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BMC Bioinformatics, Volume 18
Volume 18, Number 1, December 2017
- Dongmei Li
, Zidian Xie, Martin S. Zand, Thomas Fogg, Timothy D. Dye
Bon-EV: an improved multiple testing procedure for controlling false discovery rates. 1:1-1:10 - Annika Röhl, Alexander Bockmayr
A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks. 2:1-2:10 - Johannes W. R. Martini
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE). 3:1-3:16 - Xinyan Zhang
Negative binomial mixed models for analyzing microbiome count data. 4:1-4:10 - Davoud Torkamaneh
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. 5:1-5:7 - Fabio Cumbo
TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas. 6:1-6:9 - Michael Piechotta, Emanuel Wyler
JACUSA: site-specific identification of RNA editing events from replicate sequencing data. 7:1-7:15 - Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. 8:1-8:15 - Milos D. Radovic, Mohamed F. Ghalwash
Minimum redundancy maximum relevance feature selection approach for temporal gene expression data. 9:1-9:14 - Shirin Taghipour, Peyman Zarrineh, Mohammad Ganjtabesh, Abbas Nowzari-Dalini:
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. 10:1-10:9 - Robin Kobus, Christian Hundt, André Müller
Accelerating metagenomic read classification on CUDA-enabled GPUs. 11:1-11:10 - Fabian Grandke
PERGOLA: fast and deterministic linkage mapping of polyploids. 12:1-12:9 - Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson
T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. 13:1-13:8 - Thomas S. Wingo
MPD: multiplex primer design for next-generation targeted sequencing. 14:1-14:5 - Jinyu Li, Jörg Vervoorts
Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant. 15:1-15:9 - Sameh Eid
KinMap: a web-based tool for interactive navigation through human kinome data. 16:1-16:6 - Nicolas Bosc
The use of novel selectivity metrics in kinase research. 17:1-17:12 - Wen Zhang
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data. 18:1-18:12 - Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann:
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. 19:1-19:8 - Hashem A. Shihab, Mark F. Rogers, Michael Ferlaino, Colin Campbell, Tom R. Gaunt
GTB - an online genome tolerance browser. 20:1-20:6 - Reedik Mägi
SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes. 25:1-25:8 - Roberto A. Barrero
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. 26:1-26:12 - Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. 27:1-27:13 - Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi:
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. 30:1-30:11 - Wei-Sheng Wu, Meng-Jhun Jhou:
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. 31:1-31:10 - Nikhil Cheerla
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. 32:1-32:11 - Marco Albrecht
TTCA: an R package for the identification of differentially expressed genes in time course microarray data. 33:1-33:11 - Sylvester Olubolu Orimaye
Predicting probable Alzheimer's disease using linguistic deficits and biomarkers. 34:1-34:13 - Yi-Pin Lai, Liang-Bo Wang
iGC - an integrated analysis package of gene expression and copy number alteration. 35:1-35:9 - Carles Hernandez-Ferrer
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. 36:1-36:7 - Rashmi R. Hazarika
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. 37:1-37:9 - Claire R. Williams
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. 38:1-38:12 - Yiding Lu, Yufan Guo, Anna Korhonen:
Link prediction in drug-target interactions network using similarity indices. 39:1-39:9 - Noah Eyal-Altman
PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine. 40:1-40:7 - N. Ari Wijetunga, Andrew D. Johnston
SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. 41:1-41:13 - Fan Zhang, Patrick Flaherty
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. 45:1-45:10 - Tsukasa Fukunaga
Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants. 46:1-46:9 - Jiaoyun Yang, Haipeng Wang, Huitong Ding
Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization. 47:1-47:10 - Hatem Elshazly
MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants. 49:1-49:14 - Ying Li
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation. 51:1-51:11 - David R. Penas
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. 52:1-52:24 - Virginie Stanislas
Eigen-Epistasis for detecting gene-gene interactions. 54:1-54:14 - Victor Alexandre Padilha
A systematic comparative evaluation of biclustering techniques. 55:1-55:25 - Michal Jablonski
Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. 56:1-56:11 - Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina
Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. 57:1-57:12 - Giulia Paciello, Elisa Ficarra
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. 58:1-58:12 - Yasir Rahmatallah
GSAR: Bioconductor package for Gene Set analysis in R. 61:1-61:12 - Fereshteh Chitsazian, Mehdi Sadeghi, Elahe Elahi:
Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines. 67:1-67:14 - Rob Eisinga
Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers. 68:1-68:18 - Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiao-Tai Huang
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. 72:1-72:13 - Orsolya Pipek
Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. 73:1-73:11 - Shupeng Gui, Andrew P. Rice
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. 74:1-74:13 - Wutao Lin, Donghong Ji, Yanan Lu:
Disorder recognition in clinical texts using multi-label structured SVM. 75:1-75:11 - Zohar Zafrir, Tamir Tuller
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. 77:1-77:10 - Govind Nair
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization. 78:1-78:9 - Sinjini Sikdar, Susmita Datta:
A novel statistical approach for identification of the master regulator transcription factor. 79:1-79:11 - Cristiano Lacerda Nunes Pinto
Transductive learning as an alternative to translation initiation site identification. 81:1-81:15 - Rui Henriques
BicPAMS: software for biological data analysis with pattern-based biclustering. 82:1-82:16 - Mari van Reenen
Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp. 83:1-83:13 - Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain
Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data. 84:1-84:17 - James C. Wilgenbusch
Visualizing phylogenetic tree landscapes. 85:1-85:12 - Daniel Ian McSkimming, Khaled Rasheed, Natarajan Kannan:
Classifying kinase conformations using a machine learning approach. 86:1-86:15 - Jiapeng Zhou, Jing Xin, Yayun Niu, Shiwen Wu
DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD. 87:1-87:10 - Vitaly A. Selivanov, Adrián Benito
MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. 88:1-88:9 - Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin:
Erratum to: Integrating mean and variance heterogeneities to identify differentially expressed genes. 89:1 - Yanhui Fan
PyHLA: tests for the association between HLA alleles and diseases. 90:1-90:5 - Seung Hoan Choi, Adam Labadorf
Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis. 91:1-91:13 - Quan Zhang, Yuzhen Ye
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. 92:1-92:12 - Hirokazu Chiba
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. 93:1-93:6 - W. Duncan Wadsworth, Raffaele Argiento
An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. 94:1-94:12 - Georgios A. Dalkas
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. 95:1-95:12 - Beatriz Serrano-Solano
How can functional annotations be derived from profiles of phenotypic annotations? 96:1-96:12 - Raja Ali
VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces. 97:1-97:8 - Yanhui Hu
The Drosophila Gene Expression Tool (DGET) for expression analyses. 98:1-98:9 - Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. 99:1-99:14 - Tran Tuan Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. 100:1-100:10 - Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou:
iHMS: a database integrating human histone modification data across developmental stages and tissues. 103:1-103:9 - Gabriela F. Rodrigues-Luiz
TipMT: Identification of PCR-based taxon-specific markers. 104:1-104:8 - Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. 105:1-105:14 - Muhammad Rizwan, Anam Naz
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. 106:1-106:7 - Seyed Ziaeddin Alborzi, Marie-Dominique Devignes
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. 107:1-107:11 - Kosuke Yoshida
Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data. 108:1-108:11 - Chunwei Ma
Improvement of peptide identification with considering the abundance of mRNA and peptide. 109:1-109:8 - Marika Kaakinen
MARV: a tool for genome-wide multi-phenotype analysis of rare variants. 110:1-110:8 - Malte Petersen
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. 111:1-111:10 - Francesco Napolitano
repo: an R package for data-centered management of bioinformatic pipelines. 112:1-112:9 - Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro de Vasconcelos
Erratum to: Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction. 113:1 - Jasmit S. Shah
Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies. 114:1-114:13 - Julia Koehler Leman, Sergey Lyskov, Richard Bonneau:
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. 115:1-115:9 - Matthias Barann
Manananggal - a novel viewer for alternative splicing events. 120:1-120:13 - Sergio Gonzalez
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. 121:1-121:9 - Lina Yao
Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing. 122:1-122:11 - Diego Pasqualin
SFREEMAP - A simulation-free tool for stochastic mapping. 123:1-123:8 - Massimo Narizzano, Gabriele Arnulfo
SEEG assistant: a 3DSlicer extension to support epilepsy surgery. 124:1-124:13 - Ilya Zhbannikov
stpm: an R package for stochastic process model. 125:1-125:12 - Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi
Meta-aligner: long-read alignment based on genome statistics. 126:1-126:9 - Joshua L. Cherry:
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history. 127:1-127:12 - Florian Rohart
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. 128:1-128:13 - Li Zhang
3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data. 129:1-129:14 - Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park, Youngmi Yoon:
Drug voyager: a computational platform for exploring unintended drug action. 131:1-131:13 - Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. 132:1-132:11 - Sarah Sandmann
BBCAnalyzer: a visual approach to facilitate variant calling. 133:1-133:6 - Xiaoyong Pan, Hong-Bin Shen:
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. 136:1-136:14 - Saghi Nojoomi, Patrice Koehl
String kernels for protein sequence comparisons: improved fold recognition. 137:1-137:15 - Philip L. Tzou
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. 138:1-138:6 - M.-H. Elsensohn, N. Leblay, Sarra Dimassi, Amandine Campan-Fournier, A. Labalme, Florence Roucher Boulez
Statistical method to compare massive parallel sequencing pipelines. 139:1-139:11 - Pathima Nusrath Hameed
Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes. 140:1-140:15 - Martin Nettling, Hendrik Treutler, Jesús Cerquides
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. 141:1-141:10 - Antonio Fabregat
Reactome pathway analysis: a high-performance in-memory approach. 142:1-142:9 - Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell
Model based heritability scores for high-throughput sequencing data. 143:1-143:16 - Aidi Zhang, Libo He, Yaping Wang:
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. 145:1-145:13 - Richard J. Cotton
flippant-An R package for the automated analysis of fluorescence-based scramblase assays. 146:1-146:7 - Yong Chen, Li Zhao, Yi Wang, Ming Cao, Violet Gelowani, Mingchu Xu, Smriti A. Agrawal, Yumei Li, Stephen P. Daiger, Richard A. Gibbs, Fei Wang
SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. 147:1-147:9 - Vera Rieder
DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. 148:1-148:12 - Hao He, Dongdong Lin, Ji-Gang Zhang, Yu-Ping Wang, Hong-Wen Deng:
Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network. 149:1-149:6 - Monica H. T. Wong
Two-way learning with one-way supervision for gene expression data. 150:1-150:13 - Cedric Simillion
Avoiding the pitfalls of gene set enrichment analysis with SetRank. 151:1-151:14 - Toru Maruyama, Tetsushi Mori
SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions. 152:1-152:11 - Paolo Cifani
ProteoModlR for functional proteomic analysis. 153:1-153:7 - Christopher R. Bolen
The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. 155:1-155:8 - Grace Yoon
Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome. 156:1-156:7 - Marco Tompitak
Benchmarking and refining probability-based models for nucleosome-DNA interaction. 157:1-157:7 - Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta
Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. 158:1-158:11 - Tim O. F. Conrad
Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. 160:1-160:20 - Ricardo Olanda
A new parallel pipeline for DNA methylation analysis of long reads datasets. 161:1-161:6 - Rui Henriques
Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering. 162:1-162:2 - Andrés Becerra
Prediction of virus-host protein-protein interactions mediated by short linear motifs. 163:1-163:11 - Anke Fähnrich
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface. 164:1-164:6 - Tao Huang
MOST: most-similar ligand based approach to target prediction. 165:1-165:11 - Lan Jing, Dandan Guo, Wenjie Hu, Xiaofan Niu:
The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis. 166:1-166:13 - Soren H. Hough
Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. 167:1-167:10 - Jin Chu Wu
A novel measure and significance testing in data analysis of cell image segmentation. 168:1-168:13 - Li Ma, Suohai Fan
CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests. 169:1-169:18 - Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar
MicroRNA categorization using sequence motifs and k-mers. 170:1-170:9 - J. Harry Caufield
Bacterial protein meta-interactomes predict cross-species interactions and protein function. 171:1-171:14 - Kristian Hovde Liland
microclass: an R-package for 16S taxonomy classification. 172:1-172:9 - Daniel Fischer
Subgroup detection in genotype data using invariant coordinate selection. 173:1-173:9 - Alain B. Tchagang, François Fauteux
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. 174:1-174:16 - Andrey Smelter
A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. 175:1-175:12 - Veit Wiesmann
Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms. 176:1-176:12 - Qing Wei, Ishita K. Khan, Ziyun Ding, Satwica Yerneni
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. 177:1-177:13 - Emily Jane McTavish
TreeToReads - a pipeline for simulating raw reads from phylogenies. 178:1-178:7 - Zhi-an Huang
LW-FQZip 2: a parallelized reference-based compression of FASTQ files. 179:1-179:8 - Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing. 180:1-180:14 - Sk Md Mosaddek Hossain
Preservation affinity in consensus modules among stages of HIV-1 progression. 181:1-181:23 - Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel
EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. 182:1-182:13 - Bo Wen
metaX: a flexible and comprehensive software for processing metabolomics data. 183:1-183:14 - Sinan Abo Alchamlat, Frédéric Farnir
KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies. 184:1-184:12 - Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. 185:1
- Donghyeon Yu
Enhanced construction of gene regulatory networks using hub gene information. 186:1-186:20 - Giovanna M. M. Ventola, Teresa Maria Rosaria Noviello
Identification of long non-coding transcripts with feature selection: a comparative study. 187:1-187:16 - Romain Bourqui
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining. 188:1-188:10 - Zhenzhou Wang
Generalizing cell segmentation and quantification. 189:1-189:16 - Prabina Kumar Meher
DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins. 190:1-190:14 - Alencar Xavier
Genomic prediction using subsampling. 191:1-191:7 - Vikram E. Chhatre
StrAuto: automation and parallelization of STRUCTURE analysis. 192:1-192:5 - Hui Peng, Chaowang Lan, Yi Zheng, Gyorgy Hutvagner
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. 193:1-193:17 - Beatriz Serrano-Solano
Erratum to: How can functional annotations be derived from profiles of phenotypic annotations? 194:1-194:2 - José Santos Reyes, Ángel Monteagudo
Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability. 195:1-195:18 - Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz
The autophagy interaction network of the aging model Podospora anserina. 196:1-196:15 - Zhijiang Wan, Yishan He, Ming Hao, Jian Yang, Ning Zhong
M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree. 197:1-197:13 - Fei Li, Meishan Zhang
A neural joint model for entity and relation extraction from biomedical text. 198:1-198:11 - Tobias Madsen
Significance evaluation in factor graphs. 199:1-199:12 - Bastijn Koopmans
AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data. 200:1-200:5 - Gaurang Mahajan
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. 201:1-201:14 - Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi, Victor Dillard:
Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. 202:1 - Nathan K. Schaefer
AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. 203:1-203:22 - Ergude Bao, Lingxiao Lan:
HALC: High throughput algorithm for long read error correction. 204:1-204:12 - Garrett W. Birkel, Amit Ghosh
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. 205:1-205:11 - Jia-Feng Yu, Xianghua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. 206:1-206:5 - William W. Greenwald
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. 207:1-207:6 - Mohamed Amine Remita
A machine learning approach for viral genome classification. 208:1-208:11 - Rasha E. Boulos
Multi-scale structural community organisation of the human genome. 209:1-209:13 - Putri W. Novianti
Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia. 210:1-210:11 - Ji-Hye Choi
Pan-cancer analysis of systematic batch effects on somatic sequence variations. 211:1-211:10 - Guifang Fu, Gang Wang, Xiaotian Dai
An adaptive threshold determination method of feature screening for genomic selection. 212:1-212:10 - Clare Pacini
Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure. 213:1-213:6 - Peter Kamp Busk
Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. 214:1-214:9 - Ebrahim Afyounian
Segmentum: a tool for copy number analysis of cancer genomes. 215:1-215:10 - Akhilesh Kaushal, Hongmei Zhang
Comparison of different cell type correction methods for genome-scale epigenetics studies. 216:1-216:12 - Meiling Liu, Sanghoon Moon, Longfei Wang
On the association analysis of CNV data: a fast and robust family-based association method. 217:1-217:11 - Sarvesh Nikumbh
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. 218:1-218:16 - Garrett W. Birkel, Amit Ghosh
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. 219:1-219:2 - Tanchanok Wisitponchai, Watshara Shoombuatong
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. 220:1-220:12 - Mark D. Temple
An auditory display tool for DNA sequence analysis. 221:1-221:11 - Alencar Xavier
Erratum to: Genomic prediction using subsampling. 222:1 - You-Yu Lin
De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. 223:1-223:10 - Debangana Chakravorty
MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells. 224:1-224:10 - Loris Bertoldi
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. 225:1-225:11 - Mohammed Al-Jaff, Eric Sandström, Manfred G. Grabherr
microTaboo: a general and practical solution to the k-disjoint problem. 228:1-228:7 - Li Chen
A vascular image registration method based on network structure and circuit simulation. 229:1-229:13 - Irene Epifanio
Intervention in prediction measure: a new approach to assessing variable importance for random forests. 230:1-230:16 - Francisco Avila Cobos
Zipper plot: visualizing transcriptional activity of genomic regions. 231:1-231:9 - Jochen Kruppa
Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. 232:1-232:10 - Bertjan Broeksema, Magdalena Calusinska
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. 233:1-233:12 - Lianbo Yu
Power analysis for RNA-Seq differential expression studies. 234:1-234:9 - Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen, Carl J. Schmidt
WebGIVI: a web-based gene enrichment analysis and visualization tool. 237:1-237:10 - Jose Cleydson F. Silva
Geminivirus data warehouse: a database enriched with machine learning approaches. 240:1-240:11 - Jing Liu, Yaxiong Chi, Chen Zhu, Yaochu Jin
A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps. 241:1-241:14 - Benjamin Schubert
ImmunoNodes - graphical development of complex immunoinformatics workflows. 242:1-242:7 - Junpeng Zhang
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. 243:1-243:12 - Andrea Tangherloni
LASSIE: simulating large-scale models of biochemical systems on GPUs. 246 - Xiang Gao, Huaiying Lin, Kashi Vishwanath Revanna, Qunfeng Dong
A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy. 247:1-247:10 - Miles Aron
Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order. 254 - Ian H. Holmes
Solving the master equation for Indels. 255:1-255:10 - Joanna Zyla
Ranking metrics in gene set enrichment analysis: do they matter? 256:1-256:12 - Surabhi Maheshwari, Michal Brylinski
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. 257:1-257:14 - Sojeong Ka, Sunho Lee
HLAscan: genotyping of the HLA region using next-generation sequencing data. 258:1-258:11 - Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra
Epimetheus - a multi-profile normalizer for epigenomic sequencing data. 259:1-259:9 - Moritz Hanke
Clone temporal centrality measures for incomplete sequences of graph snapshots. 261:1-261:18 - Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo
NFPscanner: a webtool for knowledge-based deciphering of biomedical networks. 262:1-262:9 - Knut D. Rand
Coordinates and intervals in graph-based reference genomes. 263:1-263:8 - Diana Domanska
The rainfall plot: its motivation, characteristics and pitfalls. 264:1-264:11 - Hamzah Syed
SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with "time-to-event" outcomes. 265:1-265:6 - Anna Kusnezowa, Lars I. Leichert
In silico approach to designing rational metagenomic libraries for functional studies. 267:1-267:11 - Zhen Zhang, Shumin Xia, Pakorn Kanchanawong
An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs. 268:1-268:14 - Zhenqing Ye, Tao Ma, Michael Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher, Liguo Wang
CircularLogo: A lightweight web application to visualize intra-motif dependencies. 269:1-269:8 - Zhuo Wang
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data. 270:1-270:14 - Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J. Jacobs:
JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. 271:1-271:9 - Jakob Unger, Mike Mansour, Marcin Kopaczka, Nina Gronloh, Marc Spehr
An unsupervised learning approach for tracking mice in an enclosed area. 272:1-272:14 - Marijke Van Moerbeke
A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays. 273:1-273:14 - Florian Kandlinger, Maximilian G. Plach, Rainer Merkl
AGeNNT: annotation of enzyme families by means of refined neighborhood networks. 274:1-274:13 - Xiaoyang Jing
MQAPRank: improved global protein model quality assessment by learning-to-rank. 275:1-275:8 - Spela Baebler
quantGenius: implementation of a decision support system for qPCR-based gene quantification. 276:1-276:11 - Tanlin Sun, Bo Zhou, Luhua Lai, Jianfeng Pei
Sequence-based prediction of protein protein interaction using a deep-learning algorithm. 277:1-277:8 - Kazuhiro Takemoto
Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions. 278:1-278:9 - Dmitry Y. Mozzherin
"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar. 279:1-279:14 - Yong Wan
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis. 280:1-280:15 - Yan Xu
Large scale tissue histopathology image classification, segmentation, and visualization via deep convolutional activation features. 281:1-281:17 - Boris Shabash, Kay C. Wiese
Numerical integration methods and layout improvements in the context of dynamic RNA visualization. 282:1-282:18 - Jonathan Louis Golob, Elisa Margolis
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities. 283:1-283:12 - Christian Schäfer, Alexander H. Schmidt, Jürgen Sauter
Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. 284:1-284:10 - Lukasz Wróbel, Adam Gudys
Learning rule sets from survival data. 285:1-285:13 - Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny, Sheida Nabavi:
An evaluation of copy number variation detection tools for cancer using whole exome sequencing data. 286:1-286:13 - Aziz Khan
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. 287:1-287:8 - Toshiyuki Oda, Kyungtaek Lim, Kentaro Tomii
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. 288 - Kazunori D. Yamada, Satoshi Omori, Hafumi Nishi, Masaru Miyagi:
Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach. 289 - Marek Palkowski
Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing. 290 - Miha Stajdohar, Rafael D. Rosengarten
dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. 291 - Jennifer Rogers, Andrew Fishberg, Nora Youngs, Yi-Chieh Wu:
Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species. 292 - Frank Keul, Martin Hess
PFASUM: a substitution matrix from Pfam structural alignments. 293 - Jian Zhang
Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme. 294 - Atif Ali Khan
Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes. 295 - Alex M. Ascensión
NaviSE: superenhancer navigator integrating epigenomics signal algebra. 296 - Pei Fen Kuan
A systematic evaluation of nucleotide properties for CRISPR sgRNA design. 297 - Shermin Pei, Betty L. Slinger, Michelle M. Meyer
Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15. 298 - Thomas M. Poulsen, Martin C. Frith
Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads. 299 - Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu, Keliang Li:
Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences. 300 - Stephen J. Bush
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. 301 - Wen Torng
3D deep convolutional neural networks for amino acid environment similarity analysis. 302 - Kolja Stahl, Michael Schneider, Oliver Brock:
EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. 303 - Reiko Nishihara
Biomarker correlation network in colorectal carcinoma by tumor anatomic location. 304 - Atul Kamboj
Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data. 305 - Ahmet Rasit Ozturk, Tolga Can
A multiplex primer design algorithm for target amplification of continuous genomic regions. 306 - Yusuke Azuma
Biologically constrained optimization based cell membrane segmentation in C. elegans embryos. 307 - Katsuhiro Omae, Osamu Komori, Shinto Eguchi
Quasi-linear score for capturing heterogeneous structure in biomarkers. 308 - Xiting Yan
A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. 309 - Kai Battenberg
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. 310 - Andrew Bartlett
Bioinformatics: indispensable, yet hidden in plain sight? 311 - J. F. Mudge, Christopher J. Martyniuk
Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach. 312 - Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael
Early response index: a statistic to discover potential early stage disease biomarkers. 313 - Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. 314 - Xi Chen, Chen Wang
CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment. 315 - Giorgos Minas
ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. 316 - Michael I. Klein, David F. Stern, Hongyu Zhao
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. 317 - Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila
SparkBLAST: scalable BLAST processing using in-memory operations. 318 - Sheng Yang Michael Loh, Yoshitaka Ogawa, Sara Kawana, Koichiro Tamura
Semi-automated quantitative Drosophila wings measurements. 319 - Hasan Awad Aljohi, Wanfei Liu
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data. 320 - Valerio Orlandini
SLMSuite: a suite of algorithms for segmenting genomic profiles. 321 - Nicola Lazzarini
RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers. 322 - Yuxuan Yuan
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data. 323 - Axel Wedemeyer
An improved filtering algorithm for big read datasets and its application to single-cell assembly. 324 - Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. 325 - Lili Zhao
TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. 326 - Hongrui Wang, Hongwei Liu, Leixin Cai, Caixia Wang, Qiang Lv:
Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking. 327 - Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin
Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm. 328 - Yadav Kuleesha
Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis. 329 - Dianhao Guo, Jiapeng Luo, Yuenan Zhou
ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data. 330 - Jeremy P. Koelmel, Nicholas M. Kroeger, Candice Z. Ulmer
LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. 331 - Ziyi Li, Sandra E. Safo
Incorporating biological information in sparse principal component analysis with application to genomic data. 332 - Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi
SegCorr a statistical procedure for the detection of genomic regions of correlated expression. 333 - Marc Jeanmougin
HLA-check: evaluating HLA data from SNP information. 334 - Sheng Zhang, Bo Wang, Lin Wan, Lei M. Li:
Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling. 335 - Su Hee Chu
Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis. 336 - Sehrish Kanwal
Investigating reproducibility and tracking provenance - A genomic workflow case study. 337 - Ksenia Khelik, Karin Lagesen
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. 338 - Bogumil Konopka, Marta Marciniak, Witold Dyrka
Quantiprot - a Python package for quantitative analysis of protein sequences. 339 - Sara González-Pérez, Florencio Pazos
Factors affecting interactome-based prediction of human genes associated with clinical signs. 340 - John Alexander
Variant Ranker: a web-tool to rank genomic data according to functional significance. 341 - Alvin Farrel, Jun-tao Guo
An efficient algorithm for improving structure-based prediction of transcription factor binding sites. 342 - Jie Liu, Minyi Su
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints. 343 - Sharon Marie Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D. Baker, Anne P. Starling, John E. Hokanson, Debashis Ghosh:
Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications. 344 - Se-Ran Jun
Assessment of genome annotation using gene function similarity within the gene neighborhood. 345 - Jan Schröder
CLOVE: classification of genomic fusions into structural variation events. 346 - Tamás Nagy, Martin Kampmann
CRISPulator: a discrete simulation tool for pooled genetic screens. 347 - Yanan Zhu
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. 348 - Yasser B. Ruiz-Blanco
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. 349 - Guoxian Yu
NoGOA: predicting noisy GO annotations using evidences and sparse representation. 350 - Jennifer A. Tom
Identifying and mitigating batch effects in whole genome sequencing data. 351 - Antoine Basset, Patrick Bouthemy, Jérôme Boulanger, François Waharte, Jean Salamero
An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images. 352 - Syafiq Kamarul Azman
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture. 353 - James E. Barrett
Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection. 354 - Sheng Liu, Cristina Zibetti
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. 355 - Zhao Li, Jin Li, Peng Yu:
l1kdeconv: an R package for peak calling analysis with LINCS L1000 data. 356 - Jeremy R. Wang
Correcting nucleotide-specific biases in high-throughput sequencing data. 357 - Katrin Hainke, Sebastian Szugat, Roland Fried, Jörg Rahnenführer
Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV. 358 - Daniel Amsel
Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum. 359 - Yan Xu
Parallel multiple instance learning for extremely large histopathology image analysis. 360 - Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. 361 - Gregory J. Zynda, Jawon Song
Repliscan: a tool for classifying replication timing regions. 362 - Carlos Guzman
CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction. 363 - Alejandro Sune-Aunon, Álvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares
Full L1-regularized Traction Force Microscopy over whole cells. 365 - Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao:
Local sequence and sequencing depth dependent accuracy of RNA-seq reads. 364:1-364:12 - Lisa Katharina Blaß, Christian Weyler, Elmar Heinzle:
Network design and analysis for multi-enzyme biocatalysis. 366:1-366:12 - Joseph Guhlin
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. 367:1-367:8 - Gamal K. O. Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen:
A neural network multi-task learning approach to biomedical named entity recognition. 368:1-368:14 - Olivier Sheik Amamuddy
Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks. 369:1-369:7 - Seirana Hashemi, Abbas Nowzari-Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam
Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains. 370:1-370:18 - Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider
eccCL: parallelized GPU implementation of Ensemble Classifier Chains. 371:1-371:4 - K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. 372:1-372:14 - Manuel Rueda
SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort. 373:1-373:10 - Mahdi Heydari, Giles Miclotte
Evaluation of the impact of Illumina error correction tools on de novo genome assembly. 374:1-374:13 - Xin-Ping Xie, Yu-Feng Xie, Hong-Qiang Wang:
A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification. 375 - James J. Yang
Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function. 376 - Saghi Nojoomi, Patrice Koehl
A weighted string kernel for protein fold recognition. 378 - Jiyun Zhou, Qin Lu, Ruifeng Xu
EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation. 379 - Badri Adhikari, Jianlin Cheng
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. 380 - Lian Liu, Shao-Wu Zhang, Yufei Huang, Jia Meng
QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. 387:1-387:12 - Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. 388 - Suyeon Kang
Robust gene selection methods using weighting schemes for microarray data analysis. 389:1-389:15 - John Athey, Aikaterini Alexaki
A new and updated resource for codon usage tables. 391:1-391:10 - Xiaoyang Jing
RRCRank: a fusion method using rank strategy for residue-residue contact prediction. 390 - Gabriella Sferra
Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling. 396:1-396:7 - Konstantinos Zagganas
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets. 399:1-399:8 - Steve Lefever
High-throughput PCR assay design for targeted resequencing using primerXL. 400:1-400:9 - Jared Ostmeyer, Scott Christley, William Rounds, Inimary T. Toby, Benjamin M. Greenberg
Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. 401:1-401:10 - Michael Kern, Alexander Lex
Interactive visual exploration and refinement of cluster assignments. 406 - Matthias Zytnicki:
mmquant: how to count multi-mapping reads? 411:1-411:6 - Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li
Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images. 412:1-412:13 - Wei Hu, Amrapali Zaveri
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. 415:1-415:12 - Thomas J. Hardcastle
Methods for discovering genomic loci exhibiting complex patterns of differential methylation. 416:1-416:11 - Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng
Deep learning methods for protein torsion angle prediction. 417:1-417:13 - José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. 421:1-421:5 - Ying Wang
Improving contig binning of metagenomic data using (d2S) oligonucleotide frequency dissimilarity. 425:1-425:14 - Duo Xu, Yousef Jaber, Pavlos Pavlidis, Omer Gokcumen
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. 426:1-426:8 - Jerome Audoux, Mikaël Salson, Christophe F. Grosset
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. 428:1-428:14 - Sophie Molnos
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. 429:1-429:8 - Juan Carlos Aledo
A machine learning approach for predicting methionine oxidation sites. 430:1-430:14 - Jose Cleydson F. Silva
Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae. 431:1-431:14 - Maninder Sandhu, V. Sureshkumar
RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. 432:1-432:11 - Alan Beccati, Jan Gerken
SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees. 433:1-433:4 - Peng Zhai, Longshu Yang, Xiao Guo, Zhe Wang, Jiangtao Guo, Xiaoqi Wang, Huaiqiu Zhu:
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. 434:1-434:16 - Nazar Zaki
BioCarian: search engine for exploratory searches in heterogeneous biological databases. 435:1-435:15 - Jianing Gao
Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data. 436:1-436:6 - Joseph N. Paulson, Cho-Yi Chen
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. 437:1-437:10 - Enfeng Qi, Dongyu Wang, Bo Gao, Yang Li
Block-based characterization of protease specificity from substrate sequence profile. 438:1-438:9 - Jia Song
Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family. 439:1-439:8 - Bence Bolgár
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization. 440:1-440:18 - A. Eck, Luisa M. Zintgraf, E. F. J. de Groot, Tim G. J. de Meij, Taco S. Cohen, P. H. M. Savelkoul, Max Welling, A. E. Budding:
Interpretation of microbiota-based diagnostics by explaining individual classifier decisions. 441:1-441:13 - Michael Ferlaino
An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. 442:1-442:8 - Shumin Li
Protein remote homology detection based on bidirectional long short-term memory. 443:1-443:8 - Sebastian Proost
LSTrAP: efficiently combining RNA sequencing data into co-expression networks. 444:1-444:9 - Wei Zheng, Hongfei Lin, Ling Luo
An attention-based effective neural model for drug-drug interactions extraction. 445:1-445:11 - Maria Taboada
A new synonym-substitution method to enrich the human phenotype ontology. 446:1-446:12 - Xue Jiang, Han Zhang, Feng Duan, Xiongwen Quan
Identify Huntington's disease associated genes based on restricted Boltzmann machine with RNA-seq data. 447:1-447:13 - Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy Monson, William Rounds, Florian Rubelt
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. 448:1-448:5 - Marco Notaro
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. 449:1-449:18 - Jaehee Kim, Haseong Kim:
Partitioning of functional gene expression data using principal points. 450:1-450:17 - Hyejin Cho, Wonjun Choi, Hyunju Lee
A method for named entity normalization in biomedical articles: application to diseases and plants. 451:1-451:12 - Tao Chen
LiverWiki: a wiki-based database for human liver. 452:1-452:11 - Chenggang Yu, Hyung Jun Woo
A strategy for evaluating pathway analysis methods. 453:1-453:11 - Youyi Fong
chngpt: threshold regression model estimation and inference. 454:1-454:7 - Chaitanya R. Acharya
Mapping eQTL by leveraging multiple tissues and DNA methylation. 455 - Jakub Wiedemann, Tomasz Zok
LCS-TA to identify similar fragments in RNA 3D structures. 456 - R. Greg Stacey
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). 457 - Yahya Bokhari
QuaDMutEx: quadratic driver mutation explorer. 458 - Jia Wen
A heuristic model for computational prediction of human branch point sequence. 459 - Biswanath Chowdhury, Arnav Garai, Gautam Garai:
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm. 460 - Oana Carja
riboviz: analysis and visualization of ribosome profiling datasets. 461 - Yiwei Li, Lucian Ilie
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. 485:1-485:11 - Levi D. McClenny, Mahdi Imani
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems. 519:1-519:8 - Giulio Spinozzi
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. 520:1-520:12 - Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David Vocadlo
Software for rapid time dependent ChIP-sequencing analysis (TDCA). 521:1-521:16 - Megan J. Bowman
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. 522:1-522:15 - Yao-Ting Huang
An efficient error correction algorithm using FM-index. 524:1-524:9 - Wael Karain:
Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method. 525:1-525:13 - Peter Bajcsy
Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images. 526:1-526:23 - Qinxue Meng
DBNorm: normalizing high-density oligonucleotide microarray data based on distributions. 527:1-527:11 - John M. Gaspar, Ronald P. Hart
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. 528:1-528:8 - Curtis T. Rueden
ImageJ2: ImageJ for the next generation of scientific image data. 529:1-529:26 - Maxwell T. Spadafore
A proximity-based graph clustering method for the identification and application of transcription factor clusters. 530:1-530:14 - Jelena Calyseva
PON-SC - program for identifying steric clashes caused by amino acid substitutions. 531:1-531:8 - Janna L. Fierst
Decontaminating eukaryotic genome assemblies with machine learning. 533:1-533:16 - Michael T. Ganger
A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments. 534:1-534:11 - Bart Broeckx
Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations. 535:1-535:10 - Vahid Jalili
Explorative visual analytics on interval-based genomic data and their metadata. 536:1-536:15 - Vassily A. Lyubetsky
Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming. 537:1-537:18 - Kristi Gdanetz
CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. 538:1-538:9 - Kang K. Yan, Hongyu Zhao
A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. 539:1-539:13 - Ralph W. Crosby, Tiffani L. Williams:
Fast algorithms for computing phylogenetic divergence time. 514:1-514:13 - Oyetunji E. Ogundijo, Xiaodong Wang:
Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach. 541:1-541:15 - Yuangen Yao
Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction. 542:1-542:12 - Carlos Ruiz-Arenas
Redundancy analysis allows improved detection of methylation changes in large genomic regions. 553:1-553:9 - Matthias Beyens
pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data. 554:1-554:6 - Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson
Canary: an atomic pipeline for clinical amplicon assays. 555:1-555:7 - Valeria Montano
An Eigenvalue test for spatial principal component analysis. 562:1-562:7 - Jordi Martorell-Marugan
MetaGenyo: a web tool for meta-analysis of genetic association studies. 563:1-563:6 - Nilesh Khiste, Lucian Ilie
HISEA: HIerarchical SEed Aligner for PacBio data. 564:1-564:13 - Tianyu Kang, Wei Ding
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. 565:1-565:11 - Sumanta Ray
A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression. 579:1-579:21 - Fanchi Meng, Chen Wang, Lukasz A. Kurgan
fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization. 580:1-580:11 - Gayathri Thillaiyampalam
An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. 581:1-581:16 - Yuhang Liu, Jinfeng Zhang, Xing Qiu:
Super-delta: a new differential gene expression analysis procedure with robust data normalization. 582:1-582:13 - Preeti Choudhary
CSmetaPred: a consensus method for prediction of catalytic residues. 583:1-583:13 - Dennis E. te Beest
Improved high-dimensional prediction with Random Forests by the use of co-data. 584:1-584:11 - Youngmahn Han, Dongsup Kim:
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction. 585:1-585:9 - Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers, Matthew E. Hudson
A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy. 586:1-586:12 - Chen Lyu, Bo Chen, Yafeng Ren, Donghong Ji:
Long short-term memory RNN for biomedical named entity recognition. 462 - Rex Shen, Lan Luo, Hui Jiang
Identification of gene pairs through penalized regression subject to constraints. 466 - Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity. 467 - Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda
RNA inverse folding using Monte Carlo tree search. 468 - Jebediah Rosen, Kyle Handy, André Gillan, Rob Smith
JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals. 469 - Dawit Nigatu
Sequence-based information-theoretic features for gene essentiality prediction. 473 - Heidi E. L. Lischer, Kentaro K. Shimizu
Reference-guided de novo assembly approach improves genome reconstruction for related species. 474 - Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann
A fragment based method for modeling of protein segments into cryo-EM density maps. 475 - Paul M. Harrison:
fLPS: Fast discovery of compositional biases for the protein universe. 476 - Oriol Mazariegos-Canellas, Trien Do, Tim E. A. Peto, David W. Eyre
BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness. 477 - Duc-Hau Le, Lieven P. C. Verbeke, Le Hoang Son, Dinh-Toi Chu
Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs. 479 - Oluwatosin Oluwadare
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. 480 - Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang, Jianhua Wei:
Analysis of breast cancer subtypes by AP-ISA biclustering. 481 - Tao Zhu
GFF3sort: a novel tool to sort GFF3 files for tabix indexing. 482 - Maria Needhamsen
Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. 486 - Richard Elias, David Hoksza
TRAVeLer: a tool for template-based RNA secondary structure visualization. 487 - Rami Eitan, Ron Shamir:
Reconstructing cancer karyotypes from short read data: the half empty and half full glass. 488 - Eric C. Rouchka
Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics. 490 - Sérgio E. D. Dias
GPU-based detection of protein cavities using Gaussian surfaces. 493 - Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan:
dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder. 494 - Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan:
ANAT 2.0: reconstructing functional protein subnetworks. 495 - Khanh To Duc
bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests. 503 - Nathan Sloat, Jui-Wen Liu, Susan J. Schroeder
Swellix: a computational tool to explore RNA conformational space. 504 - Linlin Gao, Haiwei Pan, Qing Li
Brain medical image diagnosis based on corners with importance-values. 505 - Daniel Castillo
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. 506 - Rhys A. Farrer
Synima: a Synteny imaging tool for annotated genome assemblies. 507 - Hongwei Ge, Liang Sun
Fast batch searching for protein homology based on compression and clustering. 508 - Kosai Al-Nakeeb
Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data. 510 - Jie Tan, Matt Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
ADAGE signature analysis: differential expression analysis with data-defined gene sets. 512 - Sudipta Acharya
Unsupervised gene selection using biological knowledge : application in sample clustering. 513 - Fen-Xiang Liu, Chunfa Tong
MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species. 515 - Marco Beccuti
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. 516
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