Tabitha Bitterli, Phil F. Culverhouse, John I. Spicer, Simon Rundle:
A novel application of motion analysis for detecting stress responses in embryos at different stages of development. 37 - Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen:
FANTOM: Functional and taxonomic analysis of metagenomes. 38 - Xuejun Liu, Zhenzhu Gao, Li Zhang, Magnus Rattray:
puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis. 39 - Brendan O'Fallon:
ACG: rapid inference of population history from recombining nucleotide sequences. 40 - Yun-feng Qi, Yanxin Huang, Hong-yan Wang, Yu Zhang, Yongli Bao, Lu-guo Sun, Yin Wu, Chun-lei Yu, Zhen-bo Song, Li-hua Zheng, Ying Sun, Guan-nan Wang, Yu-xin Li:
Elucidating the crosstalk mechanism between IFN-gamma and IL-6 via mathematical modelling. 41 - Marie Verbanck, Sébastien Lê, Jérôme Pagès:
A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data. 42 - Xiaoyu Wang, Jin Yao, Yijun Sun, Volker Mai:
M-pick, a Modularity-based Method for OTU Picking of 16S rRNA Sequences. 43 - Bharat Panwar, Sudheer Gupta, Gajendra P. S. Raghava:
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information. 44 - Anthony G. Doran, Christopher J. Creevey:
Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. 45 - Alain Guénoche:
Multiple consensus trees: a method to separate divergent genes. 46 - Antonio Mora, Katerina Michalickova, Ian M. Donaldson:
A survey of protein interaction data and multigenic inherited disorders. 47 - Arpah Abu, Lee Hong Lim, Amandeep S. Sidhu, Sarinder Kaur Dhillon:
Semantic representation of monogenean haptoral Bar image annotation. 48 - Brian L. LaMarche, Kevin L. Crowell, Navdeep Jaitly, Vladislav A. Petyuk, Anuj R. Shah, Ashoka D. Polpitiya, John D. Sandoval, Gary R. Kiebel, Matthew E. Monroe, Stephen J. Callister, Thomas O. Metz, Gordon A. Anderson, Richard D. Smith:
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. 49 - Edwin J. C. G. van den Oord, József Bukszár, Gábor Rudolf, Srilaxmi Nerella, Joseph L. McClay, Lin Y. Xie, Karolina A. Åberg:
Estimation of CpG coverage in whole methylome next-generation sequencing studies. 50 - Carlo A. Trugenberger, Christoph Wälti, David Peregrim, Mark E. Sharp, Svetlana Bureeva:
Discovery of novel biomarkers and phenotypes by semantic technologies. 51 - Patricio Oyarzún, Jonathan J. Ellis, Mikael Bodén, Bostjan Kobe:
PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. 52 - Tobias Wittkop, Emily TerAvest, Uday S. Evani, K. Mathew Fleisch, Ari E. Berman, Corey Powell, Nigam H. Shah, Sean D. Mooney:
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. 53 - David Campos, Sérgio Matos, José Luís Oliveira:
Gimli: open source and high-performance biomedical name recognition. 54 - Salma Jamal, Vinita Periwal, Vinod Scaria:
Predictive modeling of anti-malarial molecules inhibiting apicoplast formation. 55 - Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach, Knut Reinert:
Optimal precursor ion selection for LC-MALDI MS/MS. 56 - Jongkeun Lee, Unjoo Lee, Baeksop Kim, Jeehee Yoon:
A computational method for detecting copy number variations using scale-space filtering. 57 - Jinseog Kim, Insuk Sohn, Dae-Soon Son, Dong Hwan Kim, TaeJin Ahn, Sin-Ho Jung:
Prediction of a time-to-event trait using genome wide SNP data. 58 - Ilana Lichtenstein, Michael A. Charleston, Tibério S. Caetano, Jennifer R. Gamble, Mathew A. Vadas:
Active Subnetwork Recovery with a Mechanism-Dependent Scoring Function; with application to Angiogenesis and Organogenesis studies. 59 - Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk, Markus Göker:
Genome sequence-based species delimitation with confidence intervals and improved distance functions. 60 - Mohsen Hajiloo, Yadav Sapkota, John R. Mackey, Paula Robson, Russell Greiner, Sambasivarao Damaraju:
ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction. 61 - Michal Jamróz, Andrzej Kolinski:
ClusCo: clustering and comparison of protein models. 62 - J. Eduardo Fajardo, András Fiser:
Protein structure based prediction of catalytic residues. 63 - Rok Blagus, Lara Lusa:
Improved shrunken centroid classifiers for high-dimensional class-imbalanced data. 64 - Bernard J. Pope, Tu Nguyen-Dumont, Fabrice Odefrey, Russell Bell, Sean V. Tavtigian, David E. Goldgar, Andrew Lonie, Melissa C. Southey, Daniel J. Park:
FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets. 65 - Andrés Varón, Ward C. Wheeler:
Local search for the generalized tree alignment. 66 - Yupeng Chen, Bertil Schmidt, Douglas L. Maskell:
A hybrid short read mapping accelerator. 67 - Jorge Alberto Jaramillo-Garzón, Joan-Josep Gallardo-Chacón, César Germán Castellanos-Domínguez, Alexandre Perera-Lluna:
Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins. 68 - Lucian Ilie, Hamid Mohamadi, Geoffrey Brian Golding, William F. Smyth:
BOND: Basic OligoNucleotide Design. 69 - Erik Kristiansson, Tobias Österlund, Lina Gunnarsson, Gabriella Arne, D. G. Joakim Larsson, Olle Nerman:
A novel method for cross-species gene expression analysis. 70 - Laura Plaza, Jorge Carrillo de Albornoz:
Evaluating the use of different positional strategies for sentence selection in biomedical literature summarization. 71 - Yunfei Li, Debjit Ray, Ping Ye:
Identification of germ cell-specific genes in mammalian meiotic prophase. 72 - Dariusz Mrozek, Bozena Malysiak-Mrozek, Artur Siaznik:
search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information. 73 - Wenan Chen, Guimin Gao, Srilaxmi Nerella, Christina M. Hultman, Patrik K. E. Magnusson, Patrick F. Sullivan, Karolina A. Åberg, Edwin J. C. G. van den Oord:
MethylPCA: a toolkit to control for confounders in methylome-wide association studies. 74 - Andreas Heider, Rüdiger Alt:
virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. 75 - Jerry Guintivano, Michal Arad, Kellie L. K. Tamashiro, Todd D. Gould, Zachary A. Kaminsky:
BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data. 76 - Björn Hammesfahr, Florian Odronitz, Stefanie Mühlhausen, Stephan Waack, Martin Kollmar:
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures. 77 - John C. Earls, James A. Eddy, Cory C. Funk, Youn-Hee Ko, Andrew T. Magis, Nathan D. Price:
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. 78 - Xiao Wu, Kathryn Berkow, Daniel N. Frank, Ellen Li, Ajay S. Gulati, Wei Zhu:
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. 79 - Zihua Yang, Zhengrong Yang:
Prediction of heterogeneous differential genes by detecting outliers to a Gaussian tight cluster. 81 - Sébastien Giguère, Mario Marchand, François Laviolette, Alexandre Drouin, Jacques Corbeil:
Learning a peptide-protein binding affinity predictor with kernel ridge regression. 82 - Adam Gudys, Michal Wojciech Szczesniak, Marek Sikora, Izabela Makalowska:
HuntMi: an efficient and taxon-specific approach in pre-miRNA identification. 83 - David Mosén-Ansorena, Ana María Aransay:
Bivariate segmentation of SNP-array data for allele-specific copy number analysis in tumour samples. 84 - Guy Baele, Philippe Lemey, Stijn Vansteelandt:
Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. 85 - Hanwen Huang, Zhongxue Chen, Xudong Huang:
Age-adjusted nonparametric detection of differential DNA methylation with case-control designs. 86 - Zhenyu Yang, Zuojing Li, David R. Bickel:
Empirical Bayes estimation of posterior probabilities of enrichment: A comparative study of five estimators of the local false discovery rate. 87 - Jesse Eickholt, Jianlin Cheng:
DNdisorder: predicting protein disorder using boosting and deep networks. 88 - Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel M. L. Chow, Zhandong Liu:
Digital sorting of complex tissues for cell type-specific gene expression profiles. 89 - Chuanxin Zou, Jiayu Gong, Honglin Li:
An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis. 90 - Charlotte Soneson, Mauro Delorenzi:
A comparison of methods for differential expression analysis of RNA-seq data. 91 - Thuc Duy Le, Lin Liu, Bing Liu, Anna Tsykin, Gregory J. Goodall, Kenji Satou, Jiuyong Li:
Inferring microRNA and transcription factor regulatory networks in heterogeneous data. 92 - Jinzhu Yang, Paloma T. Gonzalez-Bellido, Hanchuan Peng:
A distance-field based automatic neuron tracing method. 93 - Phillip D. Yates, Nitai D. Mukhopadhyay:
An inferential framework for biological network hypothesis tests. 94 - Jinkui Cheng, Xu Zeng, Guomin Ren, Zhihua Liu:
CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes. 95 - Satish Mahadevan Srinivasan, Suleyman Vural, Brian R. King, Chittibabu Guda:
Mining for class-specific motifs in protein sequence classification. 96 - Takanori Ueda, Daisuke Tominaga, Noriko Araki, Tomohiro Yoshikawa:
Estimate hidden dynamic profiles of siRNA effect on apoptosis. 97 - Anna Katharina Dehof, Simon Loew, Hans-Peter Lenhof, Andreas Hildebrandt:
NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. 98 - Cecile Bazot, Nicolas Dobigeon, Jean-Yves Tourneret, Aimee K. Zaas, Geoffrey S. Ginsburg, Alfred O. Hero III:
Unsupervised Bayesian linear unmixing of gene expression microarrays. 99 - Hsiu-Ling Chou, Chung-Tay Yao, Sui-Lun Su, Chia-Yi Lee, Kuang-Yu Hu, Harn-Jing Terng, Yun-Wen Shih, Yu-Tien Chang, Yu-Fen Lu, Chi-Wen Chang, Mark L. Wahlqvist, Thomas Wetter, Chi-Ming Chu:
Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees. 100 - Michal Marczyk, Roman Jaksik, Andrzej Polanski, Joanna Polanska:
Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition. 101 - Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti, Roberto Marangoni:
Mobilomics in Saccharomyces cerevisiae strains. 102 - Paula de Matos, Jennifer A. Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck:
The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics. 103 - Anne-Lise Veuthey, Alan J. Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios:
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. 104 - Abhijit Karnik, Rucha Karnik, Christopher Grefen:
SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites. 105 - Rok Blagus, Lara Lusa:
SMOTE for high-dimensional class-imbalanced data. 106 - Jim Jing-Yan Wang, Xiaolei Wang, Xin Gao:
Non-negative matrix factorization by maximizing correntropy for cancer clustering. 107 - Chih Lee, Chun-Hsi Huang:
LASAGNA: A novel algorithm for transcription factor binding site alignment. 108 - Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière:
TPMS: a set of utilities for querying collections of gene trees. 109 - Lisa M. Chung, John P. Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R. Montgomery, Hongyu Zhao:
Differential expression analysis for paired RNA-seq data. 110 - Emma M. Rath, Dominique Tessier, Alexander A. Campbell, Hong Ching Lee, Tim Werner, Noeris K. Salam, Lawrence K. Lee, W. Bret Church:
A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions. 111 - Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi, Peter D. Karp:
A systematic comparison of the MetaCyc and KEGG pathway databases. 112 - Francisco M. Ortuño Guzman, Ignacio Rojas, Miguel A. Andrade-Navarro, Jean-Fred Fontaine:
Using cited references to improve the retrieval of related biomedical documents. 113 - Steven Eker, Markus Krummenacker, Alexander Glennon Shearer, Ashish Tiwari, Ingrid M. Keseler, Carolyn L. Talcott, Peter D. Karp:
Computing minimal nutrient sets from metabolic networks via linear constraint solving. 114 - Katja Schulze, Ulrich M. Tillich, Thomas Dandekar, Marcus Frohme:
PlanktoVision - an automated analysis system for the identification of phytoplankton. 115 - Shaojun Tang, Alberto Riva:
PASTA: splice junction identification from RNA-Sequencing data. 116 - Yongchao Liu, Adrianto Wirawan, Bertil Schmidt:
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. 117 - Christian Theil Have, Sine Zambach, Henning Christiansen:
Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes. 118 - Silke Janitza, Carolin Strobl, Anne-Laure Boulesteix:
An AUC-based permutation variable importance measure for random forests. 119 - Cheong Xin Chan, Maisarah Mahbob, Mark A. Ragan:
Clustering evolving proteins into homologous families. 120 - David Haughton, Félix Balado:
BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA. 121 - Simon Dornseifer, Georg Sczakiel:
Computational identification of biologically functional non-hairpin GC-helices in human Argonaute mRNA. 122 - Jaesik Jeong, Xiang Zhang, Xue Shi, Seongho Kim, Changyu Shen:
An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS. 123 - Xing Qiu, Hulin Wu, Rui Hu:
The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis. 124 - Nikhil R. Garge, Georgiy V. Bobashev, Barry Eggleston:
Random forest methodology for model-based recursive partitioning: the mobForest package for R. 125 - Julien Wollbrett, Pierre Larmande, Frédéric de Lamotte, Manuel Ruiz:
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases. 126 - Joachim von Eichborn, Anna Lena Woelke, Filippo Castiglione, Robert Preissner:
VaccImm: simulating peptide vaccination in cancer therapy. 127 - Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma'ayan:
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. 128 - Shreepriya Das, Haris Vikalo:
Base calling for high-throughput short-read sequencing: dynamic programming solutions. 129 - Eszter Hazai, Istvan Hazai, Isabelle Ragueneau-Majlessi, Sophie P. Chung, Zsolt Bikádi, Qingcheng Mao:
Predicting substrates of the human breast cancer resistance protein using a support vector machine method. 130 - Pierre Grenon, Bernard de Bono:
Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology. 131 - Li Liu, Donghui Zhang, Hong Liu, Christopher Arendt:
Robust methods for population stratification in genome wide association studies. 132 - Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka Axmann, Ralf Steuer:
How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis. 133 - Boguslaw Obara, Mark A. J. Roberts, Judith P. Armitage, Vicente Grau:
Bacterial cell identification in differential interference contrast microscopy images. 134 - Thomas J. Hardcastle, Krystyna A. Kelly:
Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution. 135 - Fang Yang, Nicholas Chia, Bryan A. White, Lawrence B. Schook:
Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison. 136 - Andreas Pavlogiannis, Vadim Mozhayskiy, Ilias Tagkopoulos:
A flood-based information flow analysis and network minimization method for gene regulatory networks. 137 - François Van Lishout, Jestinah M. Mahachie John, Elena S. Gusareva, Víctor Urrea, Isabelle Cleynen, Emilie Théâtre, Benoît Charloteaux, Malu Luz Calle, Louis Wehenkel, Kristel Van Steen:
An efficient algorithm to perform multiple testing in epistasis screening. 138 - Nima Aghaeepour, Holger H. Hoos:
Ensemble-based prediction of RNA secondary structures. 139 - Josef Laimer, Clemens J. Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz, Peter Lackner:
D-Light on promoters: A client-server system for the analysis and visualization of cis-regulatory elements. 140 - Helen I. Field, Richard M. R. Coulson, Mark C. Field:
An automated graphics tool for comparative genomics: the Coulson plot generator. 141 - Ping Ge, Shaojie Zhang:
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. 142 - Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li:
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis. 143 - Afshin Sadeghi, Holger Fröhlich:
Steiner tree methods for optimal sub-network identification: an empirical study. 144 - Josh Eckels, Cory Nathe, Elizabeth K. Nelson, Sara G. Shoemaker, Elizabeth Nostrand, Nicole L. Yates, Vicki C. Ashley, Linda J. Harris, Mark Bollenbeck, Youyi Fong, Georgia D. Tomaras, Britt Piehler:
Quality control, analysis and secure sharing of Luminex(R) immunoassay data using the open source LabKey Server platform. 145 - Antonio Jimeno-Yepes, Élise Prieur-Gaston, Aurélie Névéol:
Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. 146 - Lorna Morris, Andrew Tsui, Charles Crichton, Steve Harris, Peter Maccallum, William J. Howat, Jim Davies, James D. Brenton, Carlos Caldas:
A metadata-aware application for remote scoring and exchange of tissue microarray images. 147 - Matthew V. N. O'Sullivan, Vitali Sintchenko, Gwendolyn L. Gilbert:
Software for selecting the most informative sets of genomic loci for multi-target microbial typing. 148 - James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson, Jotun Hein:
Quantifying variances in comparative RNA secondary structure prediction. 149 - Junbo Duan, Ji-Gang Zhang, Hong-Wen Deng, Yu-Ping Wang:
CNV-TV: A robust method to discover copy number variation from short sequencing reads. 150 - Chen Suo, Timothea Toulopoulou, Elvira Bramon, Muriel Walshe, Marco M. Picchioni, Robin M. Murray, Jürg Ott:
Analysis of multiple phenotypes in genome-wide genetic mapping studies. 151 - Qi Dai, Yan Li, Xiao-Qing Liu, Yuhua Yao, Yunjie Cao, Pingan He:
Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position. 152 - Eric A. Welsh, Steven Eschrich, Anders Berglund, David A. Fenstermacher:
Iterative rank-order normalization of gene expression microarray data. 153 - Vesna Memievi, Anders Wallqvist, Jaques Reifman:
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. 154 - Marie C. Galligan, Radka Saldova, Matthew P. Campbell, Pauline M. Rudd, Thomas Brendan Murphy:
Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution. 155 - David Mayerich, Michael J. Walsh, Matthew Schulmerich, Rohit Bhargava:
Real-time interactive data mining for chemical imaging information: application to automated histopathology. 156 - Jen-hwa Chu, Angela J. Rogers, Iuliana Ionita-Laza, Katayoon Darvishi, Ryan Mills, Charles Lee, Benjamin A. Raby:
Copy number variation genotyping using family information. 157 - Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Meg Pirrung, Brian C. O'Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E. Alfaro, Aaron Steele, Greg Jordan:
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. 158 - Pietro Di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini:
MIMO: an efficient tool for molecular interaction maps overlap. 159 - Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Szymon Grabowski:
Disk-based k-mer counting on a PC. 160 - Tian Mi, Sanguthevar Rajasekaran:
Efficient algorithms for biological stems search. 161 - Carlos Milovic, Carolina Oses, Manuel Villalón, Sergio Uribe, Carlos Lizama, Claudia Prieto, Marcelo E. Andia, Pablo Irarrazaval, Cristian Tejos:
Calcium (Ca2+) waves data calibration and analysis using image processing techniques. 162 - Nazar Zaki, Dmitry Efimov, Jose Berengueres:
Protein complex detection using interaction reliability assessment and weighted clustering coefficient. 163 - Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis R. Bach, Jean-Philippe Vert:
Learning smoothing models of copy number profiles using breakpoint annotations. 164 - Gordon K. Smyth, Naomi S. Altman:
Separate-channel analysis of two-channel microarrays: recovering inter-spot information. 165 - Karolina Sikorska, Emmanuel Lesaffre, Patrick J. F. Groenen, Paul H. C. Eilers:
GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies. 166 - Alireza Hadj Khodabakhshi, Anthony P. Fejes, Inanç Birol, Steven J. M. Jones:
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. 167 - Robert J. Pantazes, Costas D. Maranas:
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. 168 - Yanchun Bao, Veronica Vinciotti, Ernst Wit, Peter A. C. 't Hoen:
Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data. 169 - Siow-Wee Chang, Sameem Abdul Kareem, Amir F. Merican, Rosnah Zain:
Oral cancer prognosis based on clinicopathologic and genomic markers using a hybrid of feature selection and machine learning methods. 170 - Antonio Jimeno-Yepes, J. Caitlin Sticco, James G. Mork, Alan R. Aronson:
GeneRIF indexing: sentence selection based on machine learning. 171 - Zhe Liu, Hongwu Ma, Igor Goryanin:
A semi-automated genome annotation comparison and integration scheme. 172 - Yang Song, Weidong Cai, Heng Huang, Yue Wang, David Dagan Feng, Mei Chen:
Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling. 173 - Xiuli Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao:
PMTED: a plant microRNA target expression database. 174 - Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou:
Wide coverage biomedical event extraction using multiple partially overlapping corpora. 175 - Norbert Niklas, Johannes Pröll, Martin Danzer, Stephanie Stabentheiner, Katja Hofer, Christian Gabriel:
Routine performance and errors of 454 HLA exon sequencing in diagnostics. 176 - Jonathan P. Tyrer, Qi Guo, Douglas F. Easton, Paul D. P. Pharoah:
The admixture maximum likelihood test to test for association between rare variants and disease phenotypes. 177 - Florent Baty, Jochen Rüdiger, Nicola Miglino, Lukas Kern, Peter Borger, Martin H. Brutsche:
Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis. 178 - David Edwards:
Modelling and visualizing fine-scale linkage disequilibrium structure. 179 - Newton Shydeo Brandão Miyoshi, Daniel Guariz Pinheiro, Wilson A. Silva Jr., Joaquim Cezar Felipe:
Computational framework to support integration of biomolecular and clinical data within a translational approach. 180 - Rong Xu, QuanQiu Wang:
Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing. 181 - Han Zhang, Marcelo Fiszman, Dongwook Shin, Bartlomiej Wilkowski, Thomas C. Rindflesch:
Clustering cliques for graph-based summarization of the biomedical research literature. 182 - Thomas L. Rodgers, David Burnell, Phil D. Townsend, Ehmke Pohl, Martin J. Cann, Mark R. Wilson, Tom C. B. McLeish:
ΔΔPT: a comprehensive toolbox for the analysis of protein motion. 183 - Ayat Hatem, Doruk Bozdag, Amanda E. Toland, Ümit V. Çatalyürek:
Benchmarking short sequence mapping tools. 184 - Jean-Baptiste Pettit, John C. Marioni:
bioWeb3D: an online webGL 3D data visualisation tool. 185 - Guojun Yang:
MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements. 186 - Idoia Ochoa, Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Tsachy Weissman, Golan Yona:
QualComp: a new lossy compressor for quality scores based on rate distortion theory. 187 - George Wu, Hongkai Ji:
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking. 188 - Su Yeon Kim, Terence P. Speed:
Comparing somatic mutation-callers: Beyond Venn diagrams. 189 - Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis, Hongyu Zhao:
Utilizing protein structure to identify non-random somatic mutations. 190 - Andreas Holzinger, Mario Zupan:
KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain. 191 - Troy A. Ruths, Luay Nakhleh:
Boosting forward-time population genetic simulators through genotype compression. 192 - Chenglin Liu, Jinwen Ma, Chung-Che Jeff Chang, Xiaobo Zhou:
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. 193 - Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, Robert Stevens:
bioNerDS: exploring bioinformatics' database and software use through literature mining. 194 - Alison M. Meynert, Louise S. Bicknell, Matthew E. Hurles, Andrew P. Jackson, Martin S. Taylor:
Quantifying single nucleotide variant detection sensitivity in exome sequencing. 195 - Ahsan Raja Chowdhury, Madhu Chetty, Xuan Vinh Nguyen:
Incorporating time-delays in S-System model for reverse engineering genetic networks. 196 - Xavier I. Ambroggio, Jennifer Dommer, Vivek Gopalan, Eleca J. Dunham, Jeffery K. Taubenberger, Darrell E. Hurt:
HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. 197 - Yong Liang, Cheng Liu, Xin-Ze Luan, Kwong-Sak Leung, Tak-Ming Chan, Zongben Xu, Hai Zhang:
Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification. 198 - Ren-Hua Chung, Chung-Chin Shih:
SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies. 199 - Katherine L. Thompson, Laura Salter Kubatko:
Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies. 200 - Francesco Napolitano, Renato Mariani-Costantini, Roberto Tagliaferri:
Bioinformatic pipelines in Python with leaf. 201 - Kishori M. Konwar, Niels W. Hanson, Antoine P. Pagé, Steven J. Hallam:
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. 202 - John O. Woods, Ulf Martin Singh-Blom, Jon M. Laurent, Kriston L. McGary, Edward M. Marcotte:
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. 203 - Joshua T. Burdick, John Isaac Murray:
Deconvolution of gene expression from cell populations across the C. elegans lineage. 204 - Petr Cech, Jaromír Kukal, Jirí Cerný, Bohdan Schneider, Daniel Svozil:
Automatic workflow for the classification of local DNA conformations. 205 - Alice M. Richardson, Brett A. Lidbury:
Infection status outcome, machine learning method and virus type interact to affect the optimised prediction of hepatitis virus immunoassay results from routine pathology laboratory assays in unbalanced data. 206 - Emmanuel Bresso, Renaud Grisoni, Gino Marchetti, Arnaud Sinan Karaboga, Michel Souchet, Marie-Dominique Devignes, Malika Smaïl-Tabbone:
Integrative relational Machine-Learning Approach for Understanding Drug Side-Effect Profiles. 207 - Antonio José Jimeno-Yepes, Laura Plaza, James G. Mork, Alan R. Aronson, Alberto Díaz:
MeSH indexing based on automatically generated summaries. 208 - Joel Sjöstrand, Lars Arvestad, Jens Lagergren, Bengt Sennblad:
GenPhyloData: realistic simulation of gene family evolution. 209 - Yen-Tsung Huang, Xihong Lin:
Gene set analysis using variance component tests. 210 - Varun Jaiswal, Sree K. Chanumolu, Ankit Gupta, Rajinder S. Chauhan, Chittaranjan Rout:
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. 211 - Irina Dinu, Xiaoming Wang, Linda E. Kelemen, Shabnam Vatanpour, Saumyadipta Pyne:
Linear combination test for gene set analysis of a continuous phenotype. 212 - Lazaros Mavridis, Neetika Nath, John B. O. Mitchell:
PFClust: a novel parameter free clustering algorithm. 213 - Márcia M. Almeida-de-Macedo, Nick Ransom, Yaping Feng, Jonathan Hurst, Eve Syrkin Wurtele:
Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data. 214 - Ola Kristoffer Øye, Katarina M. Jørgensen, Sigrun M. Hjelle, André Sulen, Dag Magne Ulvang, Bjørn Tore Gjertsen:
Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data. 215 - Andre J. Aberer, Alexandros Stamatakis:
Rapid forward-in-time simulation at the chromosome and genome level. 216 - Paul T. Shannon, Mark L. Grimes, Burak Kutlu, Jan J. Bot, David J. Galas:
RCytoscape: tools for exploratory network analysis. 217 - Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich, Thomas Dandekar:
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. 218 - Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota:
TCC: an R package for comparing tag count data with robust normalization strategies. 219 - Xinyun Ma, Xuegong Zhang:
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. 220 - Brian J. Schmidt, Fergal P. Casey, Thomas Paterson, Jason R. Chan:
Alternate virtual populations elucidate the type I interferon signature predictive of the response to rituximab in rheumatoid arthritis. 221 - Shuiwang Ji:
Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering. 222 - Roger S. Day, Kevin K. McDade:
A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration. 223 - Kevin T. O'Brien, Niall J. Haslam, Denis C. Shields:
SLiMScape: a protein short linear motif analysis plugin for Cytoscape. 224 - Jiawen Bian, Chenglin Liu, Hongyan Wang, Jing Xing, Priyanka Kachroo, Xiaobo Zhou:
SNVHMM: predicting single nucleotide variants from next generation sequencing. 225 - Fernando Meyer, Stefan Kurtz, Michael Beckstette:
Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns. 226 - Caiyan Jia, Matthew B. Carson, Jian Yu:
A fast weak motif-finding algorithm based on community detection in graphs. 227 - Stefanie Seltmann, Harald Stachelscheid, Alexander Damaschun, Ludger Jansen, Fritz Lekschas, Jean-Fred Fontaine, Throng-Nghia Nguyen-Dobinsky, Ulf Leser, Andreas Kurtz:
CELDA - an ontology for the comprehensive representation of cells in complex systems. 228 - Marcos Parras-Moltó, Francisco J. Campos-Laborie, Juan García-Diéguez, M. R. Rodríguez-Griñolo, Antonio J. Pérez-Pulido:
Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels. 229 - Yu-Cheng Liu, Chun-Pei Cheng, Vincent S. Tseng:
Mining differential top-k co-expression patterns from time course comparative gene expression datasets. 230 - Cali E. Willet, Laura Bunbury-Cruickshank, Diane van Rooy, Georgina Child, Mohammad R. Shariflou, Peter C. Thomson, Claire M. Wade:
Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays. 231 - Jianya Guo, Xi Mei, Kun Tang:
Automatic landmark annotation and dense correspondence registration for 3D human facial images. 232 - Alok Sharma, Kuldip K. Paliwal, Abdollah Dehzangi, James G. Lyons, Seiya Imoto, Satoru Miyano:
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. 233 - Lifeng Zhang, Daniel Berleant, Jing Ding, Eve Syrkin Wurtele:
Automatic extraction of biomolecular interactions: an empirical approach. 234 - Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands, Joost P. Schanstra:
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases. 235 - Sutirtha Chakraborty, Somnath Datta, Susmita Datta:
svapls: an R package to correct for hidden factors of variability in gene expression studies. 236 - Aurora Torrente, Sara López-Pintado, Juan Romo:
DepthTools: an R package for a robust analysis of gene expression data. 237 - Stefan Paulus, Jan Dupuis, Anne-Katrin Mahlein, Heiner Kuhlmann:
Surface feature based classification of plant organs from 3D laserscanned point clouds for plant phenotyping. 238 - Noah Berlow, Lara E. Davis, Emma L. Cantor, Bernard Séguin, Charles Keller, Ranadip Pal:
A new approach for prediction of tumor sensitivity to targeted drugs based on functional data. 239 - Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders:
Robust flux balance analysis of multiscale biochemical reaction networks. 240 - Igor V. Deyneko, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Deineko, Edgar Wingender, Siegfried Weiss:
MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters. 241 - Ajay Kumar, Liisa Holm, Petri Törönen:
GOParGenPy: a high throughput method to generate Gene Ontology data matrices. 242 - Daniel Barker, David E. K. Ferrier, Peter W. H. Holland, John B. O. Mitchell, Heleen Plaisier, Michael G. Ritchie, Steven D. Smart:
4273pi: Bioinformatics education on low cost ARM hardware. 243 - Hongen Zhang, Paul S. Meltzer, Sean Davis:
RCircos: an R package for Circos 2D track plots. 244 - Dongdong Lin, Ji-Gang Zhang, Jingyao Li, Vince D. Calhoun, Hong-Wen Deng, Yu-Ping Wang:
Group sparse canonical correlation analysis for genomic data integration. 245 - Trevor Paterson, Andy Law:
ArkMAP: integrating genomic maps across species and data sources. 246 - Liang Zou, Mang Wang, Yi Shen, Jie Liao, Ao Li, Minghui Wang:
PKIS: computational identification of protein Kinases for experimentally discovered protein Phosphorylation sites. 247 - Maria Hauser, Christian E. Mayer, Johannes Söding:
kClust: fast and sensitive clustering of large protein sequence databases. 248 - Sara Ballouz, Jason Y. Liu, Richard A. George, Naresh Bains, Arthur Liu, Martin Oti, Bruno A. Gaëta, Diane Fatkin, Merridee A. Wouters:
Gentrepid V2.0: a web server for candidate disease gene prediction. 249 - Tobias Czauderna, Michael Wybrow, Kim Marriott, Falk Schreiber:
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. 250 - Kamal Taha, Dirar Mohammad Al Homouz, Hassan Al-Muhairi, Zaid Al Mahmoud:
GRank: a middleware search engine for ranking genes by relevance to given genes. 251 - James Hensman, Neil D. Lawrence, Magnus Rattray:
Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters. 252 - Ruby Lee, Jonathan R. Karr, Markus W. Covert:
WholeCellViz: data visualization for whole-cell models. 253 - Mikel Esnaola, Pedro Puig, David González, Robert Castelo, Juan R. González:
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. 254 - Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter T. Hraber, Cheryl Gleasner, Lance Green, Bette T. Korber, Thomas Leitner:
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets. 255 - Annette Block, Frédéric Debode, Lutz Grohmann, Julie Hulin, Isabel Taverniers, Linda Kluga, Elodie Barbau-Piednoir, Sylvia Broeders, Ingrid Huber, Marc Van den Bulcke, Petra Heinze, Gilbert Berben, Ulrich Busch, Nancy Roosens, Eric Janssen, Jana Zel, Kristina Gruden, Dany Morisset:
The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants. 256 - Stephan Beisken, Thorsten Meinl, Bernd Wiswedel, Luis F. de Figueiredo, Michael R. Berthold, Christoph Steinbeck:
KNIME-CDK: Workflow-driven Cheminformatics. 257 - Jonathan A. Gelfond, Joseph G. Ibrahim, Mayetri Gupta, Ming-Hui Chen, Jannine D. Cody:
Differential expression analysis with global network adjustment. 258 - Shuying Sun, Aaron Noviski, Xiaoqing Yu:
MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. 259 - Osman S. Osman, Joanne L. Selway, Parvathy E. Harikumar, Claire J. Stocker, Edward T. Wargent, Michael Anthony Cawthorne, Sabah A. Jassim, Kenneth Langlands:
A novel method to assess collagen architecture in skin. 260 - Ali Anaissi, Paul J. Kennedy, Madhu Goyal, Daniel R. Catchpoole:
A balanced iterative random forest for gene selection from microarray data. 261 - Yingtao Bi, Ramana V. Davuluri:
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. 262 - Terrence F. Meehan, Nicole A. Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl:
Ontology based molecular signatures for immune cell types via gene expression analysis. 263 - Patricia Soares, Renato J. Alves, Ana B. Abecasis, Carlos Penha Gonçalves, M. Gabriela Gomes, José B. Pereira-Leal:
inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. 264 - Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman:
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. 265 - Sushmita Paul, Pradipta Maji:
µHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix. 266 - Yo Son Park, Michael A. Schmidt, Eden R. Martin, Margaret A. Pericak-Vance, Ren-Hua Chung:
Pathway-PDT: a flexible pathway analysis tool for nuclear families. 267 - Alexander Solovyov, W. Ian Lipkin:
Centroid based clustering of high throughput sequencing reads based on n-mer counts. 268 - Cuncong Zhong, Shaojie Zhang:
Efficient alignment of RNA secondary structures using sparse dynamic programming. 269 - Guido H. Jajamovich, Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang:
Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA. 270 - Caroline Bérard, Michael Seifert, Tristan Mary-Huard, Marie-Laure Martin-Magniette:
MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates. 271 - Tilo Buschmann, Leonid V. Bystrykh:
Levenshtein error-correcting barcodes for multiplexed DNA sequencing. 272 - Céline Brouard, Christel Vrain, Julie Dubois, David Castel, Marie-Anne Debily, Florence d'Alché-Buc:
Learning a Markov Logic network for supervised gene regulatory network inference. 273 - Xiaoqing Yu, Shuying Sun:
Comparing a few SNP calling algorithms using low-coverage sequencing data. 274 - János András Mótyán, Péter Bagossi, Szilvia Benk, József Tzsér:
A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein. 275 - Timothy Nugent, David T. Jones:
Membrane protein orientation and refinement using a knowledge-based statistical potential. 276 - Pierre Lechat, Erika L. Souche, Ivan Moszer:
SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics. 277 - Mingzhu Zhu, Jeremy L. Dahmen, Gary Stacey, Jianlin Cheng:
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. 278 - Juliane Charlotte Thøgersen, Morten Mørup, Søren Damkiær, Søren Molin, Lars Jelsbak:
Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways. 279 - Marcin Kruczyk, Husen M. Umer, Stefan Enroth, Jan Komorowski:
Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data. 280 - David Campos, Sérgio Matos, José Luís Oliveira:
A modular framework for biomedical concept recognition. 281 - Jian Xiao, Wensheng Zhu, Jianhua Guo:
Large-scale multiple testing in genome-wide association studies via region-specific hidden Markov models. 282 - André Veríssimo, Laura Paixão, Ana Rita Neves, Susana Vinga:
BGFit: management and automated fitting of biological growth curves. 283 - Gaston K. Mazandu, Nicola J. Mulder:
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. 284 - Daniela Stojanova, Michelangelo Ceci, Donato Malerba, Saso Dzeroski:
Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction. 285 - Iain H. Moal, Mieczyslaw Torchala, Paul A. Bates, Juan Fernández-Recio:
The scoring of poses in protein-protein docking: current capabilities and future directions. 286 - Aruna Jammalamadaka, Sourav Banerjee, Kenneth S. Kosik, Bangalore S. Manjunath:
Statistical Analysis of Dendritic Spine Distributions in Rat Hippocampal Cultures. 287 - Ivan Molineris, Ugo Ala, Paolo Provero, Ferdinando Di Cunto:
Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs). 288 - Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen, Rasmus Nielsen:
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. 289 - Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau, Frédéric Bard:
ScreenSifter: analysis and visualization of RNAi screening data. 290 - Jie Zhou, Santosh Lamichhane, Gabriella Sterne, Bing Ye, Hanchuan Peng:
BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. 291 - Henrik Failmezger, Holger Fröhlich, Achim Tresch:
Unsupervised automated high throughput phenotyping of RNAi time-lapse movies. 292 - Hanchuan Peng, Badrinath Roysam, Giorgio A. Ascoli:
Automated image computing reshapes computational neuroscience. 293 - Saket Navlakha, Parvez Ahammad, Eugene W. Myers:
Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging. 294 - Yusuke Azuma, Shuichi Onami:
Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images. 295 - Cheng-Jin Du, Phillip T. Hawkins, Len R. Stephens, Till Bretschneider:
3D time series analysis of cell shape using Laplacian approaches. 296 - Felix Buggenthin, Carsten Marr, Michael Schwarzfischer, Philipp S. Hoppe, Oliver Hilsenbeck, Timm Schroeder, Fabian J. Theis:
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. 297 - Jessica L. Stringham, Adam S. Brown, Robert A. Drewell, Jacqueline M. Dresch:
Flanking sequence context-dependent transcription factor binding in early Drosophila development. 298 - George Tucker, Po-Ru Loh, Bonnie Berger:
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. 299 - Chun Fang, Tamotsu Noguchi, Daisuke Tominaga, Hayato Yamana:
MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation. 300 - Martin O. Jones, Mark L. Blaxter:
afterParty: turning raw transcriptomes into permanent resources. 301 - Chris Schmidt, Stephanie Jimenez Irausquin, Homayoun Valafar:
Advances in the REDCAT software package. 302 - Michael A. DeJesus, Thomas R. Ioerger:
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. 303 - Jhih-Siang Lai, Cheng-Wei Cheng, Allan Lo, Ting-Yi Sung, Wen-Lian Hsu:
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices. 304 - Darragh G. McArt, Peter Bankhead, Philip D. Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang:
cudaMap: a GPU accelerated program for gene expression connectivity mapping. 305 - Stefan Karl, Thomas Dandekar:
Jimena: efficient computing and system state identification for genetic regulatory networks. 306 - Noushin Ghaffari, Mohammadmahdi R. Yousefi, Charles D. Johnson, Ivan Ivanov, Edward R. Dougherty:
Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification. 307 - Grégoire Pau, Thomas Walter, Beate Neumann, Jean-Karim Hériché, Jan Ellenberg, Wolfgang Huber:
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay. 308 - Sean M. Hoban, Massimo Mezzavilla, Oscar E. Gaggiotti, Andrea Benazzo, Cock van Oosterhout, Giorgio Bertorelle:
High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study. 309 - Jaehee Kim, Robert Todd Ogden, Haseong Kim:
A method to identify differential expression profiles of time-course gene data with Fourier transformation. 310 - Yannis Pantazis, Markos A. Katsoulakis, Dionisios G. Vlachos:
Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory. 311 - James W. Baurley, David V. Conti:
A scalable, knowledge-based analysis framework for genetic association studies. 312 - Einar Andreas Rødland:
Compact representation of k-mer de Bruijn graphs for genome read assembly. 313 - Yaping Fang, Shan Gao, David Tai, C. Russell Middaugh, Jianwen Fang:
Identification of properties important to protein aggregation using feature selection. 314 - Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis:
A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms. 315 - Juan E. Ortuño, María J. Ledesma-Carbayo, Rui V. Simões, Ana-Paula Candiota, Carles Arús, Andrés Santos:
DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data. 316 - Manon Ragonnet-Cronin, Emma B. Hodcroft, Stéphane Hué, Esther Fearnhill, Valerie Delpech, Andrew J. Leigh Brown, Samantha Lycett:
Automated analysis of phylogenetic clusters. 317 - Christian Jungreuthmayer, Govind Nair, Steffen Klamt, Jürgen Zanghellini:
Comparison and improvement of algorithms for computing minimal cut sets. 318 - Assaf Zaritsky, Nathan Manor, Lior Wolf, Eshel Ben-Jacob, Ilan Tsarfaty:
Benchmark for multi-cellular segmentation of bright field microscopy images. 319 - David Sturgill, John H. Malone, Xia Sun, Harold E. Smith, Leonard Rabinow, Marie-Laure Samson, Brian Oliver:
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki). 320 - Xinbin Dai, Senjuti Sinharoy, Michael K. Udvardi, Patrick Xuechun Zhao:
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. 321 - Qi Wang, Biao Tang, Lifu Song, Biao Ren, Qun Liang, Feng Xie, Ying Zhuo, Xueting Liu, Lixin Zhang:
3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape. 322 - Hee-Jin Lee, Sang-Hyung Shim, Mi-Ryoung Song, Hyunju Lee, Jong-Chan Park:
CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations. 323 - Wellington Santos Martins, Welton Couto Carmo, Humberto J. Longo, Thierson Couto Rosa, Thiago Fernando Rangel:
SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations. 324 - Kris A. Christensen, Joseph P. Brunelli, Matthew J. Lambert, Jenefer DeKoning, Ruth B. Phillips, Gary H. Thorgaard:
Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication. 325 - Ali Al-Shahib, Anthony Underwood:
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing. 326 - Ruth Y. Eberhardt, Yuanyuan Chang, Alex Bateman, Alexey G. Murzin, Herbert L. Axelrod, William C. Hwang, L. Aravind:
Filling out the structural map of the NTF2-like superfamily. 327 - Long Chen, Leanne Lai Chan, Zhongying Zhao, Hong Yan:
A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images. 328 - Salma Jamal, Vinod Scaria:
Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana. 329 - Casey W. Dunn, Mark Howison, Felipe Zapata:
Agalma: an automated phylogenomics workflow. 330 - Fan Zhang, Ruoyan Chen, Dongbing Liu, Xiaotian Yao, Guoqing Li, Yabin Jin, Chang Yu, Yingrui Li, Lachlan James M. Coin:
YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data. 331 - Yao-ban Chan, Vincent Ranwez, Céline Scornavacca:
Reconciliation-based detection of co-evolving gene families. 332 - Qiaoyong Zhong, Chen Yang, Frederik Großerüschkamp, Angela Kallenbach-Thieltges, Peter Serocka, Klaus Gerwert, Axel Mosig:
Similarity maps and hierarchical clustering for annotating FT-IR spectral images. 333 - Mehmood Alam Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad:
fastphylo: Fast tools for phylogenetics. 334 - Peng Zhou, Kevin A. T. Silverstein, Liangliang Gao, Jonathan D. Walton, Sumitha Nallu, Joseph Guhlin, Nevin D. Young:
Detecting Small Plant Peptides Using SPADA (Small Peptide Alignment Discovery Application). 335 - Xian Zhang, Michael Boutros:
A novel phenotypic dissimilarity method for image-based high-throughput screens. 336 - Changjin Hong, Nathan L. Clement, Spencer Clement, Saher Sue Hammoud, Douglas T. Carrell, Bradley R. Cairns, Quinn Snell, Mark J. Clement, William Evan Johnson:
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. 337 - Gift Nyamundanda, Isobel Claire Gormley, Yue Fan, William M. Gallagher, Lorraine Brennan:
MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach. 338 - Andreas Sand, Martin Kristiansen, Christian N. S. Pedersen, Thomas Mailund:
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. 339 - Natalie L. Catlett, Anthony J. Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O. Elliston, Dexter Pratt:
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. 340 - William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik:
LUD, a new protein domain associated with lactate utilization. 341 - Arvind Mer, Miguel A. Andrade-Navarro:
A novel approach for protein subcellular location prediction using amino acid exposure. 342 - Ahmad Barghash, Volkhard Helms:
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. 343 - Giuseppe Facchetti, Claudio Altafini:
Partial inhibition and bilevel optimization in flux balance analysis. 344 - José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia:
wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. 345 - Douglas B. Craig, Alan A. Dombkowski:
Disulfide by design 2.0: a web-based tool for disulfide engineering in proteins. 346 - Osamu Maruyama:
Heterodimeric protein complex identification by naïve Bayes classifiers. 347 - Bernhard Misof, Benjamin Meyer, Björn Marcus von Reumont, Patrick Kück, Katharina Misof, Karen Meusemann:
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees. 348 - Arun Shivanandan, Aleksandra Radenovic, Ivo F. Sbalzarini:
MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis. 349 - Qian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye:
Image-level and group-level models for Drosophila gene expression pattern annotation. 350 - Malgorzata Kotulska, Olgierd Unold:
On the amyloid datasets used for training PAFIG - how (not) to extend the experimental dataset of hexapeptides. 351 - Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend:
Status quo of annotation of human disease variants. 352 - Alexandra M. Binder, Karin B. Michels:
The causal effect of red blood cell folate on genome-wide methylation in cord blood: a Mendelian randomization approach. 353 - Barry P. Young, Christopher J. R. Loewen:
Balony: a software package for analysis of data generated by synthetic genetic array experiments. 354 - Wan-Ting Poh, Eryu Xia, Kwanrutai Chin-inmanu, Lai-Ping Wong, Anthony Youzhi Cheng, Prida Malasit, Prapat Suriyaphol, Yik-Ying Teo, Rick Twee-Hee Ong:
Viral quasispecies inference from 454 pyrosequencing. 355 - Jerome Kelleher, Rob W. Ness, Daniel L. Halligan:
Processing genome scale tabular data with wormtable. 356 - Chung-I Li, Pei-Fang Su, Yu Shyr:
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. 357 - Adam Roberts, Harvey Feng, Lior Pachter:
Fragment assignment in the cloud with eXpress-D. 358 - Robert Lowe, Vardhman K. Rakyan:
Marmal-aid - a database for Infinium HumanMethylation450. 359 - Andrew E. Jaffe, John D. Storey, Hongkai Ji, Jeffrey T. Leek:
Gene set bagging for estimating the probability a statistically significant result will replicate. 360 - Nikolaos Berntenis, Martin Ebeling:
Detection of attractors of large Boolean networks via exhaustive enumeration of appropriate subspaces of the state space. 361 - Giorgio Giurato, Maria De Filippo, Antonio Rinaldi, Adnan Hashim, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz:
iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq. 362 - Ahrim Youn, Richard Simon:
Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations. 363 - Ashlee M. Benjamin, J. Will Thompson, Erik J. Soderblom, Scott J. Geromanos, Ricardo Henao, Virginia B. Kraus, M. Arthur Moseley, Joseph E. Lucas:
A flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information. 364 - Chao Wu, Jun Zhu, Xuegong Zhang:
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. 365 - Thorsten Schmidt, Jasmin Dürr, Margret Keuper, Thomas Blein, Klaus Palme, Olaf Ronneberger:
Variational attenuation correction in two-view confocal microscopy. 366 - Julie A. Sleep, Andreas W. Schreiber, Ute Baumann:
Sequencing error correction without a reference genome. 367 - Lun-Ching Chang, Hui-Min Lin, Etienne Sibille, George C. Tseng:
Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline. 368 - Patrick Putnam, Ge Zhang, Philip A. Wilsey:
A comparison study of succinct data structures for use in GWAS. 369 - Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach:
Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching. 370 - Tzu-Pin Lu, Eric Y. Chuang, James J. Chen:
Identification of reproducible gene expression signatures in lung adenocarcinoma. 371 - Wenlu Zhang, Daming Feng, Rongjian Li, Andrey N. Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart J. Newfeld, Sudhir Kumar, Shuiwang Ji:
A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. 372
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