Works matching IS 13674803 AND DT 2015 AND VI 31 AND IP 7

Results: 65

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1154, doi. 10.1093/bioinformatics/btv013

By:

Naldi, Aurélien;
Monteiro, Pedro T.;
Müssel, Christoph;
Kestler, Hans A.;
Thieffry, Denis;
Xenarios, Ioannis;
Saez-Rodriguez, Julio;
Helikar, Tomas;
Chaouiya, Claudine

Publication type:

Article

Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1150, doi. 10.1093/bioinformatics/btu796

By:

Ahmed, Zeeshan;
Mayr, Michel;
Zeeshan, Saman;
Dandekar, Thomas;
Mueller, Martin J.;
Fekete, Agnes

Publication type:

Article

A logical model of HIV-1 interactions with the T-cell activation signalling pathway.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1075, doi. 10.1093/bioinformatics/btu787

By:

Oyeyemi, Oyebode J.;
Davies, Oluwafemi;
Robertson, David L.;
Schwartz, Jean-Marc

Publication type:

Article

Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 986, doi. 10.1093/bioinformatics/btu785

By:

Keane, Peter;
Ceredig, Rhodri;
Seoighe, Cathal

Publication type:

Article

A bio-inspired computing model for ovarian carcinoma classification and oncogene detection.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1102, doi. 10.1093/bioinformatics/btu782

By:

Meng-Hsiun Tsai;
Mu-Yen Chen;
Huang, Steve G.;
Yao-Ching Hung;
Hsin-Chieh Wang

Publication type:

Article

Mechanotransduction map: simulation model, molecular pathway, gene set.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1053, doi. 10.1093/bioinformatics/btu776

By:

Dent, Jennifer E.;
Devescovi, Valentina;
Han Li;
Di Lena, Pietro;
Youtao Lu;
Yuanhua Liu;
Nardini, Christine

Publication type:

Article

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 991, doi. 10.1093/bioinformatics/btu770

By:

Jones, Graham;
Aydin, Zeynep;
Oxelman, Bengt

Publication type:

Article

genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1127, doi. 10.1093/bioinformatics/btu775

By:

Akalin, Altuna;
Franke, Vedran;
Vlahoviček, Kristian;
Mason, Christopher E.;
Schübeler, Dirk

Publication type:

Article

Molecular principles of human virus protein–protein interactions.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1025, doi. 10.1093/bioinformatics/btu763

By:

Halehalli, Rachita Ramachandra;
Nagarajaram, Hampapathalu Adimurthy

Publication type:

Article

NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1144, doi. 10.1093/bioinformatics/btu774

By:

Poulet, Axel;
Arganda-Carreras, Ignacio;
Legland, David;
Probst, Aline V.;
Andrey, Philippe;
Tatout, Christophe

Publication type:

Article

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1060, doi. 10.1093/bioinformatics/btu777

By:

Haifen Chen;
Jing Guo;
Mishra, Shital K.;
Robson, Paul;
Niranjan, Mahesan;
Jie Zheng

Publication type:

Article

The Victor C++ library for protein representation and advanced manipulation.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1138, doi. 10.1093/bioinformatics/btu773

By:

Hirsh, Layla;
Piovesan, Damiano;
Giollo, Manuel;
Ferrari, Carlo;
Tosatto, Silvio C. E.

Publication type:

Article

Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 981, doi. 10.1093/bioinformatics/btu753

By:

Takahiro Tsukui;
Nozomi Nagano;
Myco Umemura;
Toshitaka Kumagai;
Goro Terai;
Masayuki Machida;
Kiyoshi Asai

Publication type:

Article

HyDRA: gene prioritization via hybrid distance-score rank aggregation.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1034, doi. 10.1093/bioinformatics/btu766

By:

Minji Kim;
Farnoud, Farzad;
Milenkovic, Olgica

Publication type:

Article

Unsupervised discovery of information structure in biomedical documents.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1084, doi. 10.1093/bioinformatics/btu758

By:

Kiela, Douwe;
Yufan Guo;
Stenius, Ulla;
Korhonen, Anna

Publication type:

Article

XenoSite server: a web-available site of metabolism prediction tool.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1136, doi. 10.1093/bioinformatics/btu761

By:

Matlock, Matthew K.;
Hughes, Tyler B.;
Swamidass, S. Joshua

Publication type:

Article

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1133, doi. 10.1093/bioinformatics/btu755

By:

van Rens, Karen E.;
Mäkinen, Veli;
Tomescu, Alexandru I.

Publication type:

Article

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.

Published in:: Bioinformatics, 2015, v. 31, n. 7, p. 1093, doi. 10.1093/bioinformatics/btu786
Publication type:: Article

SAMNetWeb: identifying condition-specific networks linking signaling and transcription.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1124, doi. 10.1093/bioinformatics/btu748

By:

Gosline, Sara J. C.;
Oh, Coyin;
Fraenkel, Ernest

Publication type:

Article

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1067, doi. 10.1093/bioinformatics/btu778

By:

Liu, Zhenqiu;
Sun, Fengzhu;
Braun, Jonathan;
McGovern, Dermot P. B.;
Piantadosi, Steven

Publication type:

Article

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1141, doi. 10.1093/bioinformatics/btu788

By:

Fermin, Damian;
Avtonomov, Dmitry;
Choi, Hyungwon;
Nesvizhskii, Alexey I.

Publication type:

Article

Efficient searching and annotation of metabolic networks using chemical similarity.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1016, doi. 10.1093/bioinformatics/btu760

By:

Pertusi, Dante A.;
Stine, Andrew E.;
Broadbelt, Linda J.;
Tyo, Keith E. J.

Publication type:

Article

Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1111, doi. 10.1093/bioinformatics/btu772

By:

Xu, Ying-Ying;
Fan Yang;
Yang Zhang;
Shen, Hong-Bin

Publication type:

Article

LigDig: a web server for querying ligand–protein interactions.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1147, doi. 10.1093/bioinformatics/btu784

By:

Fuller, Jonathan C.;
Martinez, Michael;
Henrich, Stefan;
Stank, Antonia;
Richter, Stefan;
Wade, Rebecca C.

Publication type:

Article

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 999, doi. 10.1093/bioinformatics/btu791

By:

Jones, David T.;
Singh, Tanya;
Kosciolek, Tomasz;
Tetchner, Stuart

Publication type:

Article

MGAS: a powerful tool for multivariate gene-based genome-wide association analysis.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1007, doi. 10.1093/bioinformatics/btu783

By:

Van der Sluis, Sophie;
Dolan, Conor V.;
Li, Jiang;
Song, Youqiang;
Sham, Pak;
Posthuma, Danielle;
Li, Miao-Xin

Publication type:

Article

QuasR: quantification and annotation of short reads in R.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1130, doi. 10.1093/bioinformatics/btu781

By:

Gaidatzis, Dimos;
Lerch, Anita;
Hahne, Florian;
Stadler, Michael B.

Publication type:

Article

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1044, doi. 10.1093/bioinformatics/btu767

By:

Koji Kyoda;
Yukako Tohsato;
Ho, Kenneth H. L.;
Shuichi Onami

Publication type:

Article

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1120, doi. 10.1093/bioinformatics/btu743

By:

Yuki Naito;
Kimihiro Hino;
Hidemasa Bono;
Kumiko Ui-Tei

Publication type:

Article

Erratum.

Published in:: 2015
Publication type:: Correction Notice

flowCL: ontology-based cell population labelling in flow cytometry.

Published in:

2015

By:

Courtot, Mélanie;
Meskas, Justin;
Diehl, Alexander D.;
Droumeva, Radina;
Gottardo, Raphael;
Jalali, Adrin;
Taghiyar, Mohammad Jafar;
Maecker, Holden T.;
McCoy, J. Philip;
Ruttenberg, Alan;
Scheuermann, Richard H.;
Brinkman, Ryan R.

Publication type:

Product Review

SNiPA: an interactive, genetic variant-centered annotation browser.

Published in:

2015

By:

Arnold, Matthias;
Raffler, Johannes;
Pfeufer, Arne;
Suhre, Karsten;
Kastenmüller, Gabi

Publication type:

Product Review

ICMA: an integrated cardiac modeling and analysis platform.

Published in:

2015

By:

Hussan, Jagir R.;
Hunter, Peter J.;
Gladding, Patrick A.;
Greenberg, Neil;
Christie, Richard;
Wu, Alan;
Sorby, Hugh;
Thomas, James D.

Publication type:

Product Review

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

Published in:

2015

By:

Marchetti, Luca;
Manca, Vincenzo

Publication type:

Product Review

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.

Published in:

2015

By:

Woonghee Lee;
Tonelli, Marco;
Markley, John L.

Publication type:

Product Review

3Dmol.js: molecular visualization with WebGL.

Published in:

2015

By:

Rego, Nicholas;
Koes, David

Publication type:

Product Review

HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins.

Published in:

2015

By:

Rezaei-Ghaleh, Nasrollah;
Klama, Frederik;
Munari, Francesca;
Zweckstetter, Markus

Publication type:

Product Review

Detection of circular permutations within protein structures using CE-CP.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1316, doi. 10.1093/bioinformatics/btu823

By:

Bliven, Spencer E.;
Bourne, Philip E.;
Prlić, Andreas

Publication type:

Article

PEASE: predicting B-cell epitopes utilizing antibody sequence.

Published in:

2015

By:

Sela-Culang, Inbal;
Ashkenazi, Shaul;
Peters, Bjoern;
Ofran, Yanay

Publication type:

Product Review

Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier.

Published in:

2015

By:

Navarro-Gomez, Daniel;
Leipzig, Jeremy;
Lishuang Shen;
Lott, Marie;
Stassen, Alphons P. M.;
Wallace, Douglas C.;
Wiggs, Janey L.;
Falk, Marni J.;
van Oven, Mannis;
Xiaowu Gai

Publication type:

Product Review

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

Published in:

2015

By:

Bin Liu;
Fule Liu;
Longyun Fang;
Xiaolong Wang;
Kuo-Chen Chou

Publication type:

Product Review

Kablammo: an interactive, web-based BLAST results visualizer.

Published in:

2015

By:

Wintersinger, Jeff A.;
Wasmuth, James D.

Publication type:

Product Review

GenePainter v. 2.0 resolves the taxonomic distribution of intron positions.

Published in:

2015

By:

Mühlhausen, Stefanie;
Hellkamp, Marcel;
Kollmar, Martin

Publication type:

Product Review

Sputnik: ad hoc distributed computation.

Published in:

2015

By:

Völkel, Gunnar;
Lausser, Ludwig;
Schmid, Florian;
Kraus, Johann M.;
Kestler, Hans A.

Publication type:

Product Review

GSDS 2.0: an upgraded gene feature visualization server.

Published in:

2015

By:

Bo Hu;
Jinpu Jin;
An-Yuan Guo;
He Zhang;
Jingchu Luo;
Ge Gao

Publication type:

Product Review

GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences.

Published in:

2015

By:

Tetsuya Sato;
Mikita Suyama

Publication type:

Product Review

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Published in:

2015

By:

Yih-Chii Hwang;
Chiao-Feng Lin;
Otto Valladares;
Malamon, John;
Kuksa, Pavel P.;
Qi Zheng;
Gregory, Brian D.;
Li-San Wang

Publication type:

Product Review

Population-based structural variation discovery with Hydra-Multi.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1286, doi. 10.1093/bioinformatics/btu771

By:

Lindberg, Michael R.;
Hall, Ira M.;
Quinlan, Aaron R.

Publication type:

Article

Adaptive settings for the nearest-neighbor particle tracking algorithm.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1279, doi. 10.1093/bioinformatics/btu793

By:

Mazzaferri, Javier;
Roy, Joannie;
Lefrancois, Stephane;
Costantino, Santiago

Publication type:

Article

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1274, doi. 10.1093/bioinformatics/btu789

By:

Westbrook, John D.;
Chenghua Shao;
Zukang Feng;
Zhuravleva, Marina;
Velankar, Sameer;
Young, Jasmine

Publication type:

Article