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BMC Bioinformatics, Volume 16
Volume 16, 2015
- Guo-Xian Yu, Hailong Zhu, Carlotta Domeniconi:
Predicting protein functions using incomplete hierarchical labels. 1:1-1:12 - Wei Cheng, Shi Yu, Xiang Zhang, Wei Wang
:
Fast and robust group-wise eQTL mapping using sparse graphical models. 2:1-2:16 - Max Greenfeld, Jan-Willem van de Meent, Dmitri S. Pavlichin, Hideo Mabuchi
Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. 3:1-3:4 - Vikas Bansal, Ondrej Libiger:
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations. 4:1-4:11 - Martin Walker
Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study. 5:1-5:11 - Dimitar Hristovski
Biomedical question answering using semantic relations. 6:1-6:14 - Padmaja Natarajan, Marco Punta
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. 7:1-7:9 - Wandrille Duchemin, Pierre-Yves Dupont
HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species. 8:1-8:4 - Shi Yang Tan, Avirup Dutta
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. 9:1-9:13 - Eric Marinier, Daniel G. Brown, Brendan J. McConkey:
Pollux: platform independent error correction of single and mixed genomes. 10:1-10:12 - Xiaowei Wu, Ming-an Sun
Nonparametric Bayesian clustering to detect bipolar methylated genomic loci. 11:1-11:12 - Joana Vieira Silva
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. 12:1-12:12 - Robert J. Flassig
Rational selection of experimental readout and intervention sites for reducing uncertainties in computational model predictions. 13:1-13:13 - Zhong-Ru Xie
Decomposing the space of protein quaternary structures with the interface fragment pair library. 14:1-14:10 - Askar Obulkasim, Gerrit A. Meijer
Semi-supervised adaptive-height snipping of the hierarchical clustering tree. 15:1-15:11 - Nicholas Johnson, Huanan Zhang, Gang Fang, Vipin Kumar, Rui Kuang:
SubPatCNV: approximate subspace pattern mining for mapping copy-number variations. 16:1-16:12 - Frank Reinecke, Ravi Satya, John DiCarlo:
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls. 17:1-17:9 - José Torres, Andrés Domínguez, Joaquín Giménez, Ignacio Castelló, Joaquín Blázquez, Ignacio Espert:
Fast inexact mapping using advanced tree exploration on backward search methods. 18:1-18:11 - Carsten Kemena
MDAT- Aligning multiple domain arrangements. 19:1-19:7 - Ali Esmaili-Taheri, Mohammad Ganjtabesh:
ERD: a fast and reliable tool for RNA design including constraints. 20:1-20:11 - Sterling Sawaya, James Boocock
Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. 21:1-21:14 - Pilib Ó Broin
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. 22:1-22:12 - Timo Lassmann
TagDust2: a generic method to extract reads from sequencing data. 24:1-24:8 - Andrea Cassioli, Benjamin Bardiaux
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. 23:1-23:15 - Umesh K. Nandal, Wytze J. Vlietstra
Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. 25:1-25:11 - Robert Hoehndorf
Aber-OWL: a framework for ontology-based data access in biology. 26:1-26:9 - Humberto Sánchez
SFMetrics: an analysis tool for scanning force microscopy images of biomolecules. 27:1-27:9 - Natallia Kulik, Kristýna Slámová
Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility. 28:1-28:15 - Dong Seon Kim, Yoonsoo Hahn
The acquisition of novel N-glycosylation sites in conserved proteins during human evolution. 29:1-29:12 - Rowan G. Zellers, Robert A. Drewell, Jacqueline M. Dresch:
MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding. 30:1-30:14 - Jyoti Shankar
A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses. 31:1-31:18 - Federico Comoglio
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data. 32:1-32:10 - Shanshan Cheng
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. 33:1-33:12 - Juliana S. Bernardes, Fabio R. J. Vieira, Lygia Costa, Gerson Zaverucha:
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families. 34:1-34:14 - Mina Ozahata, Ester C. Sabino, Ricardo Diaz
Data-intensive analysis of HIV mutations. 35:1-35:23 - Ying Wang, Haiyan Hu, Xiaoman Li:
MBBC: an efficient approach for metagenomic binning based on clustering. 36:1-36:11 - Vittorio Fortino, Harri Alenius
BACA: bubble chArt to compare annotations. 37:1-37:5 - Chengyao Zhong, Zhiwei Hou, Jihua Huang, Qingdong Xie, Ying Zhong:
Mutations and CpG islands among hepatitis B virus genotypes in Europe. 38:1-38:11 - Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang:
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. 39:1-39:15 - Alison Callahan
An evidence-based approach to identify aging-related genes in Caenorhabditis elegans. 40:1-40:18 - Ramón Díaz-Uriarte
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. 41:1-41:26 - Aakrosh Ratan, Thomas L. Olson, Thomas P. Loughran, Webb Miller:
Identification of indels in next-generation sequencing data. 42:1-42:8 - Edgardo Mejía-Roa
NMF-mGPU: non-negative matrix factorization on multi-GPU systems. 43:1-43:12 - Jiajie Peng
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. 44:1-44:14 - Koki Tsuyuzaki
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. 45:1-45:17 - Sungho Won, Wonji Kim, Sungyoung Lee, Young Lee, Joohon Sung, Taesung Park:
Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants. 46:1-46:14 - Fengqiong Huang, James A. Macklin, Hong Cui
OTO: Ontology Term Organizer. 47:1-47:18 - Jiehuan Sun, Hongyu Zhao
The application of sparse estimation of covariance matrix to quadratic discriminant analysis. 48:1-48:9 - Michael Binns, Pedro de Atauri
Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes. 49:1-49:19 - David Kracht, Steffen Schober:
Insertion and deletion correcting DNA barcodes based on watermarks. 50:1-50:14 - Konrad Zych, Yang Li
Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. 51:1-51:8 - Lariza Laura de Oliveira, Paulo de Oliveira, Renato Tinós
A multiobjective approach to the genetic code adaptability problem. 52:1-52:20 - Ailith Pirie
The effect of rare variants on inflation of the test statistics in case-control analyses. 53:1-53:5 - Hui-Ling Huang, Yu-Chung Wu, Li-Jen Su, Yun-Ju Huang, Phasit Charoenkwan, Wen-Liang Chen, Hua-Chin Lee, William C. Chu, Shinn-Ying Ho
Discovery of prognostic biomarkers for predicting lung cancer metastasis using microarray and survival data. 54:1-54:14 - Àlex Bravo
Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research. 55:1-55:17 - Pablo A. Moreno
BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology. 56:1-56:7 - Sun Kim, Zhiyong Lu, W. John Wilbur:
Identifying named entities from PubMed®; for enriching semantic categories. 57:1-57:10 - Stanley Mbandi
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. 58:1-58:9 - Bie M. P. Verbist, Lieven Clement, Joke Reumers
ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering. 59:1-59:11 - Matthias Heinig
histoneHMM: Differential analysis of histone modifications with broad genomic footprints. 60:1-60:15 - Juan P. Steibel, Heng Wang, Ping-Shou Zhong:
A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium. 61:1-61:12 - A. Dhanasekaran, Jon L. Pearson, Balasubramanian Ganesan, Bart C. Weimer
Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction. 62:1-62:13 - Caleb K. Stein, Pingping Qu, Joshua Epstein, Amy Buros
Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat. 63:1-63:9 - Marcílio Carlos Pereira de Souto, Pablo A. Jaskowiak
Impact of missing data imputation methods on gene expression clustering and classification. 64:1-64:9 - Sandeep K. Kushwaha, Lokeshwaran Manoharan
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. 65:1-65:11 - Maochun Qin, Biao Liu, Jeffrey M. Conroy, Carl D. Morrison, Qiang Hu, Yubo Cheng, Mitsuko Murakami, Adekunle O. Odunsi, Candace S. Johnson, Lei Wei, Song Liu, Jianmin Wang:
SCNVSim: somatic copy number variation and structure variation simulator. 66:1-66:6 - Radu M. Suciu, Emir Aydin, Brian E. Chen:
GeneDig: a web application for accessing genomic and bioinformatics knowledge. 67:1-67:7 - Etienne Lord, Abdoulaye Baniré Diallo, Vladimir Makarenkov:
Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms. 68:1-68:19 - Matthias Scheuch, Dirk Höper
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. 69:1-69:17 - H. Robert Frost, Zhigang Li, Jason H. Moore
Spectral gene set enrichment (SGSE). 70:1-70:11 - Watcharaporn Tanchotsrinon, Chidchanok Lursinsap, Yong Poovorawan
A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition. 71:1-71:13 - Chuan Jiang
ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. 72:1-72:8 - Koen Herten, Matthew S. Hestand, Joris Robert Vermeesch
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. 73:1-73:6 - Wuming Gong, Naoko Koyano-Nakagawa
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. 74:1-74:16 - Yancy Lo, Hyun Min Kang, Matthew R. Nelson, Mohammad I. Othman, Stephanie L. Chissoe, Margaret G. Ehm, Gonçalo R. Abecasis, Sebastian Zöllner:
Comparing variant calling algorithms for target-exon sequencing in a large sample. 75:1-75:10 - Xi-Mei Zhang, Lin Guo, Mei-Hua Chi, Hong-Mei Sun, Xiao-Wen Chen:
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. 76:1-76:7 - Xiang Zhan, Andrew D. Patterson
Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data. 77:1-77:13 - Monika Michalovova
Fully automated pipeline for detection of sex linked genes using RNA-Seq data. 78:1-78:8 - Lars Snipen, Kristian Hovde Liland
micropanmicropan: an R-package for microbial pan-genomics. 79:1-79:8 - Bui Thang Ngoc, Tu Bao Ho, Tatsuo Kanda
A semi-supervised tensor regression model for siRNA efficacy prediction. 80:1-80:12 - Nathan Weinstein
A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva. 81:1-81:21 - Laxmi Parida, Niina Haiminen
SimBA: simulation algorithm to fit extant-population distributions. 82:1-82:9 - Nicolas Fiorini
USI: a fast and accurate approach for conceptual document annotation. 83:1-83:10 - André Lacour
Novel genetic matching methods for handling population stratification in genome-wide association studies. 84:1-84:12 - Lichun Ma
EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib. 85:1-85:10 - Rodrigo Liberal, Beata K. Lisowska, David J. Leak, John W. Pinney:
PathwayBooster: a tool to support the curation of metabolic pathways. 86:1-86:6 - Irene Pala:
BMC Bioinformatics reviewer acknowledgement 2014. 87:1-87:23 - Mohamed Mysara
NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. 88:1-88:10 - Scott Schuette, Bryan Piatkowski
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. 89:1-89:13 - Bill Hill, Richard A. Baldock
Constrained distance transforms for spatial atlas registration. 90:1-90:10 - Robert V. Baron, Yvette P. Conley
dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets. 91:1-91:15 - Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen:
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. 92:1-92:10 - Emna Harigua-Souiai
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis. 93:1-93:15 - Juyong Lee
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. 94:1-94:12 - Eugene Andres Houseman
Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective. 95:1-95:16 - Tianmin Wang
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. 96:1-96:15 - Xinan Yang
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. 97:1-97:21 - Julie M. Allen, Daisie I. Huang
aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data. 98:1-98:7 - Gabriele Arnulfo
Automatic segmentation of deep intracerebral electrodes in computed tomography scans. 99:1-99:12 - Tong Huo, Wei Liu, Yu Guo, Cheng Yang, Jianping Lin, Zihe Rao:
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. 100:1-100:9 - Calvin R. Chen
ProteinVolume: calculating molecular van der Waals and void volumes in proteins. 101:1-101:6 - Allison Chia-Yi Wu, Scott A. Rifkin
Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. 102:1-102:8 - Ninnutt Moonrin, Napat Songtawee, Siriluk Rattanabunyong, Surasuk Chunsrivirot, Wanwimon Mokmak, Sissades Tongsima
Understanding the molecular basis of EGFR kinase domain/MIG-6 peptide recognition complex using computational analyses. 103:1-103:16 - Syed Murtuza Baker
A unified framework for estimating parameters of kinetic biological models. 104:1-104:21 - John M. Gaspar, W. Kelley Thomas:
FlowClus: efficiently filtering and denoising pyrosequenced amplicons. 105:1-105:9 - Maud Tournoud, Audrey Larue, Marie-Angelique Cazalis
A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates. 106:1-106:15 - Nhung T. H. Nguyen
Wide-coverage relation extraction from MEDLINE using deep syntax. 107:1-107:11 - Joseph L. Herman, Ádám Novák, Rune B. Lyngsø, Adrienn Szabó, István Miklós, Jotun Hein:
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. 108:1-108:26 - Sawsan Khuri
Essentiality and centrality in protein interaction networks revisited. 109:1-109:8 - Yaojun Wang, Fei Yang, Peng Wu, Dongbo Bu, Shiwei Sun:
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction. 110:1-110:6 - Raluca Uricaru, Célia Michotey
YOC, A new strategy for pairwise alignment of collinear genomes. 111:1-111:16 - Fan Xu, Jing Yang, Jin Chen
Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression. 112:1-112:10 - Antonio Jimeno-Yepes
Feature engineering for MEDLINE citation categorization with MeSH. 113:1-113:12 - Kai Wang
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. 114:1-114:13 - Kimberly Glass
A network model for angiogenesis in ovarian cancer. 115:1-115:17 - Josef Laimer
MAESTRO - multi agent stability prediction upon point mutations. 116:1-116:13 - Tai-Yu Chiu, Ting-Chieh Hsu, Chia-Cheng Yen, Jia-Shung Wang:
Interpolation based consensus clustering for gene expression time series. 117:1-117:17 - Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg
IPO: a tool for automated optimization of XCMS parameters. 118:1-118:10 - Talha Bin Masood
CHEXVIS: a tool for molecular channel extraction and visualization. 119:1-119:19 - Vibha Pandey
Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera. 120:1-120:10 - Sa Kim, Tuong Nguyen, Na Seo, Seunghup Jung, Hyun An, David A. Mills, Jae Kim
Comparative proteomics: assessment of biological variability and dataset comparability. 121:1-121:10 - Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer
ContextMap 2: fast and accurate context-based RNA-seq mapping. 122:1-122:15 - Ivan Limongelli
PaPI: pseudo amino acid composition to score human protein-coding variants. 123:1-123:14 - James A. R. Dalton
Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism. 124:1-124:15 - Jimmy Van den Eynden
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. 125:1-125:12 - Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
KaBOB: ontology-based semantic integration of biomedical databases. 126:1-126:21 - Sony Malhotra, Oommen K. Mathew
DOCKSCORE: a webserver for ranking protein-protein docked poses. 127:1-127:6 - Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang, Tatsuya Akutsu
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs. 128:1-128:13 - Parisa Kordjamshidi, Dan Roth, Marie-Francine Moens:
Structured learning for spatial information extraction from biomedical text: bacteria biotopes. 129:1-129:15 - Michael Cantor, Henrik Nordberg, Tatyana Smirnova, Matthias Hess
Elviz - exploration of metagenome assemblies with an interactive visualization tool. 130:1-130:8 - Tiphaine C. Martin
coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns. 131:1-131:5 - Jessica L. Larson, Art B. Owen:
Moment based gene set tests. 132:1-132:17 - Amirhossein Manzourolajdad, Jonathan P. Arnold
Secondary structural entropy in RNA switch (Riboswitch) identification. 133:1-133:77 - Daniel Bottomly, Beth Wilmot, Shannon K. McWeeney:
plethy: management of whole body plethysmography data in R. 134:1-134:5 - Corinna Vehlow, David P. Kao
Visual analysis of biological data-knowledge networks. 135:1-135:15 - Jad Abbass
Customised fragments libraries for protein structure prediction based on structural class annotations. 136:1-136:13 - Laurent Modolo, Emmanuelle Lerat
UrQt: an efficient software for the Unsupervised Quality trimming of NGS data. 137:1-137:8 - George Tsatsaronis
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition. 138:1-138:28 - Y-h. Taguchi
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. 139:1-139:26 - Michal Dabrowski
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. 140:1-140:14 - Hieu T. Nim
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. 141:1-141:7 - Filipa Pereira
Pydna: a simulation and documentation tool for DNA assembly strategies using python. 142:1-142:10 - Maria Klodt, Katja Herzog, Reinhard Töpfer, Daniel Cremers
Field phenotyping of grapevine growth using dense stereo reconstruction. 143:1-143:11 - Benjamin Hofner
Controlling false discoveries in high-dimensional situations: boosting with stability selection. 144:1-144:17 - Peijie Lin, Sylvain Forêt, Susan R. Wilson, Conrad J. Burden
Estimation of the methylation pattern distribution from deep sequencing data. 145:1-145:11 - Xiao-Fei Zhang, Le Ou-Yang, Yuan Zhu, Meng-Yun Wu, Dao-Qing Dai:
Determining minimum set of driver nodes in protein-protein interaction networks. 146:1-146:13 - Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye, Shuiwang Ji
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain. 147:1-147:10 - Alia Dehman, Christophe Ambroise, Pierre Neuvial
Performance of a blockwise approach in variable selection using linkage disequilibrium information. 148:1-148:14 - Yan Xu
Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary. 149:1-149:10 - Claudia Angelini
Is this the right normalization? A diagnostic tool for ChIP-seq normalization. 150:1-150:15 - Michele Fratello, Angela Serra
A multi-view genomic data simulator. 151:1-151:15 - Ailan F. Arenas
MSCA: a spectral comparison algorithm between time series to identify protein-protein interactions. 152:1-152:9 - Mihaly Varadi
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. 153:1-153:9 - Tristan Bitard-Feildel
Domain similarity based orthology detection. 154:1-154:11 - Ernest D. Benavente
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. 155:1-155:5 - Catalina V. Anghel
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. 156:1-156:11 - Patrick Ernst, Amy Siu, Gerhard Weikum:
KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences. 157:1-157:13 - Nurlisa Yusuf, Ammar Zakaria
In-vitro diagnosis of single and poly microbial species targeted for diabetic foot infection using e-nose technology. 158:1-158:12 - Michaël Vyverman, Bernard De Baets
A Long Fragment Aligner called ALFALFA. 159:1-159:11 - Héloïse Gauvin, Jean-François Lefebvre, Claudia Moreau, Eve-Marie Lavoie, Damian Labuda, Hélène Vézina, Marie-Hélène Roy-Gagnon
GENLIB: an R package for the analysis of genealogical data. 160:1-160:10 - Ahmet Ay, Dihong Gong, Tamer Kahveci:
Hierarchical decomposition of dynamically evolving regulatory networks. 161:1-161:19 - Yasser B. Ruiz-Blanco
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. 162:1-162:15 - Gundián M. de Hijas-Liste, Eva Balsa-Canto
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. 163:1-163:13 - Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich, Elhanan Borenstein:
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. 164:1-164:6 - Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl J. Schmidt
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways. 165:1-165:7 - Vasily Sachnev, Saras Saraswathi, Rashid Niaz, Andrzej Kloczkowski, Suresh Sundaram:
Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer. 166:1-166:12 - Carles Hernandez-Ferrer
affy2svaffy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. 167:1-167:11 - Jesse D. Bloom
Software for the analysis and visualization of deep mutational scanning data. 168:1-168:13 - Henry Heberle
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. 169:1-169:7 - Daniel E. Russ
HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs. 170 - Saeed Saberi, Pau Farré, Olivier Cuvier
Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data. 171:1-171:12 - Jonathan R. Karr
NetworkPainter: dynamic intracellular pathway animation in Cytobank. 172:1-172:7 - Wael Karain, Nael Qaraeen:
Weighted protein residue networks based on joint recurrences between residues. 173:1-173:11 - Lun Hu, Keith C. C. Chan
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. 174:1-174:16 - Vadim Nazarov
tcR: an R package for T cell receptor repertoire advanced data analysis. 175:1-175:5 - José Lourenço
MANTIS: an R package that simulates multilocus models of pathogen evolution. 176:1-176:7 - Jonathan Sanders, Anil Singh, Gabriella Sterne
Learning-guided automatic three dimensional synapse quantification for drosophila neurons. 177:1-177:13 - Stefan Janssen
Ambivalent covariance models. 178:1-178:17 - Susan Higashi, Cyril Fournier
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. 179:1-179:14 - Felix Schönenberger, Anja Deutzmann
Discrimination of cell cycle phases in PCNA-immunolabeled cells. 180:1-180:10 - Juan Esquivel-Rodríguez
Navigating 3D electron microscopy maps with EM-SURFER. 181:1-181:9 - Thomas Lui, Nancy Tsui, Lawrence Wing-Chi Chan, Cesar Wong
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. 182:1-182:15 - Lander Willem
Optimizing agent-based transmission models for infectious diseases. 183:1-183:10 - Basel Abu-Jamous, Rui Fa, David Roberts
UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets. 184:1-184:19 - Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu:
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. 185:1-185:15 - Sejal Patel, Paola Roncaglia
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. 186:1-186:18 - Biena Mathew, Alexander Schmitz, Silvia Muñoz-Descalzo
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. 187:1-187:14 - Yongpeng Zhang, Linsen Li, Yanli Yang, Xiao Yang, Shan He, Zexuan Zhu:
Light-weight reference-based compression of FASTQ data. 188:1-188:8 - Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak K. Shah
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. 189:1-189:9 - Julien Y. Dutheil, Emeric Figuet:
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. 190:1-190:11 - Patrick Putnam, Philip A. Wilsey, Ge Zhang:
Clotho: addressing the scalability of forward time population genetic simulation. 191:1-191:14 - Haoyu Cheng
BitMapper: an efficient all-mapper based on bit-vector computing. 192:1-192:16 - Rachel Schwartz
A composite genome approach to identify phylogenetically informative data from next-generation sequencing. 193:1-193:10 - Jesper Gådin, Ferdinand van't Hooft, Per Eriksson
AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. 194:1-194:6 - Fleur Jeanquartier
Integrated web visualizations for protein-protein interaction databases. 195:1-195:16 - Sean Robinson, Garique Glonek, Inge Koch
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models. 196:1-196:9 - Jan Ruijter, Steve Lefever, Jasper Anckaert
RDML-Ninja and RDMLdb for standardized exchange of qPCR data. 197:1-197:7 - Padmini Srinivasan
Ferret: a sentence-based literature scanning system. 198:1-198:11 - Putri W. Novianti
Factors affecting the accuracy of a class prediction model in gene expression data. 199:1-199:12 - Anirban Bhar
Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes. 200:1-200:19 - Dániel Kozma, Gábor E. Tusnády:
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. 201:1-201:9 - Yang Liu, Francesca Chiaromonte, Howard Ross, Raunaq Malhotra, Daniel Elleder, Mary Poss:
Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. 202:1-202:14 - Bruno Fosso
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. 203:1-203:11 - Denis Machado
YBYRÁ facilitates comparison of large phylogenetic trees. 204:1-204:4 - Hilde Vinje, Kristian Hovde Liland
Comparing K-mer based methods for improved classification of 16S sequences. 205:1-205:13 - Santiago Ríos
GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors. 206:1-206:11 - Rocío Espada
Capturing coevolutionary signals inrepeat proteins. 207:1-207:10 - Cheng Jia, Weihua Guan, Amy Yang, Rui Xiao, W. Tang, Christine Moravec, Kenneth Margulies, Thomas P. Cappola, Mingyao Li, Chun Li
MetaDiff: differential isoform expression analysis using random-effects meta-regression. 208:1-208:12 - Todd A. Gillette, Parsa Hosseini, Giorgio A. Ascoli:
Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment. 209:1-209:17 - S. M. Ashiqul Islam
PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides. 210:1-210:11 - Catherine A. Lozupone, Rob Knight
The unifrac significance test is sensitive to tree topology. 211:1-211:3 - Jonah Hocum, Logan Battrell, Ryan Maynard, Jennifer E. Adair
VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. 212:1-212:5 - Maja Temerinac-Ott
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. 213:1-213:10 - Andrew D. Hellicar, Ashfaqur Rahman
Machine learning approach for pooled DNA sample calibration. 214:1-214:11 - Pavel Balazki
MONALISA for stochastic simulations of Petri net models of biochemical systems. 215:1-215:11 - Todd A. Gillette, Giorgio A. Ascoli:
Topological characterization of neuronal arbor morphology via sequence representation: I - motif analysis. 216:1-216:15 - Dongmei Li, Zidian Xie, Marc A. Le Pape
An evaluation of statistical methods for DNA methylation microarray data analysis. 217:1-217:20 - Theodore Gibbons, Stephen M. Mount, Endymion Cooper
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. 218:1-218:14 - Xiaoping Cheng, Hongmin Cai
Optimal combination of feature selection and classification via local hyperplane based learning strategy. 219:1-219:10 - Ke Hu, Angela Ting, Jing Li
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. 220:1-220:9 - Damien Farrell
Epitopemap: a web application for integrated whole proteome epitope prediction. 221:1-221:6 - Minho Chae, Charles G. Danko
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. 222:1-222:16 - Soyeon Ahn, Haris Vikalo:
Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm. 223:1-223:10 - Stephen Hartley, James C. Mullikin:
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. 224:1-224:7 - Julian Gingold
Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. 225:1-225:20 - Henry Ogoe
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. 226:1-226:15 - Hani Z. Girgis:
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. 227:1-227:19 - Jay Khurana, Jay Reeder, Antony Shrimpton, Juilee Thakar:
GESPA: classifying nsSNPs to predict disease association. 228:1-228:10 - Albina Asadulina, Markus Conzelmann, Elizabeth Williams
Object-based representation and analysis of light and electron microscopic volume data using Blender. 229:1-229:9 - Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman
Sealer: a scalable gap-closing application for finishing draft genomes. 230:1-230:8 - Nicholas E. Newell
Mapping side chain interactions at protein helix termini. 231:1-231:21 - Jose Samaniego Castruita, Marie Zepeda Mendoza, Ross Barnett
Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. 232:1-232:13 - Jittisak Senachak, Supapon Cheevadhanarak, Apiradee Hongsthong:
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1. 233:1-233:9 - Claudia Caudai
Inferring 3D chromatin structure using a multiscale approach based on quaternions. 234:1-234:11 - Howard Huang, James C. Mullikin, Nancy F. Hansen:
Evaluation of variant detection software for pooled next-generation sequence data. 235:1-235:9 - Benjamin Albrecht:
Computing all hybridization networks for multiple binary phylogenetic input trees. 236:1-236:15 - Mihai Pop
Use and mis-use of supplementary material in science publications. 237:1-237:4 - David Quigley:
Equalizer reduces SNP bias in Affymetrix microarrays. 238:1-238:8 - Itziar Frades
Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis. 239:1-239:13 - Mathias Kuhring
SuRankCo: supervised ranking of contigs in de novo assemblies. 240:1-240:7 - Fei Huang, Christopher J. Oldfield, Bin Xue, Wei-Lun Hsu, Jingwei Meng, Xiaowen Liu, Li Shen
Erratum to: Improving protein order-disorder classification using charge-hydropathy plots. 241:1-241:2 - Nicolas Duforet-Frebourg, Lucie Gattepaille, Michael G. B. Blum
HaploPOP: a software that improves population assignment by combining markers into haplotypes. 242:1-242:8 - Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla
Simulated unbound structures for benchmarking of protein docking in the Dockground resource. 243:1-243:6 - Binbin Lai
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads. 244:1-244:14 - Fang Yu, Ming-Hui Chen, Lynn Kuo, Heather Talbott
Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications. 245:1-245:15 - Rallis Karamichalis, Lila Kari, Stavros Konstantinidis
An investigation into inter- and intragenomic variations of graphic genomic signatures. 246:1-246:22 - Carlos Sanquetta, Jaime Wojciechowski, Ana Paula Dalla Corte
Comparison of data mining and allometric model in estimation of tree biomass. 247:1-247:9 - Mirwaes Wahabzada, Stefan Paulus
Automated interpretation of 3D laserscanned point clouds for plant organ segmentation. 248:1-248:11 - Huizhu Ren, Ying Shen:
RNA-binding residues prediction using structural features. 249:1-249:10 - Óscar Torreño Tirado, Oswaldo Trelles:
Breaking the computational barriers of pairwise genome comparison. 250:1-250:13 - Jean-Pierre Flandrois
leBIBI QBPP : a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. 251:1-251:12 - Susanne Schaller, Johannes Weinberger, Raúl Jiménez-Heredia, Martin Danzer, Rainer Oberbauer, Christian Gabriel
ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data. 252:1-252:10 - Petr Cech
MultiSETTER: web server for multiple RNA structure comparison. 253:1-253:8 - Theodore Roman, Amir Nayyeri, Brittany Fasy
A simplicial complex-based approach to unmixing tumor progression data. 254:1-254:17 - Andrew Ndhlovu
Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix. 255:1-255:14 - Clovis Galiez, François Coste
Amplitude spectrum distance: measuring the global shape divergence of protein fragments. 256:1-256:16 - Jose A. Perea, Anastasia Deckard
SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. 257:1-257:12 - Aaron T. L. Lun, Gordon K. Smyth
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. 258:1-258:11 - Mohammad R. Nezami Ranjbar, Cristina Di Poto, Yue Joseph Wang, Habtom W. Ressom:
SIMAT: GC-SIM-MS data analysis tool. 259:1-259:12 - Yi Wang, Yi Li, Hongbao Cao, Momiao Xiong, Yin Yao Shugart, Li Jin
Efficient test for nonlinear dependence of two continuous variables. 260:1-260:8 - Angela Serra
MVDA: a multi-view genomic data integration methodology. 261:1-261:13 - Elsa Bernard
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. 262:1-262:10 - Yugyung Lee, Alok Khemka, Gayathri Acharya, Namita Giri, Chi Lee:
A cascade computer model for mocrobicide diffusivity from mucoadhesive formulations. 263:1-263:12 - Edward Meeds, Michael Chiang
POPE: post optimization posterior evaluation of likelihood free models. 264:1-264:20 - Xiaoyan Ma, Daphne Ezer
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors. 265:1-265:13 - Marc Perea, Ivar Lugtenburg, Eduardo Mayol
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. 266:1-266:6 - Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. 267:1-267:12 - Aram Avila-Herrera, Katherine S. Pollard:
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. 268:1-268:18 - Peter Jehl, Fabian Sievers, Desmond G. Higgins:
OD-seq: outlier detection in multiple sequence alignments. 269:1-269:11 - Jónathan Heras
GelJ - a tool for analyzing DNA fingerprint gel images. 270:1-270:8 - Guo-Xian Yu, Hailong Zhu, Carlotta Domeniconi, Jiming Liu:
Predicting protein function via downward random walks on a gene ontology. 271:1-271:13 - Jacob A. Turner, Christopher Bolen, Derek Blankenship:
Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates. 272:1-272:12 - Shun Yao, Shinjae Yoo
Prior knowledge driven Granger causality analysis on gene regulatory network discovery. 273:1-273:18 - Theodore Gibbons, Stephen M. Mount, Endymion Cooper
Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. 274:1-274:2 - Ashley J. Waardenberg
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. 275:1-275:8 - Agnieszka Rybarczyk
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. 276:1-276:12 - Marc W. Schmid
HiCdat: a fast and easy-to-use Hi-C data analysis tool. 277:1-277:6 - Soohyun Lee
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. 278:1-278:16 - Gennaro Gambardella
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. 279:1-279:9 - Akito Taneda:
Multi-objective optimization for RNA design with multiple target secondary structures. 280:1-280:20 - Gregory K. Farrant
WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. 281:1-281:13 - Jing Tong, Jimin Pei, Nick V. Grishin:
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. 282:1-282:7 - Abel Folch-Fortuny
Enabling network inference methods to handle missing data and outliers. 283:1-283:12 - Sonja Holl, Yassene Mohammed
Scientific workflow optimization for improved peptide and protein identification. 284:1-284:13 - Eman Badr
CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements. 285:1-285:15 - Paul K. Korir
Seq-ing improved gene expression estimates from microarrays using machine learning. 286:1-286:11 - Leonardo Ricci
Statistical analysis of a Bayesian classifier based on the expression of miRNAs. 287:1-287:12 - Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk:
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. 288:1-288:14 - Michele Pelosi, Marco Alfò
Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts. 289:1-289:17 - Andres H. Gutiérrez
Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method. 290:1-290:11 - Argiris Sakellariou, George M. Spyrou:
mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics. 291:1-291:9 - Sha Zhu, James H. Degnan, Sharyn Goldstien, Bjarki Eldon
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 292:1-292:7 - Hongtai Huang, Andrea Fava
A methodology for exploring biomarker - phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations. 293:1-293:15 - Veronika Weyer, Harald Binder
A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures. 294:1-294:12 - Kai Bernd Stadermann
SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. 295:1-295:10 - Ward C. Wheeler:
Phylogenetic network analysis as a parsimony optimization problem. 296:1-296:9 - Altan Kara
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. 297:1-297:9 - Keith Inman
Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles. 298:1-298:10 - Abdulkadir Elmas
Reconstruction of novel transcription factor regulons through inference of their binding sites. 299:1-299:10 - Rok Blagus, Lara Lusa
Boosting for high-dimensional two-class prediction. 300:1-300:17 - Li C. Xia
Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. 301:1-301:14 - Hui-Wen Huang, Yao-Shen Chen, Jeff Chen, Po-Liang Lu, Yung-Cheng Lin, Bao-Chen Chen, Li-Chiu Chou, Chu-Feng Wang, Hui-Ju Su, Yi-Chien Huang, Yong-Ying Shi, Hsiu-Lin Chen, Bintou Sanno-Duanda, Tsi-Shu Huang, Kuei-Hsiang Lin, Yu-Chang Tyan, Pei-Yu Chu:
Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2. 302:1-302:9 - Edward Daniel
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. 303:1-303:6 - Kristopher Standish, Tristan M. Carland, Glenn K. Lockwood
Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies. 304:1-304:14 - Askar Obulkasim, Maarten Fornerod
Subtype prediction in pediatric acute myeloid leukemia: classification using differential network rank conservation revisited. 305:1-305:11 - Nilzair M. Barreto, Karina S. Machado
Inference of regulatory networks with a convergence improved MCMC sampler. 306:1-306:10 - Adam Richards, Anthony Herrel
htsint: a Python library for sequencing pipelines that combines data through gene set generation. 307:1-307:7 - Björn-Oliver Gohlke, Tim Overkamp, Anja Richter, Antje Richter, Peter T. Daniel, Bernd Gillissen
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib. 308:1-308:9 - Saskia Freytag
Systematic noise degrades gene co-expression signals but can be corrected. 309:1-309:17 - Federico Andrea Santoni
CATCHing putative causative variants in consanguineous families. 310:1-310:5 - Afshin Esmaeili, Timothy Davison, Andrew Wu, Joenel Alcantara
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli. 311:1-311:23 - Pau Bellot, Catharina Olsen
NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference. 312:1-312:15 - Kamal Kishore
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. 313:1-313:11 - Caroline König
Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors. 314:1-314:14 - Samreen Anjum, Sandro Morganella
VEGAWES: variational segmentation on whole exome sequencing for copy number detection. 315:1-315:10 - Tsuyoshi Kato, Raissa Relator
Segmental HOG: new descriptor for glomerulus detection in kidney microscopy image. 316:1-316:16 - Mauricio Guevara-Souza, Edgar E. Vallejo
A computer simulation model of Wolbachia invasion for disease vector population modification. 317:1-317:14 - Hugo López-Fernández
Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. 318:1-318:12 - Mohieddin Jafari
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. 319:1-319:9 - Stefan Lang, Amol Ugale, Eva Erlandsson, Göran Karlsson, David Bryder
SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data. 320:1-320:4 - Daiki Okada, Fumihiko Ino, Kenichi Hagihara:
Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences. 321:1-321:15 - Erik Wright:
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. 322:1-322:14 - Xiao Ding
DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection. 323:1-323:12 - Guy Allard, Feargal Ryan
SPINGO: a rapid species-classifier for microbial amplicon sequences. 324:1-324:8 - Qingzhen Hou
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. 325:1-325:12 - Md Mahmudul Hasan, Tamer Kahveci:
Indexing a protein-protein interaction network expedites network alignment. 326:1-326:17 - Da Ruan, Alastair Young
Differential analysis of biological networks. 327:1-327:13 - Pedro Lopes, José Luís Oliveira:
An automated real-time integration and interoperability framework for bioinformatics. 328:1-328:13 - Jacob B. Hall, Jessica Cooke Bailey
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. 329:1-329:9 - Peter Bajcsy
Survey statistics of automated segmentations applied to optical imaging of mammalian cells. 330:1-330:28 - Lingnan Ma, Maochun Qin, Biao Liu, Qiang Hu, Lei Wei, Jianmin Wang, Song Liu:
cnvCurator: an interactive visualization and editing tool for somatic copy number variations. 331:1-331:8 - Xuejun Liu, Xinxin Shi, Chunlin Chen, Li Zhang:
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate. 332:1-332:13 - Jorge Júlvez:
A straightforward method to compute average stochastic oscillations from data samples. 333:1-333:17 - Michaela Bayerlová, Klaus Jung, Frank Kramer
Comparative study on gene set and pathway topology-based enrichment methods. 334:1-334:15 - Joe G. Greener
AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis. 335:1-335:7 - Magdalena A. Machnicka
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. 336:1-336:16 - Jilong Li, Renzhi Cao, Jianlin Cheng
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. 337:1-337:11 - Jackson Nowotny, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. 338:1-338:19 - Xian Jin, Mahendra Awale, Michaël Zasso, Daniel Kostro, Luc Patiny
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. 339:1-339:15 - Yining Wang
Whole genome SNP genotype piecemeal imputation. 340:1-340:11 - Alexandra Simader, Bernhard Kluger, Nora Katharina Nicole Neumann, Christoph Bueschl
QCScreen: a software tool for data quality control in LC-HRMS based metabolomics. 341:1-341:9 - Gongning Luo
Neuron anatomy structure reconstruction based on a sliding filter. 342:1-342:19 - Jizhong Deng, Huasheng Huang, Xiaoli Yu, Ji Jin, Weisen Lin, Fagen Li, Zhijiao Song, Mei Li, Siming Gan:
DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid. 343:1-343:8 - Kimmo Kartasalo
CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels. 344:1-344:23 - Sven Thiele
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. 345:1-345:13 - Pietro di Lena, Giacomo Domeniconi
GOTA: GO term annotation of biomedical literature. 346:1-346:13 - Peipei Li, Yongjun Piao, Ho Shon, Keun Ho Ryu:
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. 347:1-347:9 - Matej Holec, Ondrej Kuzelka
Novel gene sets improve set-level classification of prokaryotic gene expression data. 348:1-348:8 - Marzia A. Cremona
Peak shape clustering reveals biological insights. 349:1-349:18 - Ivana Ihnatova
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. 350:1-350:8 - Mingming Liu, Layne T. Watson, Liqing Zhang:
HMMvar-func: a new method for predicting the functional outcome of genetic variants. 351:1-351:10 - Saulo Aflitos
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. 352:1-352:10 - Liliana Angeles-Martinez, Constantinos Theodoropoulos
A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems. 353:1-353:15 - Sara R. Selitsky, Praveen Sethupathy:
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. 354:1-354:13 - Irene Vrbik, David A. Stephens
The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data. 355:1-355:9 - Xizeng Mao, Qin Ma
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. 356:1-356:9 - Steven H. Wu
Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals. 357:1-357:12 - Gregory Ditzler, J. Calvin Morrison, Yemin Lan, Gail Rosen
Fizzy: feature subset selection for metagenomics. 358:1-358:8 - Clemens Zvácek, Gerald Friedrichs, Leonhard Heizinger
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. 359:1-359:8 - Jun Meng, Dong Liu, Yushi Luan:
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. 361:1-361:11 - Min Tang
Evaluation of methods for differential expression analysis on multi-group RNA-seq count data. 360:1-360:14 - Rok Blagus, Lara Lusa
Joint use of over- and under-sampling techniques and cross-validation for the development and assessment of prediction models. 363:1-363:10 - Michael A. Peabody, Thea Van Rossum
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. 362:1-362:19 - Preston V. Lee
BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms. 364:1-364:7 - Wen Zhang
Predicting drug side effects by multi-label learning and ensemble learning. 365:1-365:11 - Naresh Doni Jayavelu, Lasse Aasgaard, Nadav S. Bar:
Iterative sub-network component analysis enables reconstruction of large scale genetic networks. 366:1-366:13 - Paul Müller
ODTbrain: a Python library for full-view, dense diffraction tomography. 367:1-367:9 - Mark-Anthony Bray, Anne E. Carpenter
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. 369:1-369:7 - Aurélie Pirayre
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference. 368:1-368:12 - Maurits Evers, Michael Huttner
miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. 370:1-370:10 - Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems. 371:1 - Andrew E. Jaffe
Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. 372:1-372:10 - Mark R. Segal, Henrik Bengtsson
Reconstruction of 3D genome architecture via a two-stage algorithm. 373:1-373:10 - Cécile Monat
TOGGLE: toolbox for generic NGS analyses. 374:1-374:8 - Ralf Eggeling
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. 375:1-375:15 - Teri Evans
AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts. 376:1-376:11 - Joan Maynou, Erola Pairo, Santiago Marco
Sequence information gain based motif analysis. 377:1-377:13 - Victor Mocioiu, Sandra Ortega-Martorell
From raw data to data-analysis for magnetic resonance spectroscopy - the missing link: jMRUI2XML. 378:1-378:11 - Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie M. P. Verbist, Joke Reumers
QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. 379:1-379:14 - David M. Kristensen, Usman Saeed, Dmitrij Frishman, Eugene V. Koonin:
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. 380:1-380:11 - James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. 381:1-381:9 - António Ribeiro
An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome. 382:1-382:16 - David Edwards:
Two molecular measures of relatedness based on haplotype sharing. 383:1-383:11 - Thu-Hien To, Edwin Jacox, Vincent Ranwez
A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality. 384:1-384:15 - Maria Sorokina
A new network representation of the metabolism to detect chemical transformation modules. 385:1-385:9 - Xiao Zhu
misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads. 386:1-386:16 - Martin Nettling, Hendrik Treutler
DiffLogo: a comparative visualization of sequence motifs. 387:1-387:9 - Elena Landoni
Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation. 388:1-388:10 - Robert Kleinkauf, Torsten Houwaart
antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. 389:1-389:7 - Mohammed AlQuraishi
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. 390:1-390:19 - Bart Broeckx
An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors. 391:1-391:7 - Anastasiya Lapytsko, Gabriel Kollarovic
FoCo: a simple and robust quantification algorithm of nuclear foci. 392:1-392:13 - Mufleh Al-Shatnawi, M. Omair Ahmad, M. N. S. Swamy:
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions. 393:1-393:11 - Linda Dib, Xavier Meyer, Panu Artimo, Vassilios Ioannidis
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree. 394:1-394:7 - Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee, Kwong-Sak Leung:
High-order dynamic Bayesian Network learning with hidden common causes for causal gene regulatory network. 395:1-395:28 - Chen Yang, Daniel Niedieker
Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections. 396:1-396:14 - Michael Chiang
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. 397:1-397:19 - Dhany Saputra, Simon Rasmussen
Reads2Type: a web application for rapid microbial taxonomy identification. 398:1-398:10 - Tahsin M. Kurç, Xin Qi, Daihou Wang, Fusheng Wang
Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies. 399:1-399:21 - Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. 400:1-400:21 - Guillaume Rivière, Christophe Klopp
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. 401:1-401:12 - Hongchu Wang, Xuehai Hu:
Accurate prediction of nuclear receptors with conjoint triad feature. 402:1-402:13 - Gengxin Li, Hongyu Zhao
M3-S: a genotype calling method incorporating information from samples with known genotypes. 403:1-403:9 - Laval Jacquin, Tuong-Vi Cao, Cécile Grenier, Nourollah Ahmadi
DHOEM: a statistical simulation software for simulating new markers in real SNP marker data. 404:1-404:8 - Akram Yazdani, Azam Yazdani, Eric Boerwinkle:
Rare variants analysis using penalization methods for whole genome sequence data. 405:1-405:8 - Elena Rivas, Sean R. Eddy:
Parameterizing sequence alignment with an explicit evolutionary model. 406:1-406:23 - Xiaoli Gao:
Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations. 407:1-407:14 - Filippo Del Vecchio
Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model. 408:1-408:11 - Flavio Lichtenstein
MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets. 409:1-409:19 - Roozbeh Dehghannasiri
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. 410:1 - Paul Aiyetan
MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development. 411:1-411:7 - Bogdan Belean
Unsupervised image segmentation for microarray spots with irregular contours and inner holes. 412:1-412:12 - Sini Rautio
MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis. 413:1-413:12 - Christian Allende, Erik Sohn, Cedric Little
Treelink: data integration, clustering and visualization of phylogenetic trees. 414:1-414:6 - Matteo Gabetta, Ivan Limongelli
BigQ: a NoSQL based framework to handle genomic variants in i2b2. 415:1-415:11 - Andy Kilianski
Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. 416:1-416:12 - Suyu Mei, Hao Zhu:
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. 417:1-417:18
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