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ORCIDBMC Bioinformatics, Volume 17
Volume 17, 2016
- Ákos Tényi, Pedro de Atauri
, David Gomez-Cabrero, Isaac Cano, Kim Clarke, Francesco Falciani, Marta Cascante, Josep Roca, Dieter Maier:
ChainRank, a chain prioritisation method for contextualisation of biological networks. 17 - Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé, Yves Van de Peer:
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. 18 - James J. Yang, Jia Li, L. Keoki Williams, Anne Buu:
An efficient genome-wide association test for multivariate phenotypes based on the Fisher combination function. 19 - Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos, Francisco Melo:
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. 20 - Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer:
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. 21 - Van-Vinh Le, Tran Van Lang, Tran Van Hoai:
A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads. 22 - Manuel Binet, Olivier Gascuel, Céline Scornavacca, Emmanuel J. P. Douzery, Fabio Pardi:
Fast and accurate branch lengths estimation for phylogenomic trees. 23 - Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V. Uzilov, Rong Chen:
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. 24 - Kerstin Johnsson, Jonas Wallin, Magnus Fontes:
BayesFlow: latent modeling of flow cytometry cell populations. 25 - Nithin Shivashankar, Sonali Patil, Amrisha Bhosle, Nagasuma Chandra, Vijay Natarajan:
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. 26 - Roman Hornung, Anne-Laure Boulesteix, David Causeur:
Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. 27 - Yubo Zhang, Yi Ding:
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.). 28 - Arthur T. O. Melo, Radhika Bartaula, Iago Hale:
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. 29 - Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister M. Swenson:
Aligning the unalignable: bacteriophage whole genome alignments. 30 - Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro F. Santibanez-Koref, David J. Elliott, Michael S. Jackson:
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. 31 - Eugene Tseytlin, Kevin J. Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan, Rebecca S. Jacobson:
NOBLE - Flexible concept recognition for large-scale biomedical natural language processing. 32 - Mari van Reenen, Carolus J. Reinecke, Johan A. Westerhuis, J. Hendrik Venter:
Variable selection for binary classification using error rate p-values applied to metabolomics data. 33 - Kamal Taha, Paul D. Yoo:
Predicting the functions of a protein from its ability to associate with other molecules. 34 - Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass:
Deciphering transcriptional regulations coordinating the response to environmental changes. 35 - Shuai Li, Michael Woodfin, S. Seth Long, Peter G. Fuerst:
IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination. 36 - Lun-Ching Chang, Bingshan Li, Zhou Fang, Scott Vrieze, Matthew McGue, William G. Iacono, George C. Tseng, Wei Chen:
A computational method for genotype calling in family-based sequencing data. 37 - Veronika B. Dubinkina, Dmitry S. Ischenko, Vladimir Ulyantsev, Alexander V. Tyakht, Dmitry G. Alexeev:
Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. 38 - Sandeep K. Kushwaha, Lokeshwaran Manoharan, Tejashwari Meerupati, Katarina Hedlund, Dag G. Ahrén:
Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics. 39 - Vassily A. Lyubetsky, Roman Gershgorin, Alexander V. Seliverstov, Konstantin Yu. Gorbunov:
Algorithms for reconstruction of chromosomal structures. 40 - Francisco Pina-Martins, Bruno M. Vieira, Sofia G. Seabra, Dora Batista, Octávio S. Paulo:
4Pipe4 - A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. 41 - Daniele Muraro, Alison Simmons:
An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease. 42 - Elo Leung, Amy Huang, Eithon Cadag, Aldrin Montana, Jan Lorenz Soliman, Carol L. Ecale Zhou:
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations. 43 - Yuan Chen, Lifeng Wang, Lanzhi Li, Hongyan Zhang, Zheming Yuan:
Informative gene selection and the direct classification of tumors based on relative simplicity. 44 - Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer:
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. 45 - André C. A. Nascimento, Ricardo B. C. Prudêncio, Ivan G. Costa:
A multiple kernel learning algorithm for drug-target interaction prediction. 46 - Tzu-Yu Liu, Thomas Burke, Lawrence P. Park, Christopher W. Woods, Aimee K. Zaas, Geoffrey S. Ginsburg, Alfred O. Hero III:
An individualized predictor of health and disease using paired reference and target samples. 47 - Daniel A. Janies, Zachary L. Witter, Gregorio V. Linchangco, David W. Foltz, Allison K. Miller, Alexander M. Kerr, Jeremy J. Jay, Robert W. Reid, Gregory A. Wray:
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. 48 - David Rio Deiros, Richard A. Gibbs, Jeffrey Rogers:
DNAism: exploring genomic datasets on the web with Horizon Charts. 49 - Giovanni Mele:
Arabidopsis Motif Scanner. 50 - Virginie Uhlmann, Shantanu Singh, Anne E. Carpenter:
CP-CHARM: segmentation-free image classification made accessible. 51 - Wei Zhang, Huiyun Li, Zhaohai Li, Qizhai Li:
A two-phase procedure for non-normal quantitative trait genetic association study. 52 - Patrick Schorderet:
NEAT: a framework for building fully automated NGS pipelines and analyses. 53 - Alencar Xavier, William M. Muir, Katy Martin Rainey:
Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans. 55 - Ram Vinay Pandey, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel:
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research. 56 - Liguo Wang, Jinfu J. Nie, Hugues Sicotte, Ying Li, Jeanette E. Eckel-Passow, Surendra Dasari, Peter T. Vedell, Poulami Barman, Liewei Wang, Richard Weinshiboum, Jin Jen, Haojie Huang, Manish Kohli, Jean-Pierre A. Kocher:
Measure transcript integrity using RNA-seq data. 58 - Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos, Raquel M. Silva:
The exceptional genomic word symmetry along DNA sequences. 59 - Hua-zhen Wang, Fan Yang, Zhiyuan Luo:
An experimental study of the intrinsic stability of random forest variable importance measures. 60 - Christos Kozanitis, David A. Patterson:
GenAp: a distributed SQL interface for genomic data. 63 - Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti:
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. 64 - Anthony O'Hare, Samantha Lycett, Thomas Doherty, Liliana C. M. Salvador, Rowland R. Kao:
Broadwick: a framework for computational epidemiology. 65 - Benjamin K. Johnson, Matthew B. Scholz, Tracy K. Teal, Robert B. Abramovitch:
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. 66 - Katharina Imkeller, Peter F. Arndt, Hedda Wardemann, Christian E. Busse:
sciReptor: analysis of single-cell level immunoglobulin repertoires. 67 - Ludmil B. Alexandrov, Alan R. Bishop, Kim Ø. Rasmussen, Boian S. Alexandrov:
The role of structural parameters in DNA cyclization. 68 - Jincheol Park, Shili Lin:
Impact of data resolution on three-dimensional structure inference methods. 70 - Shabnam Shamriz, Hamideh Ofoghi:
Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant. 71 - Mario Deng, Johannes Brägelmann, Joachim L. Schultze, Sven Perner:
Web-TCGA: an online platform for integrated analysis of molecular cancer data sets. 72 - Xiaochun Sun, Rita H. Mumm:
Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation. 73 - Huey-miin Hsueh, Chen-An Tsai:
Gene set analysis using sufficient dimension reduction. 74 - Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf-Dieter Schubert, Alan Christoffels:
Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis. 75 - Joeri Ruyssinck, Piet Demeester, Tom Dhaene, Yvan Saeys:
Netter: re-ranking gene network inference predictions using structural network properties. 76 - Renée X. de Menezes, Leila Mohammadi, Jelle J. Goeman, Judith M. Boer:
Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. 77 - Adam S. Brown, Sek Won Kong, Isaac S. Kohane, Chirag J. Patel:
ksRepo: a generalized platform for computational drug repositioning. 78 - Dirk Krüger:
BMC Bioinformatics reviewer acknowledgement 2015. 79 - Giorgio E. M. Melloni, Stefano de Pretis, Laura Riva, Mattia Pelizzola, Arnaud Céol, Jole Costanza, Heiko Müller, Luca Zammataro:
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. 80 - Jeff Daily:
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. 81 - Simon Dellicour, Rebecca Rose, Oliver G. Pybus:
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. 82 - Suvir Jain, Kashyap R. Tumkur, Tsung-Ting Kuo, Shitij Bhargava, Gordon Lin, Chun-Nan Hsu:
Erratum to: Weakly supervised learning of biomedical information extraction from curated data. 84 - Marcin Piechota, Michal Korostynski, Joanna Ficek, Andrzej Tomski, Ryszard Przewlocki:
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators. 85 - Jiadong Ji, Zhongshang Yuan, Xiaoshuai Zhang, Fuzhong Xue:
A powerful score-based statistical test for group difference in weighted biological networks. 86 - Klaus Hahn, Peter R. Massopust, Sergei Prigarin:
A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain. 87 - Diana L. Delibaltov, Utkarsh Gaur, Jennifer Kim, Matthew Kourakis, Erin Newman-Smith, William Smith, Samuel A. Belteton, Daniel Szymanski, B. S. Manjunath:
CellECT: cell evolution capturing tool. 88 - Kahn Rhrissorrakrai, Kristin C. Gunsalus:
Erratum to: MINE: Module Identification in Networks. 89 - Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie:
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. 90 - Ivan Vujaklija, Ana Bielen, Tina Paradzik, Sinisa Bidin, Pavle Goldstein, Dusica Vujaklija:
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. 91 - Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro F. Santibanez-Koref, David J. Elliott, Michael S. Jackson:
Erratum to: PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. 92 - Jared S. Fowles, Kristen C. Brown, Ann M. Hess, Dawn L. Duval, Daniel L. Gustafson:
Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma. 93 - Minji Kim, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli, Olgica Milenkovic:
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. 94 - Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Keles:
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. 96 - Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung:
Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins. 97 - Nicholas C. Wong, Bernard J. Pope, Ida L. Candiloro, Darren Korbie, Matt Trau, Stephen Q. Wong, Thomas Mikeska, Xinmin Zhang, Mark Pitman, Stefanie Eggers, Stephen R. Doyle, Alexander Dobrovic:
MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. 98 - Chan-seok Jeong, Dongsup Kim:
Structure-based Markov random field model for representing evolutionary constraints on functional sites. 99 - Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai, Xiaoli Li, Hong Yan:
A two-layer integration framework for protein complex detection. 100 - M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Seth M. Bybee:
Detecting false positive sequence homology: a machine learning approach. 101 - Timothy DeFreitas, Hachem Saddiki, Patrick Flaherty:
GEMINI: a computationally-efficient search engine for large gene expression datasets. 102 - Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim:
Trimming of sequence reads alters RNA-Seq gene expression estimates. 103 - Anjana Grandhi, Wenge Guo, Shyamal D. Peddada:
A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies. 104 - Kamal Taha, Paul D. Yoo:
Erratum to: Predicting the functions of a protein from its ability to associate with other molecules. 105 - Hanyu Jiang, Narayan Ganesan:
CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU. 106 - Joaquín Tárraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquín Dopazo:
HPG pore: an efficient and scalable framework for nanopore sequencing data. 107 - Meng-Yun Wu, Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Yuan Zhu, Hong Yan:
Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer. 108 - Shihai Feng, Chien-Chi Lo, Po-E Li, Patrick S. G. Chain:
ADEPT, a dynamic next generation sequencing data error-detection program with trimming. 109 - Mihails Delmans, Martin Hemberg:
Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data. 110 - Mingon Kang, Liping Tang, Jean Gao:
Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice. 111 - Biao Liu, Jessica L. Childs-Disney, Brent M. Znosko, Dan Wang, Mohammad Fallahi, Steven M. Gallo, Matthew D. Disney:
Analysis of secondary structural elements in human microRNA hairpin precursors. 112 - Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao, Tatsuya Akutsu:
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order. 113 - Youzhong Liu, Kirill Smirnov, Marianna Lucio, Régis D. Gougeon, Hervé Alexandre, Philippe Schmitt-Kopplin:
MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics. 114 - Mohammed-Amin Madoui, Carole Dossat, Léo d'Agata, Jan van Oeveren, Edwin van der Vossen, Jean-Marc Aury:
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. 115 - Binghuang Cai, Xia Jiang:
Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences. 116 - Javier Pérez-Rodríguez, Nicolás García-Pedrajas:
Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences. 117 - Armin Rauschenberger, Marianne A. Jonker, Mark A. van de Wiel, Renée X. de Menezes:
Testing for association between RNA-Seq and high-dimensional data. 118 - Frazier N. Baker, Aleksey A. Porollo:
CoeViz: a web-based tool for coevolution analysis of protein residues. 119 - Devin C. Koestler, Meaghan J. Jones, Joseph Usset, Brock C. Christensen, Rondi A. Butler, Michael S. Kobor, John K. Wiencke, Karl T. Kelsey:
Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). 120 - Sumanta Ray, Sanghamitra Bandyopadhyay:
A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs. 121 - Yafang Li, Jinyoung Byun, Guoshuai Cai, Xiangjun Xiao, Younghun Han, Olivier Cornelis, James E. Dinulos, Joe Dennis, Douglas F. Easton, Ivan P. Gorlov, Michael F. Seldin, Christopher I. Amos:
FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data. 122 - Aristeidis G. Telonis, Phillipe Loher, Yohei Kirino, Isidore Rigoutsos:
Consequential considerations when mapping tRNA fragments. 123 - Mirela Domijan, Paul E. Brown, Boris V. Shulgin, David A. Rand:
PeTTSy: a computational tool for perturbation analysis of complex systems biology models. 124 - Melanie Schirmer, Rosalinda D'Amore, Umer Zeeshan Ijaz, Neil Hall, Christopher Quince:
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. 125 - Kevin C. Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew C. Parnell, Stephen V. Gordon, David E. MacHugh:
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. 126 - Luis de la Garza, Johannes Veit, András Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert, Oliver Kohlbacher:
From the desktop to the grid: scalable bioinformatics via workflow conversion. 127 - Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. 128 - Shailesh Tripathi, Salissou Moutari, Matthias Dehmer, Frank Emmert-Streib:
Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules. 129 - Matteo Comin, Morris Antonello:
On the comparison of regulatory sequences with multiple resolution Entropic Profiles. 130 - Bo Yao, Zhong Li, Meng Ding, Minhong Chen:
Three-dimensional protein model similarity analysis based on salient shape index. 131 - Sapna Kumari, Wenping Deng, Chathura Gunasekara, Vincent Chiang, Huann-Sheng Chen, Hao Ma, Xin Davis, Hairong Wei:
Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. 132 - Kiyoshi Ezawa:
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. 133 - Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp:
Modeling the integration of bacterial rRNA fragments into the human cancer genome. 134 - Bo Yang, Yong Wang, Pei-Yuan Qian:
Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. 135 - Wei Cheng, Yu Shi, Xiang Zhang, Wei Wang:
Sparse regression models for unraveling group and individual associations in eQTL mapping. 136 - Gregory A. Ryslik, Yuwei Cheng, Yorgo Modis, Hongyu Zhao:
Leveraging protein quaternary structure to identify oncogenic driver mutations. 137 - Matthew N. McCall, Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer, Marc K. Halushka:
A benchmark for microRNA quantification algorithms using the OpenArray platform. 138 - Sanja Glisic, David P. Cavanaugh, Krishnan K. Chittur, Milan Sencanski, Vladimir Perovic, Tijana Bojic:
Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3. 139 - Justina Zurauskiene, Christopher Yau:
pcaReduce: hierarchical clustering of single cell transcriptional profiles. 140 - Hongen Zhang, Paul S. Meltzer, Sean R. Davis:
caOmicsV: an R package for visualizing multidimensional cancer genomic data. 141 - Ruiquan Ge, Manli Zhou, Youxi Luo, Qinghan Meng, Guoqin Mai, Dongli Ma, Guoqing Wang, Fengfeng Zhou:
McTwo: a two-step feature selection algorithm based on maximal information coefficient. 142 - Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis:
Does the choice of nucleotide substitution models matter topologically? 143 - Joshua D. Starmer, Terry Magnuson:
Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains. 144 - Marvin N. Wright, Andreas Ziegler, Inke R. König:
Do little interactions get lost in dark random forests? 145 - Ran Bi, Peng Liu:
Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments. 146 - Miguel Ángel Vadillo, Pablo Garaizar:
The effect of noise-induced variance on parameter recovery from reaction times. 147 - Gianvito Urgese, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra:
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. 148 - Kerstin Johnsson, Jonas Wallin, Magnus Fontes:
Erratum to: BayesFlow: latent modeling of flow cytometry cell populations. 149 - Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun, Philip M. Kim:
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. 150 - Joost B. Beltman, Jos Urbanus, Arno Velds, Nienke van Rooij, Jan C. Rohr, Shalin H. Naik, Ton N. Schumacher:
Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. 151 - Matteo Paolo Ferla:
Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling. 152 - Likun Wang, Cong Zhang, Johnathan Watkins, Yan Jin, Michael McNutt, Yuxin Yin:
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels. 153 - Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gaël Jalowicki, Martina Kutmon, Kedar Nath Natarajan, David Tolnay, Melanie I. Stefan, Chris T. A. Evelo, Nicolas Le Novère:
The systems biology format converter. 154 - Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Lustrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford:
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. 155 - Kaiyin Zhong, Lennart C. Karssen, Manfred Kayser, Fan Liu:
CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies. 156 - Gianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna, Stefano Di Carlo:
CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction. 157 - Mohamed F. Ghalwash, Xi Hang Cao, Ivan Stojkovic, Zoran Obradovic:
Structured feature selection using coordinate descent optimization. 158 - Anders Ellern Bilgrau, Steffen Falgreen, Anders Petersen, Malene Krag Kjeldsen, Julie Støve Bødker, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted:
Unaccounted uncertainty from qPCR efficiency estimates entails uncontrolled false positive rates. 159 - Gang Fu, Ying Ding, Abhik Seal, Bin Chen, Yizhou Sun, Evan Bolton:
Predicting drug target interactions using meta-path-based semantic network analysis. 160 - Niklaus Johner, Daniel Harries, George Khelashvili:
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations. 161 - Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu:
Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. 162 - Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch:
Sortal anaphora resolution to enhance relation extraction from biomedical literature. 163 - G. Traver Hart, Jason Moffat:
BAGEL: a computational framework for identifying essential genes from pooled library screens. 164 - Daniel J. Park, Roger Li, Edmund Lau, Peter Georgeson, Tu Nguyen-Dumont, Bernard J. Pope:
UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. 165 - Padet Siriyasatien, Atchara Phumee, Phatsavee Ongruk, Katechan Jampachaisri, Kraisak Kesorn:
Analysis of significant factors for dengue fever incidence prediction. 166 - Emily Chia-Yu Su, Yu-Sing Chen, Yun-Cheng Tien, Jeff Liu, Bing-Ching Ho, Sung-Liang Yu, Sher Singh:
ChemiRs: a web application for microRNAs and chemicals. 167 - Giriraj Acharya, Gurmeet Kaur, Srikrishna Subramanian:
Evolutionary relationships between heme-binding ferredoxin α + β barrels. 168 - Zuguang Gu, Roland Eils, Matthias Schlesner:
gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. 169 - Maude Ardin, Vincent Cahais, Xavier Castells, Liacine Bouaoun, Graham B. Byrnes, Zdenko Herceg, Jiri Zavadil, Magali Olivier:
MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes. 170 - Hong Liu, Jessica Liu, Michelle Toups, Timothy Soos, Christopher Arendt:
Gene signature-based mapping of immunological systems and diseases. 171 - Kathleen Sprouffske, Andreas Wagner:
Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves. 172 - Thomas S. Rask, Bent Petersen, Donald S. Chen, Karen P. Day, Anders Gorm Pedersen:
Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data. 176 - Xuan Zhu, Jian Wang, Bo Peng, Sanjay Shete:
Empirical estimation of sequencing error rates using smoothing splines. 177 - Andrew E. Teschendorff, Allison Jones, Martin Widschwendter:
Stochastic epigenetic outliers can define field defects in cancer. 178 - Ashley J. Waardenberg, Samuel D. Bassett, Romaric Bouveret, Richard P. Harvey:
Erratum to: 'CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments'. 179 - Yingbo Li, France Rose, Florencia di Pietro, Xavier Morin, Auguste Genovesio:
Detection and tracking of overlapping cell nuclei for large scale mitosis analyses. 183 - Yu-An Huang, Zhu-Hong You, Xing Chen, Keith C. C. Chan, Xin Luo:
Sequence-based prediction of protein-protein interactions using weighted sparse representation model combined with global encoding. 184 - Bhusan K. Kuntal, Anirban Dutta, Sharmila S. Mande:
CompNet: a GUI based tool for comparison of multiple biological interaction networks. 185 - Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang:
Construction of dynamic probabilistic protein interaction networks for protein complex identification. 186 - Adam Spiro, Ehud Shapiro:
eSTGt: a programming and simulation environment for population dynamics. 187 - Navin Rustagi, Oliver A. Hampton, Jie Li, Liu Xi, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel, David A. Wheeler:
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. 188 - Martin Hess, Frank Keul, Michael Goesele, Kay Hamacher:
Addressing inaccuracies in BLOSUM computation improves homology search performance. 189 - Bridget C. Ryan, Torben S. Werner, Perry L. Howard, Robert L. Chow:
ImiRP: a computational approach to microRNA target site mutation. 190 - Mohamed Mysara, Natalie Leys, Jeroen Raes, Pieter Monsieurs:
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. 192 - Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M. Johnson, Lei Song, Adil Alaoui, Michael Harris, Robert Clarke, Louis M. Weiner, Yuriy Gusev, Subha Madhavan:
G-DOC Plus - an integrative bioinformatics platform for precision medicine. 193 - Lu Cao, Marjo de Graauw, Kuan Yan, Leah Winkel, Fons J. Verbeek:
Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening. 196 - Patrice Dosset, Patrice Rassam, Laurent Fernandez, Cedric Espenel, Eric Rubinstein, Emmanuel Margeat, Pierre-Emmanuel Milhiet:
Automatic detection of diffusion modes within biological membranes using back-propagation neural network. 197 - Paul G. O'Reilly, Qing Wen, Peter Bankhead, Philip D. Dunne, Darragh G. McArt, Suzanne McPherson, Peter Hamilton, Ken I. Mills, Shu-Dong Zhang:
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. 198 - Christian Brueffer, Lao H. Saal:
TopHat-Recondition: a post-processor for TopHat unmapped reads. 199 - Moritz von Stosch, Cristiana Rodrigues de Azevedo, Mauro Luis, Sebastião Feyo de Azevedo, Rui Oliveira:
A principal components method constrained by elementary flux modes: analysis of flux data sets. 200 - Richard J. Cotton, Johannes Graumann:
readat: An R package for reading and working with SomaLogic ADAT files. 201 - Naiem T. Issa, Jordan Kruger, Henri Wathieu, Rajarajan Raja, Stephen W. Byers, Dakshanamurthy Sivanesan:
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. 202 - Risa Kawaguchi, Hisanori Kiryu:
Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. 203 - Sébastien Guizard, Benoît Piégu, Yves Bigot:
DensityMap: a genome viewer for illustrating the densities of features. 204 - Allison Chia-Yi Wu, Scott A. Rifkin:
Erratum to: 'Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images'. 207 - Marc Sturm, Christopher M. Schroeder, Peter Bauer:
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data. 208 - Vlad Popovici, Eva Budinska, Lenka Capkova, Daniel Schwarz, Ladislav Dusek, Josef Feit, Rolf Jaggi:
Joint analysis of histopathology image features and gene expression in breast cancer. 209 - Julia Bayer, Carsten Kuenne, Jens Preussner, Mario Looso:
LimiTT: link miRNAs to targets. 210 - Qing Wen, Chang Sik Kim, Peter Hamilton, Shu-Dong Zhang:
A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping. 211 - Christos Karapiperis, Stefan J. Kempf, Roel Quintens, Omid Azimzadeh, Victoria Linares Vidal, Simonetta Pazzaglia, Dimitry Bazyka, Pier G. Mastroberardino, Zacharias G. Scouras, Soile Tapio, Mohammed Abderrafi Benotmane, Christos A. Ouzounis:
Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery. 212 - Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou:
A novel procedure on next generation sequencing data analysis using text mining algorithm. 213 - Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang, Chun-Hou Zheng:
CINOEDV: a co-information based method for detecting and visualizing n-order epistatic interactions. 214 - Nathan D. Berkowitz, Ian M. Silverman, Daniel M. Childress, Hilal Kazan, Li-San Wang, Brian D. Gregory:
A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). 215 - Ladislav Rampásek, Randi M. Jimenez, Andrej Lupták, Tomás Vinar, Brona Brejová:
RNA motif search with data-driven element ordering. 216 - Fengchao Yu, Ning Li, Weichuan Yu:
ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database. 217 - Suyash S. Shringarpure, Carlos D. Bustamante, Kenneth Lange, David H. Alexander:
Efficient analysis of large datasets and sex bias with ADMIXTURE. 218 - Zexian Zeng, Xia Jiang, Richard E. Neapolitan:
Discovering causal interactions using Bayesian network scoring and information gain. 221 - Liangcai Zhang, Ying Yuan, Karen H. Lu, Li Zhang:
Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer. 222 - Yupeng Li, Scott A. Jackson:
Crowdsourcing the nodulation gene network discovery environment. 223 - Ivani de Oliveira Negrão Lopes, Alexander Schliep, André Carlos Ponce de Leon Ferreira de Carvalho:
Automatic learning of pre-miRNAs from different species. 224 - Lina Zhang, Chengjin Zhang, Rui Gao, Runtao Yang, Qing Song:
Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes. 225 - Neel Prabh, Christian Rödelsperger:
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? 226 - Jin Tae Kwak, Stephen M. Hewitt, André Alexander Kajdacsy-Balla, Saurabh Sinha, Rohit Bhargava:
Automated prostate tissue referencing for cancer detection and diagnosis. 227 - Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach, Hubert Rehrauer:
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. 228 - Cyprien Mbogning, Philippe Broët:
Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patients. 230 - Meijian Sun, Xia Wang, Chuanxin Zou, Zenghui He, Wei Liu, Honglin Li:
Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors. 231 - Hirotaka Matsumoto, Hisanori Kiryu:
SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation. 232 - Christopher E. Gillies, Edgar A. Otto, Virginia Vega-Warner, Catherine C. Robertson, Simone Sanna-Cherchi, Ali Gharavi, Brendan Crawford, Rajendra Bhimma, Cheryl A. Winkler, Hyun Min Kang, Matthew G. Sampson:
tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine. 233 - Sukantadev Bag, Michael B. Prentice, Mingzhi Liang, Martin J. Warren, Kingshuk Roy Choudhury:
Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions. 234 - José Ignacio Requeno, José Manuel Colom:
Evaluation of properties over phylogenetic trees using stochastic logics. 235 - Niklaus Johner, Daniel Harries, George Khelashvili:
Erratum to: Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations. 236 - Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo:
Read mapping on de Bruijn graphs. 237 - Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro:
Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. 242 - Arnav Kapur, Kshitij Marwah, Gil Alterovitz:
Gene expression prediction using low-rank matrix completion. 243 - Bo Wen, Shaohang Xu, Ruo Zhou, Bing Zhang, Xiaojing Wang, Xin Liu, Xun Xu, Siqi Liu:
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. 244 - Dongdong Lin, Ji-Gang Zhang, Jingyao Li, Chao Xu, Hong-Wen Deng, Yu-Ping Wang:
An integrative imputation method based on multi-omics datasets. 247 - Guangliang Kang, Li Du, Hong Zhang:
multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions. 248 - Luciano Fernandez-Ricaud, Olga Kourtchenko, Martin Zackrisson, Jonas Warringer, Anders Blomberg:
PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics. 249 - Rainer Winnenburg, Nigam H. Shah:
Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. 250 - Zhiming Qian, Shuohong Wang, Xi En Cheng, Yan Qiu Chen:
An effective and robust method for tracking multiple fish in video image based on fish head detection. 251 - S. M. Minhaz Ud-Dean, Sandra Heise, Steffen Klamt, Rudiyanto Gunawan:
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. 252 - John J. Andersen, Bradley J. Nelson, Jeremy M. Brown:
EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics. 253 - Veronica Vinciotti, Ernst C. Wit, Rick Jansen, Eco J. C. de Geus, Brenda W. J. H. Penninx, Dorret I. Boomsma, Peter A. C. 't Hoen:
Consistency of biological networks inferred from microarray and sequencing data. 254 - Violeta N. Kovacheva, David R. J. Snead, Nasir M. Rajpoot:
A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue. 255 - Paul A. Wilkinson, Mark O. Winfield, Gary L. A. Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Cáccamo, Robert P. Davey, Keith J. Edwards:
CerealsDB 3.0: expansion of resources and data integration. 256 - Chaitanya R. Acharya, Janice M. McCarthy, Kouros Owzar, Andrew S. Allen:
Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. 257 - Francesca Rizzato, Alex Rodriguez, Alessandro Laio:
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates. 258 - Eugene Andres Houseman, Molly L. Kile, David C. Christiani, Tan A. Ince, Karl T. Kelsey, Carmen J. Marsit:
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. 259 - Shalabh Thakur, David S. Guttman:
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. 260 - Achal Rastogi, Omer Murik, Chris Bowler, Leïla Tirichine:
PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing. 261 - Mohammad Tanvir Ahamed, Anna Danielsson, Szilárd Nemes, Helena Carén:
MethPed: an R package for the identification of pediatric brain tumor subtypes. 262 - Trevor Clancy, Eivind Hovig:
Profiling networks of distinct immune-cells in tumors. 263 - Nathan Cormier, Tyler Kolisnik, Mark Bieda:
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. 270 - Renaud Vanhoutrève, Arnaud Kress, Baptiste Legrand, Hélène Gass, Olivier Poch, Julie Dawn Thompson:
LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. 271 - Pei-Yuan Sung, Yi-Ting Wang, Chao A. Hsiung, Ren-Hua Chung:
GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs. 273 - Ankur Dhanik, Jessica R. Kirshner, Douglas MacDonald, Gavin Thurston, Hsin C. Lin, Andrew J. Murphy, Wen Zhang:
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. 286 - Shunpu Zhang, Zhong Li, Kevin Beland, Guoqing Lu:
Model-based clustering with certainty estimation: implication for clade assignment of influenza viruses. 287 - Andreas Mayr, Benjamin Hofner, Matthias Schmid:
Boosting the discriminatory power of sparse survival models via optimization of the concordance index and stability selection. 288 - Hanwei Yan, Xiaogang Dai, Kai Feng, Qiuyue Ma, Tongming Yin:
IGDD: a database of intronless genes in dicots. 289 - Vincenzo Lagani, Argyro D. Karozou, David Gomez-Cabrero, Gilad Silberberg, Ioannis Tsamardinos:
Erratum to: A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. 290 - Ariful Azad, Bartek Rajwa, Alex Pothen:
flowVS: channel-specific variance stabilization in flow cytometry. 291 - Aaron Y. Lee, Cecilia S. Lee, Russell N. Van Gelder:
Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations. 292 - Paolo Romano, Francesca Cordero:
Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'. 293 - Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fei Li, Xiaochen Bo:
RevEcoR: an R package for the reverse ecology analysis of microbiomes. 294 - Umar Khan Niazi, Kathrin K. Geyer, Martin J. Vickers, Karl F. Hoffmann, Martin T. Swain:
DISMISS: detection of stranded methylation in MeDIP-Seq data. 295 - Rezvan Ehsani, Finn Drabløs:
TopoICSim: a new semantic similarity measure based on gene ontology. 296 - Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. 298 - Hong Pan, Joanna D. Holbrook, Neerja Karnani, Chee Keong Kwoh:
Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment. 299 - William R. Taylor:
Reduction, alignment and visualisation of large diverse sequence families. 300 - Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou:
Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm. 301 - Andrew E. Jaffe, Thomas Hyde, Joel Kleinman, Daniel R. Weinberger, Joshua Chenoweth, Ronald McKay, Jeffrey T. Leek, Carlo Colantuoni:
Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. 302 - Adam Spiro, Ehud Shapiro:
Erratum to: eSTGt: a programming and simulation environment for population dynamics. 303 - Kiyoshi Ezawa:
General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable? 304:1-304:25 - Andre P. Masella, Christopher M. Lalansingh, Pragash Sivasundaram, Michael Fraser, Robert G. Bristow, Paul C. Boutros:
BAMQL: a query language for extracting reads from BAM files. 305 - Pongsakorn Kanjanatanin, Rath Pichyangkura, Surasak Chunsrivirot:
Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths. 306 - Thammakorn Saethang, D. Michael Payne, Yingyos Avihingsanon, Trairak Pisitkun:
A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. 307 - Jianlong Zhou, Xiuying Wang, Hui Cui, Peng Gong, Xianglin Miao, Yalin Miao, Chun Xiao, Fang Chen, Dagan Feng:
Topology-aware illumination design for volume rendering. 309 - Zhenhua Yu, Ao Li, Minghui Wang:
CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data. 310 - Anestis Gkanogiannis, Stéphane Gazut, Marcel Salanoubat, Sawsan Kanj, Thomas Brüls:
A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. 311 - SongLu Li, Sejong Oh:
Improving feature selection performance using pairwise pre-evaluation. 312 - Rallis Karamichalis, Lila Kari, Stavros Konstantinidis, Steffen Kopecki, Stephen Solis-Reyes:
Additive methods for genomic signatures. 313 - Mona Riemenschneider, Thomas Hummel, Dominik Heider:
SHIVA - a web application for drug resistance and tropism testing in HIV. 314 - David DeTomaso, Nir Yosef:
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. 315 - Ming-an Sun, Qing Zhang, Yejun Wang, Wei Ge, Dianjing Guo:
Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features. 316 - Naamah Bloch, David Harel:
The tumor as an organ: comprehensive spatial and temporal modeling of the tumor and its microenvironment. 317 - Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek, Kourosh Zarringhalam:
Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. 318 - Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo, Tatsuhiko Tsunoda:
Stepwise iterative maximum likelihood clustering approach. 319 - Xue Zhang, Wangxin Xiao, Marcio Luis Acencio, Ney Lemke, Xujing Wang:
An ensemble framework for identifying essential proteins. 322 - Jian Zhang, Bo Gao, Haiting Chai, Zhiqiang Ma, Guifu Yang:
Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm. 323 - Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma:
Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model. 324 - David Buzatto, Suzelei de Castro França, Sônia Marli Zingaretti:
CryGetter: a tool to automate retrieval and analysis of Cry protein data. 325 - Ping Li, Yaling Nie, Jingkai Yu:
Fusing literature and full network data improves disease similarity computation. 326 - Stefanie Hieke, Axel Benner, Richard F. Schlenl, Martin Schumacher, Lars Bullinger, Harald Binder:
Integrating multiple molecular sources into a clinical risk prediction signature by extracting complementary information. 327 - Sumudu P. Leelananda, Andrzej Kloczkowski, Robert L. Jernigan:
Fold-specific sequence scoring improves protein sequence matching. 328 - Dingfang Li, Longqiang Luo, Wen Zhang, Feng Liu, Fei Luo:
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs. 329 - Juan Antonio Gómez Pulido, Jose L. Cerrada-Barrios, Sebastian Trinidad-Amado, José Manuel Lanza-Gutiérrez, Ramón Ángel Fernández Díaz, Broderick Crawford, Ricardo Soto:
Fine-grained parallelization of fitness functions in bioinformatics optimization problems: gene selection for cancer classification and biclustering of gene expression data. 330 - Barbara F. F. Huang, Paul C. Boutros:
The parameter sensitivity of random forests. 331 - Yalchin Oytam, Fariborz Sobhanmanesh, Konsta Duesing, Joshua C. Bowden, Megan Osmond-McLeod, Jason Ross:
Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets. 332 - Helena Mendes-Soares, Michael B. Mundy, Luis Mendes Soares, Nicholas Chia:
MMinte: an application for predicting metabolic interactions among the microbial species in a community. 343 - Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe, Arnoldo Frigessi:
Tilting the lasso by knowledge-based post-processing. 344 - Mirko Signorelli, Veronica Vinciotti, Ernst C. Wit:
NEAT: an efficient network enrichment analysis test. 352 - Marziyeh Movahedi, Fatemeh Zare-Mirakabad, Seyed Shahriar Arab:
Evaluating the accuracy of protein design using native secondary sub-structures. 353 - Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vítor V. Vasconcelos, Agostinho Antunes:
LMAP: Lightweight Multigene Analyses in PAML. 354 - Chee Yee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher, Berthold Göttgens:
BTR: training asynchronous Boolean models using single-cell expression data. 355 - Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu, Hong Yan:
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. 358 - Xi Hang Cao, Ivan Stojkovic, Zoran Obradovic:
A robust data scaling algorithm to improve classification accuracies in biomedical data. 359 - Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard A. Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata, Fuli Yu:
A hybrid computational strategy to address WGS variant analysis in >5000 samples. 361 - Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram, Andrzej Kolinski:
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. 362 - David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani, Koji Tsuda:
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. 363 - Alan Hodgkinson, Jean-Christophe Grenier, Elias Gbeha, Philip Awadalla:
A haplotype-based normalization technique for the analysis and detection of allele specific expression. 364 - Santhilal Subhash, Chandrasekhar Kanduri:
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. 365 - David Angeles-Albores, Raymond Y. N. Lee, Juancarlos Chan, Paul W. Sternberg:
Tissue enrichment analysis for C. elegans genomics. 366 - Kai Dong, Hongyu Zhao, Tiejun Tong, Xiang Wan:
NBLDA: negative binomial linear discriminant analysis for RNA-Seq data. 369 - Qiu-Zhong Zhou, Bindan Zhang, Quan-You Yu, Ze Zhang:
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. 370 - Le Ou-Yang, Xiao-Fei Zhang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu, Zhiyong Liu, Hong Yan:
Protein complex detection based on partially shared multi-view clustering. 371 - Ricardo Cerri, Rodrigo C. Barros, André C. P. L. F. de Carvalho, Yaochu Jin:
Reduction strategies for hierarchical multi-label classification in protein function prediction. 373 - José María Fernández-Calabozo, Francisco J. Valverde-Albacete, Carmen Peláez-Moreno:
Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis. 374 - Shenghua Cheng, Tingwei Quan, Xiaomao Liu, Shaoqun Zeng:
Large-scale localization of touching somas from 3D images using density-peak clustering. 375 - Lydia Müller, Daniel Gerighausen, Mariam Farman, Dirk Zeckzer:
Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. 377 - Shunsuke Shigemitsu, Cao Wei, Tohru Terada, Kentaro Shimizu:
Development of a prediction system for tail-anchored proteins. 378 - Wenling E. Chang, Matthew W. Peterson, Christopher D. Garay, Tonia Korves:
Pathogen metadata platform: software for accessing and analyzing pathogen strain information. 379 - Bertrand S. Clarke, Saeid Amiri, Jennifer Clarke:
EnsCat: clustering of categorical data via ensembling. 380 - Maciej Antczak, Marta Kasprzak, Piotr Lukasiak, Jacek Blazewicz:
Structural alignment of protein descriptors - a combinatorial model. 383 - Changsheng Zhang, Hongmin Cai, Jingying Huang, Yan Song:
nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data. 384 - Lev I. Rubanov, Alexander V. Seliverstov, Oleg A. Zverkov, Vassily A. Lyubetsky:
A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata. 385 - Wonjun Choi, Baeksoo Kim, Hyejin Cho, Doheon Lee, Hyunju Lee:
A corpus for plant-chemical relationships in the biomedical domain. 386 - Vesna Memisevic, Kamal Kumar, Nela Zavaljevski, David DeShazer, Anders Wallqvist, Jaques Reifman:
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. 387 - Tyler W. H. Backman, Thomas Girke:
systemPipeR: NGS workflow and report generation environment. 388 - Siguna Müller, Farhad Jafari, Don Roth:
A covert authentication and security solution for GMOs. 389 - Bohdan B. Khomtchouk, James R. Hennessy, Claes Wahlestedt:
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. 390 - Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson:
solveME: fast and reliable solution of nonlinear ME models. 391 - Ignacio Atal, Jean-David Zeitoun, Aurélie Névéol, Philippe Ravaud, Raphaël Porcher, Ludovic Trinquart:
Automatic classification of registered clinical trials towards the Global Burden of Diseases taxonomy of diseases and injuries. 392 - Behrooz Torabi Moghadam, Michal Dabrowski, Bozena Kaminska, Manfred G. Grabherr, Jan Komorowski:
Combinatorial identification of DNA methylation patterns over age in the human brain. 393 - Christian Hundt, Andreas Hildebrandt, Bertil Schmidt:
rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. 394 - Kiyoshi Ezawa:
General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation. 397 - Yijie Ding, Jijun Tang, Fei Guo:
Predicting protein-protein interactions via multivariate mutual information of protein sequences. 398 - Samuel T. Westreich, Ian Korf, David A. Mills, Danielle G. Lemay:
SAMSA: a comprehensive metatranscriptome analysis pipeline. 399 - Daniel R. Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey, David Haussler:
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. 400 - Felix Lam, Christopher M. Lalansingh, Holly E. Babaran, Zhiyuan Wang, Stephenie D. Prokopec, Natalie S. Fox, Paul C. Boutros:
VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams. 401 - Valentin Voillet, Philippe Besse, Laurence Liaubet, Magali San Cristobal, Ignacio González:
Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework. 402 - Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L. Slager:
Impact of post-alignment processing in variant discovery from whole exome data. 403 - Qian Qin, Shenglin Mei, Qiu Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Han Xu, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry Long:
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. 404 - Long Pei, Min Xu, Zachary Frazier, Frank Alber:
Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking. 405 - Patrick K. O'Neill, Ivan Erill:
Parametric bootstrapping for biological sequence motifs. 406 - Junli Du, Man-Lin Li, Zhifa Yuan, Mancai Guo, Jiuzhou Song, Xiaozhen Xie, Yulin Chen:
A decision analysis model for KEGG pathway analysis. 407 - Rasha Elhesha, Tamer Kahveci:
Identification of large disjoint motifs in biological networks. 408 - John Christian Givhan Spainhour, Peng Qiu:
Identification of gene-drug interactions that impact patient survival in TCGA. 409 - Julien Dorier, Isaac Crespo, Anne Niknejad, Robin Liechti, Martin Ebeling, Ioannis Xenarios:
Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. 410 - Pritha Ghosh, Oommen K. Mathew, Ramanathan Sowdhamini:
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. 411 - Charles Girardot, Jelle Scholtalbers, Sajoscha Sauer, Shu-Yi Su, Eileen E. M. Furlong:
Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. 419 - Jiwoong Kim, Min Soo Kim, Andrew Y. Koh, Yang Xie, Xiaowei Zhan:
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. 420 - Philip J. Wilson, Stephen L. R. Ellison:
Extending digital PCR analysis by modelling quantification cycle data. 421 - Hussein A. Hejase, Kevin J. Liu:
A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. 422 - Elena Grassi, Elisa Mariella, Antonio Lembo, Ivan Molineris, Paolo Provero:
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. 423 - Juan Antonio García-Martín, Amir H. Bayegan, Iván Dotú, Peter Clote:
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. 424 - Ibrahim Tanyalcin, Katrien Stouffs, Dorien Daneels, Carla Al Assaf, Willy Lissens, Anna C. Jansen, Alexander Gheldof:
Convert your favorite protein modeling program into a mutation predictor: "MODICT". 425:1-425:19 - Sergi Sayols, Denise Scherzinger, Holger Klein:
dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data. 428 - German Demidov, Tamara Simakova, Julia Vnuchkova, Anton Bragin:
A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data. 429 - Violeta N. Kovacheva, Nasir M. Rajpoot:
Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images. 430 - Sheng-Jou Hung, Yi-Lin Chen, Chia-Hung Chu, Chuan-Chun Lee, Wan-Li Chen, Ya-Lan Lin, Ming-Ching Lin, Chung-Liang Ho, Tsunglin Liu:
TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences. 433 - Thomas Shafee, Ira Cooke:
AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments. 434 - Ka-Kit Lam, Richard Hall, Alicia Clum, Satish Rao:
BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly. 435 - Jorge Álvarez-Jarreta, Eduardo Ruiz-Pesini:
MEvoLib v1.0: the first molecular evolution library for Python. 436 - Yiling Lee, Rozieffa Roslan, Shariza Azizan, Mohd Firdaus Raih, Effirul I. Ramlan:
An analysis of simple computational strategies to facilitate the design of functional molecular information processors. 438 - Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro:
Erratum to: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. 439 - H. Robert Frost, Christopher I. Amos:
Unsupervised gene set testing based on random matrix theory. 442:1-442:16 - Jing Zhang, Sanchit Misra, Hao Wang, Wu-chun Feng:
muBLASTP: database-indexed protein sequence search on multicore CPUs. 443:1-443:14 - Lian He, Stephen Gang Wu, Muhan Zhang, Yixin Chen, Yinjie J. Tang:
WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism. 444:1-444:7 - Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng:
SGFSC: speeding the gene functional similarity calculation based on hash tables. 445:1-445:14 - David M. Budden, Edmund J. Crampin:
Distributed gene expression modelling for exploring variability in epigenetic function. 446:1-446:8 - Dmitry S. Ischenko, Dmitry G. Alexeev, Egor Shitikov, Alexandra Kanygina, Maja Malakhova, Elena S. Kostryukova, Andrey Larin, Sergey Kovalchuk, Olga Pobeguts, Ivan Butenko, Nikolay A. Kolchanov, Ilya A. Altukhov, Elena Ilina, Vadim Govorun:
Large scale analysis of amino acid substitutions in bacterial proteomics. 450:1-450:10 - Ruifeng Hu, Guibo Sun, Xiaobo Sun:
LSCplus: a fast solution for improving long read accuracy by short read alignment. 451:1-451:9 - Jingchao Ni, Mehmet Koyutürk, Hanghang Tong, Jonathan L. Haines, Rong Xu, Xiang Zhang:
Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model. 453:1-453:13 - Lorraine A. K. Ayad, Solon P. Pissis, Ahmad Retha:
libFLASM: a software library for fixed-length approximate string matching. 454:1-454:12 - Kiyoshi Ezawa:
Erratum to: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable? 457:1-457:2 - Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow:
DASP3: identification of protein sequences belonging to functionally relevant groups. 458:1-458:13 - Rezvan Ehsani, Shahram Bahrami, Finn Drabløs:
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function. 459:1-459:16 - Casey P. Shannon, Virginia Chen, Mandeep Takhar, Zsuzsanna Hollander, Robert Balshaw, Bruce McManus, Scott J. Tebbutt, Don D. Sin, Raymond T. Ng:
SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations. 460:1-460:11 - Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicolas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma'ayan:
GEN3VA: aggregation and analysis of gene expression signatures from related studies. 461:1-461:12 - Doulaye Dembélé, Philippe Kastner:
Comments on: fold change rank ordering statistics: a new method for detecting differentially expressed genes. 462:1-462:3 - Yang Song, Weidong Cai, Heng Huang, Dagan Feng, Yue Wang, Mei Chen:
Bioimage classification with subcategory discriminant transform of high dimensional visual descriptors. 465:1-465:15 - Xiuzhen Hu, Kai Wang, Qiwen Dong:
Protein ligand-specific binding residue predictions by an ensemble classifier. 470:1-470:12 - Hong Cui, Dongfang Xu, Steven S. Chong, Martin Ramirez, Thomas Rodenhausen, James A. Macklin, Bertram Ludäscher, Robert A. Morris, Eduardo M. Soto, Nicolás Mongiardino Koch:
Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building. 471:1-471:22 - Natalia Acevedo-Luna, Leonardo Mariño-Ramírez, Armand Halbert, Ulla Hansen, David Landsman, John L. Spouge:
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. 479:1-479:12 - Leonie Weinhold, Simone Wahl, Sonali Pechlivanis, Per Hoffmann, Matthias Schmid:
A statistical model for the analysis of beta values in DNA methylation studies. 480:1-480:11 - David T. Barkan, Xiao-li Cheng, Herodion Celino, Tran Trung Tran, Ashok Bhandari, Charles S. Craik, Andrej Sali, Mark L. Smythe:
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. 481:1-481:16 - Sang Y. Chun, Caitlin M. Rodriguez, Peter K. Todd, Ryan Mills:
SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data. 482:1-482:6 - Gabriel E. Hoffman, Eric E. Schadt:
variancePartition: interpreting drivers of variation in complex gene expression studies. 483:1-483:13 - Giovanni Scala, Ornella Affinito, Domenico A. Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sergio Cocozza:
ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons. 484:1-484:12 - Sophie Trefely, Peter Ashwell, Nathaniel W. Snyder:
FluxFix: automatic isotopologue normalization for metabolic tracer analysis. 485:1-485:8 - Rajat Anand, Srikanth Ravichandran, Samrat Chatterjee:
A new method of finding groups of coexpressed genes and conditions of coexpression. 486:1-486:14 - Yu Bao, Morihiro Hayashida, Tatsuya Akutsu:
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length. 487:1-487:11 - Grace Tzun-Wen Shaw, Yueh-Yang Pao, Daryi Wang:
MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles. 488:1-488:12 - Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter:
The Lair: a resource for exploratory analysis of published RNA-Seq data. 490:1-490:6 - Hardik I. Parikh, Vishal N. Koparde, Steven P. Bradley, Gregory A. Buck, Nihar U. Sheth:
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. 491:1-491:6 - Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi:
Predicting the recurrence of noncoding regulatory mutations in cancer. 492:1-492:11 - Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor A. S. Saqi, Ron Henkel, Johann Pellet, Charles Auffray:
STON: exploring biological pathways using the SBGN standard and graph databases. 494:1-494:9 - Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng:
DeepQA: improving the estimation of single protein model quality with deep belief networks. 495:1-495:9 - Eleanor Stanley, Eleni Ioanna Delatola, Esther Nkuipou-Kenfack, William Spooner, Walter Kolch, Joost P. Schanstra, Harald Mischak, Thomas Koeck:
Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease. 496:1-496:10 - Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin:
Integrating mean and variance heterogeneities to identify differentially expressed genes. 497:1-497:14 - Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng:
ConEVA: a toolbox for comprehensive assessment of protein contacts. 517:1-517:12 - Patrice Godard, Matthew Page:
PCAN: phenotype consensus analysis to support disease-gene association. 518:1-518:9 - Fouad Zahdeh, Liran Carmel:
The role of nucleotide composition in premature termination codon recognition. 519:1-519:14 - Sony Hartono Wijaya, Farit Mochamad Afendi, Irmanida Batubara, Latifah K. Darusman, Md. Altaf-Ul-Amin, Shigehiko Kanaya:
Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines. 520:1-520:19 - Mark C. Hiner, Curtis Rueden, Kevin W. Eliceiri:
SCIFIO: an extensible framework to support scientific image formats. 521:1-521:5 - Camilo Andrés Mora Osorio, Andrés Fernando González Barrios:
Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations. 522:1-522:9 - Hamzah Syed, Andrea L. Jorgensen, Andrew P. Morris:
SurvivalGWAS_Power: a user friendly tool for power calculations in pharmacogenetic studies with "time to event" outcomes. 523:1-523:8 - Nicolas Cerveau, Daniel J. Jackson:
Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms. 525:1-525:13 - Pashupati P. Mishra, Alan Medlar, Liisa Holm, Petri Törönen:
Robust multi-group gene set analysis with few replicates. 526:1-526:12 - Ehsan Kazemi, Seyed Hamed Hassani, Matthias Grossglauser, Hassan Pezeshgi Modarres:
PROPER: global protein interaction network alignment through percolation matching. 527:1-527:16 - Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade, Hong Cui:
Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources. 528:1-528:16 - Suzanne M. Paley, Paul E. O'Maille, Daniel S. Weaver, Peter D. Karp:
Pathway collages: personalized multi-pathway diagrams. 529:1-529:10 - Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote:
New tools to analyze overlapping coding regions. 530:1-530:15 - Yunli Wang, Rene Richard, Youlian Pan:
Prior knowledge guided eQTL mapping for identifying candidate genes. 531:1-531:12 - Svetlana Bulashevska, Colin Priest, Daniel Speicher, Jörg Zimmermann, Frank Westermann, Armin B. Cremers:
SwitchFinder - a novel method and query facility for discovering dynamic gene expression patterns. 532:1-532:15 - Reda Rawi, Raghvendra Mall, Khalid Kunji, Mohammed El Anbari, Michaël Aupetit, Ehsan Ullah, Halima Bensmail:
COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. 533:1-533:9 - Yuanzhe Bei, Pengyu Hong:
Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes. 541:1-541:19 - Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez:
Efficient randomization of biological networks while preserving functional characterization of individual nodes. 542:1-542:14 - Markus Lux, Jan Krüger, Christian Rinke, Irena Maus, Andreas Schlüter, Tanja Woyke, Alexander Sczyrba, Barbara Hammer:
acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data. 543:1-543:11 - Zeina Shreif, Daniel M. Gatti, Vipul Periwal:
Block network mapping approach to quantitative trait locus analysis. 544:1-544:13 - Shun Guo, Qingshan Jiang, Lifei Chen, Donghui Guo:
Gene regulatory network inference using PLS-based methods. 545:1-545:10 - Rafal Adamczak, Jarek Meller:
UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data. 546:1-546:8 - Narayan Jayaram, Daniel Usvyat, Andrew C. R. Martin:
Evaluating tools for transcription factor binding site prediction. 547 - Jianqiu Yang, Xinyi Shi, Lun Hu, Daipeng Luo, Jing Peng, Shengwu Xiong, Fanjing Kong, Baohui Liu, Xiaohui Yuan:
InDel marker detection by integration of multiple softwares using machine learning techniques. 548
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