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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, Yuxin 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 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