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ORCIDBioinformatics, Volume 32
Volume 32, Number 1, January 2016
Genome Analysis
- Zi Yang, George Michailidis:
A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data. 1-8
- Adam Krejci, Ted R. Hupp
, Matej Lexa, Borivoj Vojtesek, Petr Müller:
Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. 9-16 - Paul M. Bodily, M. Stanley Fujimoto, Quinn Snell, Dan Ventura, Mark J. Clement:
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction. 17-24
- Maciej Dziubinski, Pawel Daniluk, Bogdan Lesyng:
ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins. 25-34
- Benoît Liquet, Pierre Lafaye de Micheaux, Boris P. Hejblum, Rodolphe Thiébaut:
Group and sparse group partial least square approaches applied in genomics context. 35-42 - Brendan A. Veeneman, Sudhanshu Shukla, Saravana M. Dhanasekaran, Arul M. Chinnaiyan, Alexey I. Nesvizhskii:
Two-pass alignment improves novel splice junction quantification. 43-49
- Kevin He, Yanming Li, Ji Zhu, Hongliang Liu, Jeffrey E. Lee, Christopher I. Amos, Terry Hyslop, Jiashun Jin, Huazhen Lin, Qinyi Wei, Yi Li:
Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates. 50-57 - Paulo C. Rodrigues, Andreia Monteiro, Vanda M. Lourenço:
A robust AMMI model for the analysis of genotype-by-environment data. 58-66
- Qiaozi Gao, Elisabeth Ostendorf, Jeffrey A. Cruz, Rong Jin, David M. Kramer, Jin Chen:
Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis. 67-76 - Begüm Genç, Ugur Dogrusoz:
An algorithm for automated layout of process description maps drawn in SBGN. 77-84 - Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin:
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. 85-95 - Eunjee Lee, Koichi Ito, Yong Zhao, Eric E. Schadt, Hanna Y. Irie, Jun Zhu:
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. 96-105
- Emily K. Mallory, Ce Zhang, Christopher Ré, Russ B. Altman:
Large-scale extraction of gene interactions from full-text literature using DeepDive. 106-113
- Wei Shao, Mingxia Liu, Daoqiang Zhang:
Human cell structure-driven model construction for predicting protein subcellular location from biological images. 114-121 - Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach. 122-129
Genome Analysis
- Utkarsh J. Dang, Geoffrey Brian Golding:
markophylo: Markov chain analysis on phylogenetic trees. 130-132 - Jonathan S. Packer, Evan K. Maxwell, Colm O'Dushlaine, Alexander E. Lopez, Frederick E. Dewey, Rostislav Chernomorsky, Aris Baras, John D. Overton, Lukas Habegger, Jeffrey G. Reid:
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. 133-135
- Karel Brinda, Valentina Boeva, Gregory Kucherov:
RNF: a general framework to evaluate NGS read mappers. 136-139 - Arna Óskarsdóttir, Gísli Másson, Páll Melsted:
BamHash: a checksum program for verifying the integrity of sequence data. 140-141 - Richard M. Leggett, Darren Heavens, Mario Cáccamo, Matthew D. Clark, Robert P. Davey:
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. 142-144
- Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger:
SHAPE directed RNA folding. 145-147
- Diego A. Hartasánchez, Marina Brasó-Vives, Juanma Fuentes-Díaz, Oriol Vallès-Codina, Arcadi Navarro:
SeDuS: segmental duplication simulator. 148-150 - Wei-Yi Cheng, Jörg Hakenberg, Shuyu Dan Li, Rong Chen:
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. 151-153
- Christian Jungreuthmayer, Stefan Neubauer, Teresa Mairinger, Jürgen Zanghellini, Stephan Hann:
ICT: isotope correction toolbox. 154-156
- Noah Fahlgren, Steven T. Hill, James C. Carrington, Alberto Carbonell:
P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design. 157-158 - William Gilpin:
PyPDB: a Python API for the Protein Data Bank. 159-160
Volume 32, Number 2, January 2016
Sequence Analysis
- Jimmy Caroli, Cristian Taccioli, A. De La Fuente, P. Serafini, Silvio Bicciato:
APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data. 161-164 - Van-Minh Bui, Cheng-Tsung Lu, Trang-Thi Ho, Tzong-Yi Lee:
MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs. 165-172 - Zhiying Wang, Tsachy Weissman, Olgica Milenkovic:
smallWig: parallel compression of RNA-seq WIG files. 173-180
- Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary:
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. 181-186 - Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Pseudoknots in RNA folding landscapes. 187-194
- Thomas J. Hardcastle:
Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology. 195-202
- Recep Colak, TaeHyung Kim, Hilal Kazan, Yoomi Oh, Miguel Cruz, Adan Valladares-Salgado, Jesus Peralta, Jorge Escobedo, Esteban J. Parra, Philip M. Kim, Anna Goldenberg:
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. 203-210 - Shuang Wang, Yuchen Zhang, Wenrui Dai, Kristin E. Lauter, Miran Kim, Yuzhe Richard Tang, Hongkai Xiong, Xiaoqian Jiang:
HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS. 211-218
- Miquel Marin-Riera, Miguel Brun-Usan, Roland Zimm, Tommi Välikangas, Isaac Salazar-Ciudad:
Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model. 219-225 - Yong-Cui Wang, Shi-Long Chen, Nai-Yang Deng, Yong Wang:
Computational probing protein-protein interactions targeting small molecules. 226-234 - Francesco Napolitano, Francesco Sirci, Diego Carrella, Diego di Bernardo:
Drug-set enrichment analysis: a novel tool to investigate drug mode of action. 235-241 - Allison N. Tegge, Nicholas Sharp, T. M. Murali:
Xtalk: a path-based approach for identifying crosstalk between signaling pathways. 242-251 - Pengyi Yang, Sean J. Humphrey, David E. James, Yee Hwa Yang, Raja Jothi:
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. 252-259 - Jiyang Yu, José Silva, Andrea Califano:
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. 260-267
- Nathaniel G. Mahieu, Jonathan L. Spalding, Gary J. Patti:
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis. 268-275 - Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo:
Cell line name recognition in support of the identification of synthetic lethality in cancer from text. 276-282
Genome Analysis
- Tomaz Berisa, Joseph K. Pickrell:
Approximately independent linkage disequilibrium blocks in human populations. 283-285 - Belinda Phipson, Jovana Maksimovic, Alicia Oshlack:
missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform. 286-288 - Bernat Gel, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A. Peinado, Roberto Malinverni:
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. 289-291 - Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde:
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. 292-294 - Donghyung Lee, Vernell S. Williamson, T. Bernard Bigdeli, Brien P. Riley, Bradley Todd Webb, Ayman H. Fanous, Kenneth S. Kendler, Vladimir I. Vladimirov, Silviu-Alin Bacanu:
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts. 295-297
- James Dunbar, Charlotte M. Deane:
ANARCI: antigen receptor numbering and receptor classification. 298-300 - Paul Hodor, Amandeep Chawla, Andrew Clark, Lauren Neal:
cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud. 301-303 - Sergey Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge:
ALP & FALP: C++ libraries for pairwise local alignment E-values. 304-305
- Devin K. Schweppe, Juan D. Chavez, James E. Bruce:
XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. 306-308
- Max Franz, Christian Tannus Lopes, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader:
Cytoscape.js: a graph theory library for visualisation and analysis. 309-311
- James M. Melott, John N. Weinstein, Bradley M. Broom:
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. 312-314
- Andreas Bartschat, Eduard Hübner, Markus Reischl, Ralf Mikut, Johannes Stegmaier:
XPIWIT - an XML pipeline wrapper for the Insight Toolkit. 315-317 - Pavel Krízek, Tomás Lukes, Martin Ovesný, Karel Fliegel, Guy M. Hagen:
SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. 318-320
Volume 32, Number 3, February 2016
Genome Analysis
- Ka-Chun Wong, Yue Li, Chengbin Peng:
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. 321-324
- Michael Knudsen, Dan Søndergaard, Claus Tofting-Olesen, Frederik T. Hansen, Ditlev Egeskov Brodersen, Christian N. S. Pedersen:
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. 325-329
Genome Analysis
- Shaolong Cao, Huaizhen Qin, Alexej Gossmann, Hong-Wen Deng, Yu-Ping Wang:
Unified tests for fine-scale mapping and identifying sparse high-dimensional sequence associations. 330-337
- Swati Kaushik, Anu G. Nair, Eshita Mutt, Hari Prasanna Subramanian, Ramanathan Sowdhamini:
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. 338-344 - Juliana S. Bernardes, Fabio R. J. Vieira, Gerson Zaverucha, Alessandra Carbone:
A multi-objective optimization approach accurately resolves protein domain architectures. 345-353 - Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards:
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. 354-361 - Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou:
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. 362-369
- Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou:
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. 370-377 - Haiyou Deng, Ya Jia, Yang Zhang:
3DRobot: automated generation of diverse and well-packed protein structure decoys. 378-387
- Isik Baris Fidaner, Ayca Cankorur-Cetinkaya, Duygu Dikicioglu, Betül Kirdar, Ali Taylan Cemgil, Stephen G. Oliver:
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data. 388-397
- Mehrshad Khosraviani, Morteza Saheb Zamani, Gholamreza Bidkhori:
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction. 398-408 - Tin Chi Nguyen, Rebecca Tagett, Michele Donato, Cristina Mitrea, Sorin Draghici:
A novel bi-level meta-analysis approach: applied to biological pathway analysis. 409-416 - Jeremy Hyrkas, Sophie Clayton, Francois Ribalet, Daniel Halperin, E. Virginia Armbrust, Bill Howe:
Scalable clustering algorithms for continuous environmental flow cytometry. 417-423 - Marcel Mischnik, Francesca Sacco, Jürgen Cox, Hans-Christoph Schneider, Matthias Schäfer, Manfred Hendlich, Daniel Crowther, Matthias Mann, Thomas Klabunde:
IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. 424-431
- Simon Baker, Ilona Silins, Yufan Guo, Imran Ali, Johan Högberg, Ulla Stenius, Anna Korhonen:
Automatic semantic classification of scientific literature according to the hallmarks of cancer. 432-440
Genome Analysis
- Mitchell J. Sullivan, Nathan L. Bachmann, Peter Timms, Adam Polkinghorne:
HapFlow: visualizing haplotypes in sequencing data. 441-443
- Johannes Köster:
Rust-Bio: a fast and safe bioinformatics library. 444-446 - Ibrahim Tanyalcin, Carla Al Assaf, Alexander Gheldof, Katrien Stouffs, Willy Lissens, Anna C. Jansen:
I-PV: a CIRCOS module for interactive protein sequence visualization. 447-449 - Parth Patel, S. Deepthi Ramachandruni, Atul Kakrana, Mayumi Nakano, Blake C. Meyers:
miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis. 450-452 - Ivan Borozan, Vincent Ferretti:
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads. 453-455 - Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Nabihoudine Ibouniyamine, Céline Noirot, Marie-Stéphane Trotard, Christine Gaspin, Christophe Klopp:
Jflow: a workflow management system for web applications. 456-458
- Danny Incarnato, Francesco Neri, Francesca Anselmi, Salvatore Oliviero:
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data. 459-461 - Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu:
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. 462-464
- Christoph Müssel, Florian Schmid, Tamara J. Blätte, Martin Hopfensitz, Ludwig Lausser, Hans A. Kestler:
BiTrinA - multiscale binarization and trinarization with quality analysis. 465-468
- Jun Chen, Allan C. Just, Joel Schwartz, Lifang Hou, Nadereh Jafari, Zhifu Sun, Jean-Pierre A. Kocher, Andrea A. Baccarelli, Xihong Lin:
CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. 469-471
- Weizhong Tu, Haoran Zhang, Juan Liu, Qian-Nan Hu:
BioSynther: a customized biosynthetic potential explorer. 472-473
- Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, Ina Koch:
The new protein topology graph library web server. 474-476 - Gaston K. Mazandu, Emile R. Chimusa, Mamana Mbiyavanga, Nicola J. Mulder:
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. 477-479
Volume 32, Number 4, February 2016
Structural Bioinformatics
- Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody:
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts. 481-489
Genome Analysis
- Haoyang Zeng, Tatsunori B. Hashimoto, Daniel D. Kang, David K. Gifford:
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. 490-496 - Uwe Baier, Timo Beller, Enno Ohlebusch:
Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform. 497-504
- M. Kroon, Eric-Wubbo Lameijer, N. Lakenberg, Jayne Y. Hehir-Kwa, D. T. Thung, P. Eline Slagboom, Joost N. Kok, Kai Ye:
Detecting dispersed duplications in high-throughput sequencing data using a database-free approach. 505-510 - Massimo Andreatta, Morten Nielsen:
Gapped sequence alignment using artificial neural networks: application to the MHC class I system. 511-517
- Sarah Bastkowski, Vincent Moulton, Andreas Spillner, Taoyang Wu:
The minimum evolution problem is hard: a link between tree inference and graph clustering problems. 518-522
- Alex Lewin, Habib Saadi, James E. Peters, Aida Moreno-Moral, James C. Lee, Kenneth G. C. Smith, Enrico Petretto, Leonardo Bottolo, Sylvia Richardson:
MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues. 523-532 - Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck:
EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes. 533-541
- Qiongshi Lu, Xinwei Yao, Yiming Hu, Hongyu Zhao:
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation. 542-548 - Emile R. Chimusa, Mamana Mbiyavanga, Gaston K. Mazandu, Nicola J. Mulder:
ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. 549-556 - Po-Ju Yao, Ren-Hua Chung:
SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. 557-562
- Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath:
An algorithm to detect and communicate the differences in computational models describing biological systems. 563-570 - Thorsten Will, Volkhard Helms:
PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. 571-578
- Chen Wang, Gang Hu, Kui Wang, Michal Brylinski, Lei Xie, Lukasz A. Kurgan:
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. 579-586
Genome Analysis
- Nathan C. Sheffield, Christoph Bock:
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. 587-589 - Heng Li:
BGT: efficient and flexible genotype query across many samples. 590-592 - Kathleen Oros Klein, Stepan Grinek, Sasha Bernatsky, Luigi Bouchard, Antonio Ciampi, Ines Colmegna, Jean-Philippe Fortin, Long Gao, Marie-France Hivert, Marie Hudson, Michael S. Kobor, Aurélie Labbe, Julia L. MacIsaac, Michael J. Meaney, Alexander M. Morin, Kieran J. O'Donnell, Tomi Pastinen, Marinus H. Van Ijzendoorn, Gregory Voisin, Celia M. T. Greenwood:
funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types. 593-595 - Jeffrey Staples, Lynette Ekunwe, Ethan M. Lange, James G. Wilson, Deborah A. Nickerson, Jennifer E. Below:
PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes. 596-598 - Cyril Denby Wilkes, Olivier Arnaiz, Linda Sperling:
ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. 599-601
- Mayya Sedova, Lukasz Jaroszewski, Adam Godzik:
Protael: protein data visualization library for the web. 602-604 - Yu-Wei Wu, Blake A. Simmons, Steven W. Singer:
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. 605-607
- François Chevenet, Jean-Philippe Doyon, Céline Scornavacca, Edwin Jacox, Emmanuelle Jousselin, Vincent Berry:
SylvX: a viewer for phylogenetic tree reconciliations. 608-610