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ORCIDBMC Bioinformatics, Volume 16
Volume 16, 2015
- Guo-Xian Yu, Hailong Zhu, Carlotta Domeniconi:
Predicting protein functions using incomplete hierarchical labels. 1:1-1:12 - Wei Cheng, Shi Yu, Xiang Zhang, Wei Wang
:
Fast and robust group-wise eQTL mapping using sparse graphical models. 2:1-2:16 - Max Greenfeld, Jan-Willem van de Meent, Dmitri S. Pavlichin, Hideo Mabuchi, Chris H. Wiggins, Ruben L. Gonzalez, Daniel Herschlag:
Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. 3:1-3:4 - Vikas Bansal, Ondrej Libiger:
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations. 4:1-4:11 - Martin Walker, María-Gloria Basáñez, André Ouédraogo, Cornelus Hermsen, Teun Bousema, Thomas S. Churcher:
Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study. 5:1-5:11 - Dimitar Hristovski, Dejan Dinevski, Andrej Kastrin, Thomas C. Rindflesch:
Biomedical question answering using semantic relations. 6:1-6:14 - Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew P. Yeh, Adam Godzik, L. Aravind:
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. 7:1-7:9 - Wandrille Duchemin, Pierre-Yves Dupont, Matthew A. Campbell, Austen Ganley, Murray P. Cox:
HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species. 8:1-8:4 - Shi Yang Tan, Avirup Dutta, Nick S. Jakubovics, Mia Yang Ang, Cheuk C. Siow, Naresh V. R. Mutha, Hamed Heydari, Guat Jah Wong, Siew Woh Choo:
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. 9:1-9:13 - Eric Marinier, Daniel G. Brown, Brendan J. McConkey:
Pollux: platform independent error correction of single and mixed genomes. 10:1-10:12 - Xiaowei Wu, Ming-an Sun, Hongxiao Zhu, Hehuang Xie:
Nonparametric Bayesian clustering to detect bipolar methylated genomic loci. 11:1-11:12 - Joana Vieira Silva, Sooyeon Yoon, Sara Domingues, Sofia Guimarães, Alexander V. Goltsev, Edgar da Cruz e Silva, José F. F. Mendes, Odete da Cruz e Silva, Margarida Fardilha:
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. 12:1-12:12 - Robert J. Flassig, Iryna Migal, Esther der Zalm, Liisa K. Rihko-Struckmann, Kai Sundmacher:
Rational selection of experimental readout and intervention sites for reducing uncertainties in computational model predictions. 13:1-13:13 - Zhong-Ru Xie, Jiawen Chen, Yinghao Wu:
Decomposing the space of protein quaternary structures with the interface fragment pair library. 14:1-14:10 - Askar Obulkasim, Gerrit A. Meijer, Mark A. van de Wiel:
Semi-supervised adaptive-height snipping of the hierarchical clustering tree. 15:1-15:11 - Nicholas Johnson, Huanan Zhang, Gang Fang, Vipin Kumar, Rui Kuang:
SubPatCNV: approximate subspace pattern mining for mapping copy-number variations. 16:1-16:12 - Frank Reinecke, Ravi Satya, John DiCarlo:
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls. 17:1-17:9 - José Torres, Andrés Domínguez, Joaquín Giménez, Ignacio Castelló, Joaquín Blázquez, Ignacio Espert:
Fast inexact mapping using advanced tree exploration on backward search methods. 18:1-18:11 - Carsten Kemena, Tristan Feildel, Erich Bornberg-Bauer:
MDAT- Aligning multiple domain arrangements. 19:1-19:7 - Ali Esmaili-Taheri, Mohammad Ganjtabesh:
ERD: a fast and reliable tool for RNA design including constraints. 20:1-20:11 - Sterling Sawaya, James Boocock, Michael A. Black, Neil J. Gemmell:
Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. 21:1-21:14 - Pilib Ó Broin, Terry J. Smith, Aaron Golden:
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. 22:1-22:12 - Timo Lassmann:
TagDust2: a generic method to extract reads from sequencing data. 24:1-24:8 - Andrea Cassioli, Benjamin Bardiaux, Guillaume Bouvier, Antonio Mucherino, Rafael Alves, Leo Liberti, Michael Nilges, Carlile Lavor, Thérèse E. Malliavin:
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. 23:1-23:15 - Umesh K. Nandal, Wytze J. Vlietstra, Carsten Byrman, Rienk E. Jeeninga, Jeffrey H. Ringrose, Antoine H. C. van Kampen, Dave Speijer, Perry D. Moerland:
Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. 25:1-25:11 - Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: a framework for ontology-based data access in biology. 26:1-26:9 - Humberto Sánchez, Claire Wyman:
SFMetrics: an analysis tool for scanning force microscopy images of biomolecules. 27:1-27:9 - Natallia Kulik, Kristýna Slámová, Rüdiger Ettrich, Vladimír Kren:
Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility. 28:1-28:15 - Dong Seon Kim, Yoonsoo Hahn:
The acquisition of novel N-glycosylation sites in conserved proteins during human evolution. 29:1-29:12 - Rowan G. Zellers, Robert A. Drewell, Jacqueline M. Dresch:
MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding. 30:1-30:14 - Jyoti Shankar, Sebastian Szpakowski, Norma V. Solis, Stephanie Mounaud, Hong Liu, Liliana Losada, William C. Nierman, Scott G. Filler:
A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses. 31:1-31:18 - Federico Comoglio, Cem Sievers, Renato Paro:
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data. 32:1-32:10 - Shanshan Cheng, Yang Zhang, Charles L. Brooks III:
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. 33:1-33:12 - Juliana S. Bernardes, Fabio R. J. Vieira, Lygia Costa, Gerson Zaverucha:
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families. 34:1-34:14 - Mina Ozahata, Ester C. Sabino, Ricardo Diaz, Roberto Marcondes Cesar Jr., João Eduardo Ferreira:
Data-intensive analysis of HIV mutations. 35:1-35:23 - Ying Wang, Haiyan Hu, Xiaoman Li:
MBBC: an efficient approach for metagenomic binning based on clustering. 36:1-36:11 - Vittorio Fortino, Harri Alenius, Dario Greco:
BACA: bubble chArt to compare annotations. 37:1-37:5 - Chengyao Zhong, Zhiwei Hou, Jihua Huang, Qingdong Xie, Ying Zhong:
Mutations and CpG islands among hepatitis B virus genotypes in Europe. 38:1-38:11 - Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang:
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. 39:1-39:15 - Alison Callahan, Juan Cifuentes, Michel Dumontier:
An evidence-based approach to identify aging-related genes in Caenorhabditis elegans. 40:1-40:18 - Ramón Díaz-Uriarte:
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. 41:1-41:26 - Aakrosh Ratan, Thomas L. Olson, Thomas P. Loughran, Webb Miller:
Identification of indels in next-generation sequencing data. 42:1-42:8 - Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos García, Francisco Tirado, Alberto D. Pascual-Montano:
NMF-mGPU: non-negative matrix factorization on multi-GPU systems. 43:1-43:12 - Jiajie Peng, Sahra Uygun, Taehyong Kim, Yadong Wang, Seung Y. Rhee, Jin Chen:
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. 44:1-44:14 - Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido:
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. 45:1-45:17 - Sungho Won, Wonji Kim, Sungyoung Lee, Young Lee, Joohon Sung, Taesung Park:
Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants. 46:1-46:14 - Fengqiong Huang, James A. Macklin, Hong Cui, Heather A. Cole, Lorena Endara:
OTO: Ontology Term Organizer. 47:1-47:18 - Jiehuan Sun, Hongyu Zhao:
The application of sparse estimation of covariance matrix to quadratic discriminant analysis. 48:1-48:9 - Michael Binns, Pedro de Atauri, Anestis Vlysidis, Marta Cascante, Constantinos Theodoropoulos:
Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes. 49:1-49:19 - David Kracht, Steffen Schober:
Insertion and deletion correcting DNA barcodes based on watermarks. 50:1-50:14 - Konrad Zych, Yang Li, K. Joeri van der Velde, Ronny Joosen, Wilco Ligterink, Ritsert C. Jansen, Danny Arends:
Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. 51:1-51:8 - Lariza Laura de Oliveira, Paulo de Oliveira, Renato Tinós:
A multiobjective approach to the genetic code adaptability problem. 52:1-52:20 - Ailith Pirie, Angela M. Wood, Michael Lush, Jonathan P. Tyrer, Paul D. P. Pharoah:
The effect of rare variants on inflation of the test statistics in case-control analyses. 53:1-53:5 - Hui-Ling Huang, Yu-Chung Wu, Li-Jen Su, Yun-Ju Huang, Phasit Charoenkwan, Wen-Liang Chen, Hua-Chin Lee, William C. Chu, Shinn-Ying Ho:
Discovery of prognostic biomarkers for predicting lung cancer metastasis using microarray and survival data. 54:1-54:14 - Àlex Bravo, Janet Piñero González, Núria Queralt-Rosinach, Michael Rautschka, Laura Inés Furlong:
Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research. 55:1-55:17 - Pablo A. Moreno, Stephan Beisken, Bhavana Harsha, Venkatesh Muthukrishnan, Ilinca Tudose, Adriano Dekker, Stefanie Dornfeldt, Franziska Taruttis, Ivo Grosse, Janna Hastings, Steffen Neumann, Christoph Steinbeck:
BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology. 56:1-56:7 - Sun Kim, Zhiyong Lu, W. John Wilbur:
Identifying named entities from PubMed®; for enriching semantic categories. 57:1-57:10 - Stanley Mbandi, Uljana Hesse, Peter van Heusden, Alan Christoffels:
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. 58:1-58:9 - Bie M. P. Verbist, Lieven Clement, Joke Reumers, Kim Thys, Alexander Vapirev, Willem Talloen, Yves Wetzels, Joris Meys, Jeroen Aerssens, Luc Bijnens, Olivier Thas:
ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering. 59:1-59:11 - Matthias Heinig, Maria Colomé-Tatché, Aaron Taudt, Carola Rintisch, Sebastian Schafer, Michal Pravenec, Norbert Hübner, Martin Vingron, Frank Johannes:
histoneHMM: Differential analysis of histone modifications with broad genomic footprints. 60:1-60:15 - Juan P. Steibel, Heng Wang, Ping-Shou Zhong:
A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium. 61:1-61:12 - A. Dhanasekaran, Jon L. Pearson, Balasubramanian Ganesan, Bart C. Weimer:
Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction. 62:1-62:13 - Caleb K. Stein, Pingping Qu, Joshua Epstein, Amy Buros, Adam Rosenthal, John Crowley, Gareth Morgan, Bart Barlogie:
Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat. 63:1-63:9 - Marcílio Carlos Pereira de Souto, Pablo A. Jaskowiak, Ivan G. Costa:
Impact of missing data imputation methods on gene expression clustering and classification. 64:1-64:9 - Sandeep Kumar Kushwaha, Lokeshwaran Manoharan, Tejashwari Meerupati, Katarina Hedlund, Dag G. Ahrén:
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. 65:1-65:11 - Maochun Qin, Biao Liu, Jeffrey M. Conroy, Carl D. Morrison, Qiang Hu, Yubo Cheng, Mitsuko Murakami, Adekunle O. Odunsi, Candace S. Johnson, Lei Wei, Song Liu, Jianmin Wang:
SCNVSim: somatic copy number variation and structure variation simulator. 66:1-66:6 - Radu M. Suciu, Emir Aydin, Brian E. Chen:
GeneDig: a web application for accessing genomic and bioinformatics knowledge. 67:1-67:7 - Etienne Lord, Abdoulaye Baniré Diallo, Vladimir Makarenkov:
Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms. 68:1-68:19 - Matthias Scheuch, Dirk Höper, Martin Beer:
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. 69:1-69:17 - H. Robert Frost, Zhigang Li, Jason H. Moore:
Spectral gene set enrichment (SGSE). 70:1-70:11 - Watcharaporn Tanchotsrinon, Chidchanok Lursinsap, Yong Poovorawan:
A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition. 71:1-71:13 - Chuan Jiang, Chao Chen, Ziyue Huang, Renyi Liu, Jerome Verdier:
ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. 72:1-72:8 - Koen Herten, Matthew S. Hestand, Joris Robert Vermeesch, Jeroen K. J. Van Houdt:
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. 73:1-73:6 - Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry:
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. 74:1-74:16 - Yancy Lo, Hyun Min Kang, Matthew R. Nelson, Mohammad I. Othman, Stephanie L. Chissoe, Margaret G. Ehm, Gonçalo R. Abecasis, Sebastian Zöllner:
Comparing variant calling algorithms for target-exon sequencing in a large sample. 75:1-75:10 - Xi-Mei Zhang, Lin Guo, Mei-Hua Chi, Hong-Mei Sun, Xiao-Wen Chen:
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. 76:1-76:7 - Xiang Zhan, Andrew D. Patterson, Debashis Ghosh:
Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data. 77:1-77:13 - Monika Michalovova, Zdenek Kubat, Roman Hobza, Boris Vyskot, Eduard Kejnovský:
Fully automated pipeline for detection of sex linked genes using RNA-Seq data. 78:1-78:8 - Lars Snipen, Kristian Hovde Liland:
micropanmicropan: an R-package for microbial pan-genomics. 79:1-79:8 - Bui Thang Ngoc, Tu Bao Ho, Tatsuo Kanda:
A semi-supervised tensor regression model for siRNA efficacy prediction. 80:1-80:12 - Nathan Weinstein, Elizabeth Ortiz-Gutiérrez, Stalin Muñoz, David A. Rosenblueth, Elena R. Álvarez-Buylla, Luis Mendoza:
A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva. 81:1-81:21 - Laxmi Parida, Niina Haiminen:
SimBA: simulation algorithm to fit extant-population distributions. 82:1-82:9 - Nicolas Fiorini, Sylvie Ranwez, Jacky Montmain, Vincent Ranwez:
USI: a fast and accurate approach for conceptual document annotation. 83:1-83:10 - André Lacour, Vitalia Schüller, Dmitriy Drichel, Christine Herold, Frank Jessen, Markus Leber, Wolfgang Maier, Markus M. Nöthen, Alfredo Ramirez, Tatsiana Vaitsiakhovich, Tim Becker:
Novel genetic matching methods for handling population stratification in genome-wide association studies. 84:1-84:12 - Lichun Ma, Debby Dan Wang, Yiqing Huang, Hong Yan, Maria P. Wong, Victor C. S. Lee:
EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib. 85:1-85:10 - Rodrigo Liberal, Beata K. Lisowska, David J. Leak, John W. Pinney:
PathwayBooster: a tool to support the curation of metabolic pathways. 86:1-86:6 - Irene Pala:
BMC Bioinformatics reviewer acknowledgement 2014. 87:1-87:23 - Mohamed Mysara, Natalie Leys, Jeroen Raes, Pieter Monsieurs:
NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. 88:1-88:10 - Scott Schuette, Bryan Piatkowski, Aaron Corley, Daniel Lang, Matt Geisler:
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. 89:1-89:13 - Bill Hill, Richard A. Baldock:
Constrained distance transforms for spatial atlas registration. 90:1-90:10 - Robert V. Baron, Yvette P. Conley, Michael B. Gorin, Daniel E. Weeks:
dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets. 91:1-91:15 - Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen:
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. 92:1-92:10 - Emna Harigua-Souiai, Isidro Cortes-Ciriano, Nathan Desdouits, Thérèse E. Malliavin, Ikram Guizani, Michael Nilges, Arnaud Blondel, Guillaume Bouvier:
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis. 93:1-93:15 - Juyong Lee, Kiho Lee, InSuk Joung, Keehyoung Joo, Bernard R. Brooks, Jooyoung Lee:
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. 94:1-94:12 - Eugene Andres Houseman, Karl T. Kelsey, John K. Wiencke, Carmen J. Marsit:
Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective. 95:1-95:16 - Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin-Hui Xing, Takuji Yamada:
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. 96:1-96:15 - Xinan Yang, Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan Onel, Jill de Jong, Jianjun Chen, Luonan Chen, John M. Cunningham:
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. 97:1-97:21 - Julie M. Allen, Daisie I. Huang, Quentin C. Cronk, Kevin P. Johnson:
aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data. 98:1-98:7 - Gabriele Arnulfo, Massimo Narizzano, Francesco Cardinale, Marco Fato, Jaakko Palva:
Automatic segmentation of deep intracerebral electrodes in computed tomography scans. 99:1-99:12 - Tong Huo, Wei Liu, Yu Guo, Cheng Yang, Jianping Lin, Zihe Rao:
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. 100:1-100:9 - Calvin R. Chen, George I. Makhatadze:
ProteinVolume: calculating molecular van der Waals and void volumes in proteins. 101:1-101:6 - Allison Chia-Yi Wu, Scott A. Rifkin:
Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. 102:1-102:8 - Ninnutt Moonrin, Napat Songtawee, Siriluk Rattanabunyong, Surasuk Chunsrivirot, Wanwimon Mokmak, Sissades Tongsima, Kiattawee Choowongkomon:
Understanding the molecular basis of EGFR kinase domain/MIG-6 peptide recognition complex using computational analyses. 103:1-103:16 - Syed Murtuza Baker, C. Hart Poskar, Falk Schreiber, Björn H. Junker:
A unified framework for estimating parameters of kinetic biological models. 104:1-104:21 - John M. Gaspar, W. Kelley Thomas:
FlowClus: efficiently filtering and denoising pyrosequenced amplicons. 105:1-105:9 - Maud Tournoud, Audrey Larue, Marie-Angelique Cazalis, Fabienne Venet, Alexandre Pachot, Guillaume Monneret, Alain Lepape, Jean-Baptiste Veyrieras:
A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates. 106:1-106:15 - Nhung T. H. Nguyen, Makoto Miwa, Yoshimasa Tsuruoka, Takashi Chikayama, Satoshi Tojo:
Wide-coverage relation extraction from MEDLINE using deep syntax. 107:1-107:11 - Joseph L. Herman, Ádám Novák, Rune B. Lyngsø, Adrienn Szabó, István Miklós, Jotun Hein:
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. 108:1-108:26 - Sawsan Khuri, Stefan Wuchty:
Essentiality and centrality in protein interaction networks revisited. 109:1-109:8 - Yaojun Wang, Fei Yang, Peng Wu, Dongbo Bu, Shiwei Sun:
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction. 110:1-110:6 - Raluca Uricaru, Célia Michotey, Hélène Chiapello, Eric Rivals:
YOC, A new strategy for pairwise alignment of collinear genomes. 111:1-111:16 - Fan Xu, Jing Yang, Jin Chen, Qingyuan Wu, Wei Gong, Jianguo Zhang, Weihua Shao, Jun Mu, Deyu Yang, Yongtao Yang, Zhiwei Li, Peng Xie:
Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression. 112:1-112:10 - Antonio Jimeno-Yepes, Laura Plaza, Jorge Carrillo de Albornoz, James G. Mork, Alan R. Aronson:
Feature engineering for MEDLINE citation categorization with MeSH. 113:1-113:12 - Kai Wang, Hiroki Nishida:
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. 114:1-114:13 - Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan:
A network model for angiogenesis in ovarian cancer. 115:1-115:17 - Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner:
MAESTRO - multi agent stability prediction upon point mutations. 116:1-116:13 - Tai-Yu Chiu, Ting-Chieh Hsu, Chia-Cheng Yen, Jia-Shung Wang:
Interpolation based consensus clustering for gene expression time series. 117:1-117:17 - Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber, Christoph Magnes:
IPO: a tool for automated optimization of XCMS parameters. 118:1-118:10 - Talha Bin Masood, Sankaran Sandhya, Nagasuma R. Chandra, Vijay Natarajan:
CHEXVIS: a tool for molecular channel extraction and visualization. 119:1-119:19 - Vibha Pandey, Yogeshwar Dhar, Parul Gupta, Sumit K. Bag, Neelam Atri, Mehar Asif, Prabodh Trivedi, Pratibha Misra:
Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera. 120:1-120:10 - Sa Kim, Tuong Nguyen, Na Seo, Seunghup Jung, Hyun An, David A. Mills, Jae Kim:
Comparative proteomics: assessment of biological variability and dataset comparability. 121:1-121:10 - Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel:
ContextMap 2: fast and accurate context-based RNA-seq mapping. 122:1-122:15 - Ivan Limongelli, Simone Marini, Riccardo Bellazzi:
PaPI: pseudo amino acid composition to score human protein-coding variants. 123:1-123:14 - James A. R. Dalton, Isaias Lans, Jesús Giraldo:
Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism. 124:1-124:15 - Jimmy Van den Eynden, Ana Carolina Fierro, Lieven P. C. Verbeke, Kathleen Marchal:
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. 125:1-125:12 - Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
KaBOB: ontology-based semantic integration of biomedical databases. 126:1-126:21 - Sony Malhotra, Oommen K. Mathew, Ramanathan Sowdhamini:
DOCKSCORE: a webserver for ranking protein-protein docked poses. 127:1-127:6 - Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang, Tatsuya Akutsu:
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs. 128:1-128:13 - Parisa Kordjamshidi, Dan Roth, Marie-Francine Moens:
Structured learning for spatial information extraction from biomedical text: bacteria biotopes. 129:1-129:15 - Michael Cantor, Henrik Nordberg, Tatyana Smirnova, Matthias Hess, Susannah Tringe, Inna Dubchak:
Elviz - exploration of metagenome assemblies with an interactive visualization tool. 130:1-130:8 - Tiphaine C. Martin, Idil Yet, Pei-Chien Tsai, Jordana T. Bell:
coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns. 131:1-131:5 - Jessica L. Larson, Art B. Owen:
Moment based gene set tests. 132:1-132:17 - Amirhossein Manzourolajdad, Jonathan P. Arnold:
Secondary structural entropy in RNA switch (Riboswitch) identification. 133:1-133:77 - Daniel Bottomly, Beth Wilmot, Shannon K. McWeeney:
plethy: management of whole body plethysmography data in R. 134:1-134:5 - Corinna Vehlow, David P. Kao, Michael R. Bristow, Lawrence E. Hunter, Daniel Weiskopf, Carsten Görg:
Visual analysis of biological data-knowledge networks. 135:1-135:15 - Jad Abbass, Jean-Christophe Nebel:
Customised fragments libraries for protein structure prediction based on structural class annotations. 136:1-136:13 - Laurent Modolo, Emmanuelle Lerat:
UrQt: an efficient software for the Unsupervised Quality trimming of NGS data. 137:1-137:8 - George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R. Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, Yannis Almirantis, John Pavlopoulos, Nicolas Baskiotis, Patrick Gallinari, Thierry Artières, Axel-Cyrille Ngonga Ngomo, Norman Heino, Éric Gaussier, Liliana Barrio-Alvers, Michael Schroeder, Ion Androutsopoulos, Georgios Paliouras:
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition. 138:1-138:28 - Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama:
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. 139:1-139:26 - Michal Dabrowski, Norbert Dojer, Izabella Krystkowiak, Bozena Kaminska, Bartek Wilczynski:
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. 140:1-140:14 - Hieu T. Nim, Milena B. Furtado, Mauro W. Costa, Nadia A. Rosenthal, Hiroaki Kitano, Sarah E. Boyd:
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. 141:1-141:7 - Filipa Pereira, Flávio Azevedo, Ângela Carvalho, Gabriela F. Ribeiro, Mark W. Budde, Björn Johansson:
Pydna: a simulation and documentation tool for DNA assembly strategies using python. 142:1-142:10 - Maria Klodt, Katja Herzog, Reinhard Töpfer, Daniel Cremers:
Field phenotyping of grapevine growth using dense stereo reconstruction. 143:1-143:11 - Benjamin Hofner, Luigi Boccuto, Markus Göker:
Controlling false discoveries in high-dimensional situations: boosting with stability selection. 144:1-144:17 - Peijie Lin, Sylvain Forêt, Susan R. Wilson, Conrad J. Burden:
Estimation of the methylation pattern distribution from deep sequencing data. 145:1-145:11 - Xiao-Fei Zhang, Le Ou-Yang, Yuan Zhu, Meng-Yun Wu, Dao-Qing Dai:
Determining minimum set of driver nodes in protein-protein interaction networks. 146:1-146:13 - Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye, Shuiwang Ji:
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain. 147:1-147:10 - Alia Dehman, Christophe Ambroise, Pierre Neuvial:
Performance of a blockwise approach in variable selection using linkage disequilibrium information. 148:1-148:14 - Yan Xu, Luoxin Chen, Junsheng Wei, Sophia Ananiadou, Yubo Fan, Yi Qian, Eric I-Chao Chang, Jun'ichi Tsujii:
Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary. 149:1-149:10 - Claudia Angelini, Ruth Heller, Rita Volkinshtein, Daniel Yekutieli:
Is this the right normalization? A diagnostic tool for ChIP-seq normalization. 150:1-150:15 - Michele Fratello, Angela Serra, Vittorio Fortino, Giancarlo Raiconi, Roberto Tagliaferri, Dario Greco:
A multi-view genomic data simulator. 151:1-151:15 - Ailan F. Arenas, Gladys E. Salcedo, Andrey M. Montoya, Jorge E. Gomez-Marin:
MSCA: a spectral comparison algorithm between time series to identify protein-protein interactions. 152:1-152:9 - Mihaly Varadi, Mainak Guharoy, Fruzsina Zsolyomi, Peter Tompa:
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. 153:1-153:9 - Tristan Bitard-Feildel, Carsten Kemena, Jenny M. Greenwood, Erich Bornberg-Bauer:
Domain similarity based orthology detection. 154:1-154:11 - Ernest D. Benavente, Francesc Coll, Nick Furnham, Ruth McNerney, Judith R. Glynn, Susana G. Campino, Arnab Pain, Fady R. Mohareb, Taane G. Clark:
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. 155:1-155:5 - Catalina V. Anghel, Gerald T. Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros:
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. 156:1-156:11 - Patrick Ernst, Amy Siu, Gerhard Weikum:
KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences. 157:1-157:13 - Nurlisa Yusuf, Ammar Zakaria, Mohammad Omar, Ali Yeon Md Shakaff, Maz Jamilah Masnan, Latifah Kamarudin, Norasmadi Abdul Rahim, Nur Zawatil Isqi Zakaria, Azian Abdullah, Amizah Othman, Mohd Yasin:
In-vitro diagnosis of single and poly microbial species targeted for diabetic foot infection using e-nose technology. 158:1-158:12 - Michaël Vyverman, Bernard De Baets, Veerle Fack, Peter Dawyndt:
A Long Fragment Aligner called ALFALFA. 159:1-159:11 - Héloïse Gauvin, Jean-François Lefebvre, Claudia Moreau, Eve-Marie Lavoie, Damian Labuda, Hélène Vézina, Marie-Hélène Roy-Gagnon:
GENLIB: an R package for the analysis of genealogical data. 160:1-160:10 - Ahmet Ay, Dihong Gong, Tamer Kahveci:
Hierarchical decomposition of dynamically evolving regulatory networks. 161:1-161:19 - Yasser B. Ruiz-Blanco, Waldo Paz, James Green, Yovani Marrero-Ponce:
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. 162:1-162:15 - Gundián M. de Hijas-Liste, Eva Balsa-Canto, Jan Ewald, Martin Bartl, Pu Li, Julio R. Banga, Christoph Kaleta:
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. 163:1-163:13 - Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich, Elhanan Borenstein:
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. 164:1-164:6 - Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl J. Schmidt, Jinglong Fang, Jian Chen:
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways. 165:1-165:7 - Vasily Sachnev, Saras Saraswathi, Rashid Niaz, Andrzej Kloczkowski, Suresh Sundaram:
Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer. 166:1-166:12 - Carles Hernandez-Ferrer, Ines Quintela Garcia, Katharina Danielski, Ángel Carracedo, Luis A. Pérez-Jurado, Juan R. González:
affy2svaffy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. 167:1-167:11 - Jesse D. Bloom:
Software for the analysis and visualization of deep mutational scanning data. 168:1-168:13 - Henry Heberle, Gabriela Meirelles, Felipe R. da Silva, Guilherme P. Telles, Rosane Minghim:
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. 169:1-169:7 - Daniel E. Russ, Kwan-Yuet Ho, Nancy S. Longo:
HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs. 170 - Saeed Saberi, Pau Farré, Olivier Cuvier, Eldon Emberly:
Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data. 171:1-171:12 - Jonathan R. Karr, Harendra Guturu, Edward Y. Chen, Stuart L. Blair, Jonathan M. Irish, Nikesh Kotecha, Markus W. Covert:
NetworkPainter: dynamic intracellular pathway animation in Cytobank. 172:1-172:7 - Wael Karain, Nael Qaraeen:
Weighted protein residue networks based on joint recurrences between residues. 173:1-173:11 - Lun Hu, Keith C. C. Chan:
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. 174:1-174:16 - Vadim Nazarov, Mikhail Pogorelyy, Ekaterina Komech, Ivan Zvyagin, Dmitry Bolotin, Mikhail Shugay, Dmitry Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov:
tcR: an R package for T cell receptor repertoire advanced data analysis. 175:1-175:5 - José Lourenço, Paul S. Wikramaratna, Sunetra Gupta:
MANTIS: an R package that simulates multilocus models of pathogen evolution. 176:1-176:7 - Jonathan Sanders, Anil Singh, Gabriella Sterne, Bing Ye, Jie Zhou:
Learning-guided automatic three dimensional synapse quantification for drosophila neurons. 177:1-177:13 - Stefan Janssen, Robert Giegerich:
Ambivalent covariance models. 178:1-178:17 - Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot:
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. 179:1-179:14 - Felix Schönenberger, Anja Deutzmann, Elisa Ferrando-May, Dorit Merhof:
Discrimination of cell cycle phases in PCNA-immunolabeled cells. 180:1-180:10 - Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara:
Navigating 3D electron microscopy maps with EM-SURFER. 181:1-181:9 - Thomas Lui, Nancy Tsui, Lawrence Wing-Chi Chan, Cesar Wong, Parco Siu, Benjamin Y. M. Yung:
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. 182:1-182:15 - Lander Willem, Sean Stijven, Engelbert Tijskens, Philippe Beutels, Niel Hens, Jan Broeckhove:
Optimizing agent-based transmission models for infectious diseases. 183:1-183:10 - Basel Abu-Jamous, Rui Fa, David Roberts, Asoke K. Nandi:
UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets. 184:1-184:19 - Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu:
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. 185:1-185:15 - Sejal Patel, Paola Roncaglia, Ruth C. Lovering:
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. 186:1-186:18 - Biena Mathew, Alexander Schmitz, Silvia Muñoz-Descalzo, Nariman Ansari, Francesco Pampaloni, Ernst H. K. Stelzer, Sabine Christine Fischer:
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. 187:1-187:14 - Yongpeng Zhang, Linsen Li, Yanli Yang, Xiao Yang, Shan He, Zexuan Zhu:
Light-weight reference-based compression of FASTQ data. 188:1-188:8 - Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak K. Shah, Zidong Yu, Javier Marquina-Solis, Abhishek Kumar, Yicong Wu, James C. Schaff, Daniel Colón-Ramos, Hari Shroff, William Mohler, Zhirong Bao:
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. 189:1-189:9 - Julien Y. Dutheil, Emeric Figuet:
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. 190:1-190:11 - Patrick Putnam, Philip A. Wilsey, Ge Zhang:
Clotho: addressing the scalability of forward time population genetic simulation. 191:1-191:14 - Haoyu Cheng, Huaipan Jiang, Jiaoyun Yang, Yun Xu, Yi Shang:
BitMapper: an efficient all-mapper based on bit-vector computing. 192:1-192:16 - Rachel Schwartz, Kelly Harkins, Anne Stone, Reed A. Cartwright:
A composite genome approach to identify phylogenetically informative data from next-generation sequencing. 193:1-193:10 - Jesper Gådin, Ferdinand van't Hooft, Per Eriksson, Lasse Folkersen:
AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. 194:1-194:6 - Fleur Jeanquartier, Claire Jean-Quartier, Andreas Holzinger:
Integrated web visualizations for protein-protein interaction databases. 195:1-195:16 - Sean Robinson, Garique Glonek, Inge Koch, Mark Thomas, Christopher Davies:
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models. 196:1-196:9 - Jan Ruijter, Steve Lefever, Jasper Anckaert, Jan Hellemans, Michael W. Pfaffl, Vladimir Benes, Stephen Bustin, Jo Vandesompele, Andreas Untergasser:
RDML-Ninja and RDMLdb for standardized exchange of qPCR data. 197:1-197:7 - Padmini Srinivasan, Xiao-Ning Zhang, Roxane Bouten, Caren Chang:
Ferret: a sentence-based literature scanning system. 198:1-198:11 - Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J. C. Eijkemans:
Factors affecting the accuracy of a class prediction model in gene expression data. 199:1-199:12 - Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Edgar Wingender:
Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes. 200:1-200:19 - Dániel Kozma, Gábor E. Tusnády:
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. 201:1-201:9 - Yang Liu, Francesca Chiaromonte, Howard Ross, Raunaq Malhotra, Daniel Elleder, Mary Poss:
Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. 202:1-202:14 - Bruno Fosso, Monica Santamaria, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo, Graziano Pesole:
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. 203:1-203:11 - Denis Machado:
YBYRÁ facilitates comparison of large phylogenetic trees. 204:1-204:4 - Hilde Vinje, Kristian Hovde Liland, Trygve Almøy, Lars Snipen:
Comparing K-mer based methods for improved classification of 16S sequences. 205:1-205:13 - Santiago Ríos, Marta Fernandez, Gianluigi Caltabiano, Mercedes Campillo, Leonardo Pardo, Angel Gonzalez:
GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors. 206:1-206:11 - Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro:
Capturing coevolutionary signals inrepeat proteins. 207:1-207:10 - Cheng Jia, Weihua Guan, Amy Yang, Rui Xiao, W. Tang, Christine Moravec, Kenneth Margulies, Thomas P. Cappola, Mingyao Li, Chun Li:
MetaDiff: differential isoform expression analysis using random-effects meta-regression. 208:1-208:12 - Todd A. Gillette, Parsa Hosseini, Giorgio A. Ascoli:
Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment. 209:1-209:17 - S. M. Ashiqul Islam, Tanvir Sajed, Christopher Kearney, Erich J. Baker:
PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides. 210:1-210:11 - Catherine A. Lozupone, Rob Knight:
The unifrac significance test is sensitive to tree topology. 211:1-211:3 - Jonah Hocum, Logan Battrell, Ryan Maynard, Jennifer E. Adair, Brian Beard, David Rawlings, Hans-Peter Kiem, Daniel G. Miller, Grant Trobridge:
VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. 212:1-212:5 - Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy:
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. 213:1-213:10 - Andrew D. Hellicar, Ashfaqur Rahman, Daniel V. Smith, John M. Henshall:
Machine learning approach for pooled DNA sample calibration. 214:1-214:11 - Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch:
MONALISA for stochastic simulations of Petri net models of biochemical systems. 215:1-215:11 - Todd A. Gillette, Giorgio A. Ascoli:
Topological characterization of neuronal arbor morphology via sequence representation: I - motif analysis. 216:1-216:15 - Dongmei Li, Zidian Xie, Marc A. Le Pape, Timothy D. Dye:
An evaluation of statistical methods for DNA methylation microarray data analysis. 217:1-217:20 - Theodore Gibbons, Stephen M. Mount, Endymion Cooper, Charles F. Delwiche:
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. 218:1-218:14 - Xiaoping Cheng, Hongmin Cai, Yue Zhang, Bo Xu, Weifeng Su:
Optimal combination of feature selection and classification via local hyperplane based learning strategy. 219:1-219:10 - Ke Hu, Angela Ting, Jing Li:
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. 220:1-220:9 - Damien Farrell, Stephen V. Gordon:
Epitopemap: a web application for integrated whole proteome epitope prediction. 221:1-221:6 - Minho Chae, Charles G. Danko, W. Kraus:
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. 222:1-222:16 - Soyeon Ahn, Haris Vikalo:
Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm. 223:1-223:10 - Stephen Hartley, James C. Mullikin:
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. 224:1-224:7 - Julian Gingold, Ed Coakley, Jie Su, Dung-Fang Lee, Zerlina Lau, Hongwei Zhou, Dan Felsenfeld, Christoph Schaniel, Ihor Lemischka:
Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. 225:1-225:20 - Henry Ogoe, Shyam Visweswaran, Xinghua Lu, Vanathi Gopalakrishnan:
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. 226:1-226:15 - Hani Z. Girgis:
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. 227:1-227:19 - Jay Khurana, Jay Reeder, Antony Shrimpton, Juilee Thakar:
GESPA: classifying nsSNPs to predict disease association. 228:1-228:10 - Albina Asadulina, Markus Conzelmann, Elizabeth Williams, Aurora Panzera, Gáspár Jékely:
Object-based representation and analysis of light and electron microscopic volume data using Blender. 229:1-229:9 - Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Inanç Birol:
Sealer: a scalable gap-closing application for finishing draft genomes. 230:1-230:8 - Nicholas E. Newell:
Mapping side chain interactions at protein helix termini. 231:1-231:21 - Jose Samaniego Castruita, Marie Lisandra Zepeda Mendoza, Ross Barnett, Nathan Wales, Marcus Gilbert:
Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. 232:1-232:13 - Jittisak Senachak, Supapon Cheevadhanarak, Apiradee Hongsthong:
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1. 233:1-233:9 - Claudia Caudai, Emanuele Salerno, Monica Zoppè, Anna Tonazzini:
Inferring 3D chromatin structure using a multiscale approach based on quaternions. 234:1-234:11 - Howard Huang, James C. Mullikin, Nancy F. Hansen:
Evaluation of variant detection software for pooled next-generation sequence data. 235:1-235:9 - Benjamin Albrecht:
Computing all hybridization networks for multiple binary phylogenetic input trees. 236:1-236:15 - Mihai Pop, Steven Salzberg:
Use and mis-use of supplementary material in science publications. 237:1-237:4 - David Quigley:
Equalizer reduces SNP bias in Affymetrix microarrays. 238:1-238:8 - Itziar Frades, Svante Resjö, Erik Andreasson:
Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis. 239:1-239:13 - Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor Piro, Andreas Nitsche, Bernhard Y. Renard:
SuRankCo: supervised ranking of contigs in de novo assemblies. 240:1-240:7 - Fei Huang, Christopher J. Oldfield, Bin Xue, Wei-Lun Hsu, Jingwei Meng, Xiaowen Liu, Li Shen, Pedro Romero, Vladimir N. Uversky, A. Keith Dunker:
Erratum to: Improving protein order-disorder classification using charge-hydropathy plots. 241:1-241:2 - Nicolas Duforet-Frebourg, Lucie Gattepaille, Michael G. B. Blum, Mattias Jakobsson:
HaploPOP: a software that improves population assignment by combining markers into haplotypes. 242:1-242:8 - Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser:
Simulated unbound structures for benchmarking of protein docking in the Dockground resource. 243:1-243:6 - Binbin Lai, Fumeng Wang, Xiaoqi Wang, Liping Duan, Huaiqiu Zhu:
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads. 244:1-244:14 - Fang Yu, Ming-Hui Chen, Lynn Kuo, Heather Talbott, John D. Davis:
Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications. 245:1-245:15 - Rallis Karamichalis, Lila Kari, Stavros Konstantinidis, Steffen Kopecki:
An investigation into inter- and intragenomic variations of graphic genomic signatures. 246:1-246:22 - Carlos Sanquetta, Jaime Wojciechowski, Ana Paula Dalla Corte, Alexandre Behling, Sylvio Péllico Netto, Aurélio Rodrigues, Mateus Sanquetta:
Comparison of data mining and allometric model in estimation of tree biomass. 247:1-247:9 - Mirwaes Wahabzada, Stefan Paulus, Kristian Kersting, Anne-Katrin Mahlein:
Automated interpretation of 3D laserscanned point clouds for plant organ segmentation. 248:1-248:11 - Huizhu Ren, Ying Shen:
RNA-binding residues prediction using structural features. 249:1-249:10 - Óscar Torreño Tirado, Oswaldo Trelles:
Breaking the computational barriers of pairwise genome comparison. 250:1-250:13 - Jean-Pierre Flandrois, Guy Perrière, Manolo Gouy:
leBIBI QBPP : a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. 251:1-251:12 - Susanne Schaller, Johannes Weinberger, Raúl Jiménez-Heredia, Martin Danzer, Rainer Oberbauer, Christian Gabriel, Stephan M. Winkler:
ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data. 252:1-252:10 - Petr Cech, David Hoksza, Daniel Svozil:
MultiSETTER: web server for multiple RNA structure comparison. 253:1-253:8 - Theodore Roman, Amir Nayyeri, Brittany Terese Fasy, Russell Schwartz:
A simplicial complex-based approach to unmixing tumor progression data. 254:1-254:17 - Andrew Ndhlovu, Scott Hazelhurst, Pierre M. Durand:
Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix. 255:1-255:14 - Clovis Galiez, François Coste:
Amplitude spectrum distance: measuring the global shape divergence of protein fragments. 256:1-256:16 - Jose A. Perea, Anastasia Deckard, Steven B. Haase, John Harer:
SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. 257:1-257:12 - Aaron T. L. Lun, Gordon K. Smyth:
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. 258:1-258:11 - Mohammad R. Nezami Ranjbar, Cristina Di Poto, Yue Joseph Wang, Habtom W. Ressom:
SIMAT: GC-SIM-MS data analysis tool. 259:1-259:12 - Yi Wang, Yi Li, Hongbao Cao, Momiao Xiong, Yin Yao Shugart, Li Jin:
Efficient test for nonlinear dependence of two continuous variables. 260:1-260:8 - Angela Serra, Michele Fratello, Vittorio Fortino, Giancarlo Raiconi, Roberto Tagliaferri, Dario Greco:
MVDA: a multi-view genomic data integration methodology. 261:1-261:13 - Elsa Bernard, Laurent Jacob, Julien Mairal, Eric Viara, Jean-Philippe Vert:
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. 262:1-262:10 - Yugyung Lee, Alok Khemka, Gayathri Acharya, Namita Giri, Chi Lee:
A cascade computer model for mocrobicide diffusivity from mucoadhesive formulations. 263:1-263:12 - Edward Meeds, Michael Chiang, Mary Lee, Olivier Cinquin, John S. Lowengrub, Max Welling:
POPE: post optimization posterior evaluation of likelihood free models. 264:1-264:20 - Xiaoyan Ma, Daphne Ezer, Carmen Navarro, Boris Adryan:
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors. 265:1-265:13 - Marc Perea, Ivar Lugtenburg, Eduardo Mayol, Arnau Cordomí, Xavier Deupí, Leonardo Pardo, Mireia Olivella:
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. 266:1-266:6 - Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard, Chris T. A. Evelo:
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. 267:1-267:12 - Aram Avila-Herrera, Katherine S. Pollard:
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. 268:1-268:18 - Peter Jehl, Fabian Sievers, Desmond G. Higgins:
OD-seq: outlier detection in multiple sequence alignments. 269:1-269:11 - Jónathan Heras, César Domínguez, Eloy J. Mata, Vico Pascual, Carmen Lozano, Carmen Torres, Myriam Zarazaga:
GelJ - a tool for analyzing DNA fingerprint gel images. 270:1-270:8 - Guo-Xian Yu, Hailong Zhu, Carlotta Domeniconi, Jiming Liu:
Predicting protein function via downward random walks on a gene ontology. 271:1-271:13 - Jacob A. Turner, Christopher Bolen, Derek Blankenship:
Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates. 272:1-272:12 - Shun Yao, Shinjae Yoo, Dantong Yu:
Prior knowledge driven Granger causality analysis on gene regulatory network discovery. 273:1-273:18 - Theodore Gibbons, Stephen M. Mount, Endymion Cooper, Charles F. Delwiche:
Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. 274:1-274:2 - Ashley J. Waardenberg, Samuel D. Bassett, Romaric Bouveret, Richard P. Harvey:
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. 275:1-275:8 - Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk:
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. 276:1-276:12 - Marc W. Schmid, Stefan Grob, Ueli Grossniklaus:
HiCdat: a fast and easy-to-use Hi-C data analysis tool. 277:1-277:6 - Soohyun Lee, Chae Hwa Seo, Burak Han Alver, Sanghyuk Lee, Peter J. Park:
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. 278:1-278:16 - Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil D. Lawrence, Diego di Bernardo:
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. 279:1-279:9 - Akito Taneda:
Multi-objective optimization for RNA design with multiple target secondary structures. 280:1-280:20 - Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Le Corre, Laurence Garczarek:
WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. 281:1-281:13 - Jing Tong, Jimin Pei, Nick V. Grishin:
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. 282:1-282:7 - Abel Folch-Fortuny, Alejandro Fernández Villaverde, Alberto Ferrer, Julio R. Banga:
Enabling network inference methods to handle missing data and outliers. 283:1-283:12 - Sonja Holl, Yassene Mohammed, Olav Zimmermann, Magnus Palmblad:
Scientific workflow optimization for improved peptide and protein identification. 284:1-284:13 - Eman Badr, Lenwood S. Heath:
CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements. 285:1-285:15 - Paul K. Korir, Paul Geeleher, Cathal Seoighe:
Seq-ing improved gene expression estimates from microarrays using machine learning. 286:1-286:11 - Leonardo Ricci, Valerio Vescovo, Chiara Cantaloni, Margherita Grasso, Mattia Barbareschi, Michela Alessandra Denti:
Statistical analysis of a Bayesian classifier based on the expression of miRNAs. 287:1-287:12 - Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk:
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. 288:1-288:14 - Michele Pelosi, Marco Alfò, Francesca Martella, Elisa Pappalardo, Antonio Musaro:
Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts. 289:1-289:17 - Andres H. Gutiérrez, William D. Martin, Chris Bailey-Kellogg, Frances Terry, Leonard Moise, Anne S. De Groot:
Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method. 290:1-290:11 - Argiris Sakellariou, George M. Spyrou:
mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics. 291:1-291:9 - Sha Zhu, James H. Degnan, Sharyn Goldstien, Bjarki Eldon:
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 292:1-292:7 - Hongtai Huang, Andrea Fava, Tara Guhr, Raffaello Cimbro, Antony Rosen, Francesco Boin, Hugh Ellis:
A methodology for exploring biomarker - phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations. 293:1-293:15 - Veronika Weyer, Harald Binder:
A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures. 294:1-294:12 - Kai Bernd Stadermann, Bernd Weisshaar, Daniela Holtgräwe:
SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. 295:1-295:10 - Ward C. Wheeler:
Phylogenetic network analysis as a parsimony optimization problem. 296:1-296:9 - Altan Kara, Martin J. Vickers, Martin T. Swain, David E. Whitworth, Narcis Fernandez-Fuentes:
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. 297:1-297:9 - Keith Inman, Norah Rudin, Ken Cheng, Chris Robinson, Adam Kirschner, Luke Inman-Semerau, Kirk E. Lohmueller:
Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles. 298:1-298:10 - Abdulkadir Elmas, Xiaodong Wang, Michael S. Samoilov:
Reconstruction of novel transcription factor regulons through inference of their binding sites. 299:1-299:10 - Rok Blagus, Lara Lusa:
Boosting for high-dimensional two-class prediction. 300:1-300:17 - Li C. Xia, Dongmei Ai, Jacob A. Cram, Xiaoyi Liang, Jed A. Fuhrman, Fengzhu Sun:
Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. 301:1-301:14 - Hui-Wen Huang, Yao-Shen Chen, Jeff Chen, Po-Liang Lu, Yung-Cheng Lin, Bao-Chen Chen, Li-Chiu Chou, Chu-Feng Wang, Hui-Ju Su, Yi-Chien Huang, Yong-Ying Shi, Hsiu-Lin Chen, Bintou Sanno-Duanda, Tsi-Shu Huang, Kuei-Hsiang Lin, Yu-Chang Tyan, Pei-Yu Chu:
Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2. 302:1-302:9 - Edward Daniel, Goodluck Onwukwe, Rik Wierenga, Susan Quaggin, Seppo Vainio, Mirja Krause:
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. 303:1-303:6 - Kristopher Standish, Tristan M. Carland, Glenn K. Lockwood, Wayne Pfeiffer, Mahidhar Tatineni, C. Huang, Sarah Lamberth, Yauheniya Cherkas, Carrie Brodmerkel, Ed Jaeger, Lance Smith, Gunaretnam Rajagopal, Mark Curran, Nicholas J. Schork:
Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies. 304:1-304:14 - Askar Obulkasim, Maarten Fornerod, Michel Zwaan, Dirk Reinhardt, Marry M. van den Heuvel-Eibrink:
Subtype prediction in pediatric acute myeloid leukemia: classification using differential network rank conservation revisited. 305:1-305:11 - Nilzair M. Barreto, Karina S. Machado, Adriano Velasque Werhli:
Inference of regulatory networks with a convergence improved MCMC sampler. 306:1-306:10 - Adam Richards, Anthony Herrel, Camille Bonneaud:
htsint: a Python library for sequencing pipelines that combines data through gene set generation. 307:1-307:7 - Björn-Oliver Gohlke, Tim Overkamp, Anja Richter, Antje Richter, Peter T. Daniel, Bernd Gillissen, Robert Preissner:
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib. 308:1-308:9 - Saskia Freytag, Johann Gagnon-Bartsch, Terence P. Speed, Melanie Bahlo:
Systematic noise degrades gene co-expression signals but can be corrected. 309:1-309:17 - Federico Andrea Santoni, Periklis Makrythanasis, Stylianos E. Antonarakis:
CATCHing putative causative variants in consanguineous families. 310:1-310:5 - Afshin Esmaeili, Timothy Davison, Andrew Wu, Joenel Alcantara, Christian Jacob:
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli. 311:1-311:23 - Pau Bellot, Catharina Olsen, Philippe Salembier, Albert Oliveras-Vergés, Patrick E. Meyer:
NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference. 312:1-312:15 - Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker, Mattia Pelizzola:
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. 313:1-313:11 - Caroline König, Martha Ivón Cárdenas, Jesús Giraldo, René Alquézar, Alfredo Vellido:
Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors. 314:1-314:14 - Samreen Anjum, Sandro Morganella, Fulvio D'Angelo, Antonio Iavarone, Michele Ceccarelli:
VEGAWES: variational segmentation on whole exome sequencing for copy number detection. 315:1-315:10 - Tsuyoshi Kato, Raissa Relator, Hayliang Ngouv, Yoshihiro Hirohashi, Osamu Takaki, Tetsuhiro Kakimoto, Kinya Okada:
Segmental HOG: new descriptor for glomerulus detection in kidney microscopy image. 316:1-316:16 - Mauricio Guevara-Souza, Edgar E. Vallejo:
A computer simulation model of Wolbachia invasion for disease vector population modification. 317:1-317:14 - Hugo López-Fernández, Hugo Miguel Santos, José L. Capelo, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato:
Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. 318:1-318:12 - Mohieddin Jafari, Mehdi Mirzaie, Mehdi Sadeghi:
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. 319:1-319:9 - Stefan Lang, Amol Ugale, Eva Erlandsson, Göran Karlsson, David Bryder, Shamit Soneji:
SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data. 320:1-320:4 - Daiki Okada, Fumihiko Ino, Kenichi Hagihara:
Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences. 321:1-321:15 - Erik Wright:
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. 322:1-322:14 - Xiao Ding, Fudong Cheng, Chang-Chang Cao, Xiao Sun:
DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection. 323:1-323:12 - Guy Allard, Feargal Ryan, Ian B. Jeffery, Marcus J. Claesson:
SPINGO: a rapid species-classifier for microbial amplicon sequences. 324:1-324:8 - Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra:
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. 325:1-325:12 - Md Mahmudul Hasan, Tamer Kahveci:
Indexing a protein-protein interaction network expedites network alignment. 326:1-326:17 - Da Ruan, Alastair Young, Giovanni Montana:
Differential analysis of biological networks. 327:1-327:13 - Pedro Lopes, José Luís Oliveira:
An automated real-time integration and interoperability framework for bioinformatics. 328:1-328:13 - Jacob B. Hall, Jessica Cooke Bailey, Joshua Hoffman, Margaret A. Pericak-Vance, William K. Scott, Jaclyn Kovach, Stephen G. Schwartz, Anita Agarwal, Milam Brantley, Jonathan L. Haines, William S. Bush:
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. 329:1-329:9 - Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael Halter, Derek Juba, Marcin Kociolek, Michael Majurski, Adele P. Peskin, Carl G. Simon, Mylene Simon, Antoine Vandecreme, Mary Brady:
Survey statistics of automated segmentations applied to optical imaging of mammalian cells. 330:1-330:28 - Lingnan Ma, Maochun Qin, Biao Liu, Qiang Hu, Lei Wei, Jianmin Wang, Song Liu:
cnvCurator: an interactive visualization and editing tool for somatic copy number variations. 331:1-331:8 - Xuejun Liu, Xinxin Shi, Chunlin Chen, Li Zhang:
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate. 332:1-332:13 - Jorge Júlvez:
A straightforward method to compute average stochastic oscillations from data samples. 333:1-333:17 - Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth:
Comparative study on gene set and pathway topology-based enrichment methods. 334:1-334:15 - Joe G. Greener, Michael J. E. Sternberg:
AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis. 335:1-335:7 - Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki:
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. 336:1-336:16 - Jilong Li, Renzhi Cao, Jianlin Cheng:
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. 337:1-337:11 - Jackson Nowotny, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, Jianlin Cheng:
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. 338:1-338:19 - Xian Jin, Mahendra Awale, Michaël Zasso, Daniel Kostro, Luc Patiny, Jean-Louis Reymond:
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. 339:1-339:15 - Yining Wang, Tim Wylie, Paul Stothard, Guohui Lin:
Whole genome SNP genotype piecemeal imputation. 340:1-340:11 - Alexandra Simader, Bernhard Kluger, Nora Katharina Nicole Neumann, Christoph Bueschl, Marc Lemmens, Gerald Lirk, Rudolf Krska, Rainer Schuhmacher:
QCScreen: a software tool for data quality control in LC-HRMS based metabolomics. 341:1-341:9 - Gongning Luo, Dong Sui, Kuanquan Wang, Jinseok Chae:
Neuron anatomy structure reconstruction based on a sliding filter. 342:1-342:19 - Jizhong Deng, Huasheng Huang, Xiaoli Yu, Ji Jin, Weisen Lin, Fagen Li, Zhijiao Song, Mei Li, Siming Gan:
DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid. 343:1-343:8 - Kimmo Kartasalo, Risto-Pekka Pölönen, Marisa Ojala, Jyrki Rasku, Jukka Lekkala, Katriina Aalto-Setälä, Pasi Kallio:
CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels. 344:1-344:23 - Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt:
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. 345:1-345:13 - Pietro di Lena, Giacomo Domeniconi, Luciano Margara, Gianluca Moro:
GOTA: GO term annotation of biomedical literature. 346:1-346:13 - Peipei Li, Yongjun Piao, Ho Shon, Keun Ho Ryu:
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. 347:1-347:9 - Matej Holec, Ondrej Kuzelka, Filip Zelezný:
Novel gene sets improve set-level classification of prokaryotic gene expression data. 348:1-348:8 - Marzia A. Cremona, Laura M. Sangalli, Simone Vantini, Gaetano Dellino, Pier Giuseppe Pelicci, Piercesare Secchi, Laura Riva:
Peak shape clustering reveals biological insights. 349:1-349:18 - Ivana Ihnatova, Eva Budinska:
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. 350:1-350:8 - Mingming Liu, Layne T. Watson, Liqing Zhang:
HMMvar-func: a new method for predicting the functional outcome of genetic variants. 351:1-351:10 - Saulo Aflitos, Edouard Severing, Gabino Sanchez-Perez, Sander Peters, Hans de Jong, Dick de Ridder:
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. 352:1-352:10 - Liliana Angeles-Martinez, Constantinos Theodoropoulos:
A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems. 353:1-353:15 - Sara R. Selitsky, Praveen Sethupathy:
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. 354:1-354:13 - Irene Vrbik, David A. Stephens, Michel Roger, Bluma Brenner:
The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data. 355:1-355:9 - Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, Ying Xu:
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. 356:1-356:9 - Steven H. Wu, Allen G. Rodrigo:
Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals. 357:1-357:12 - Gregory Ditzler, J. Calvin Morrison, Yemin Lan, Gail Rosen:
Fizzy: feature subset selection for metagenomics. 358:1-358:8 - Clemens Zvácek, Gerald Friedrichs, Leonhard Heizinger, Rainer Merkl:
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. 359:1-359:8 - Jun Meng, Dong Liu, Yushi Luan:
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. 361:1-361:11 - Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota:
Evaluation of methods for differential expression analysis on multi-group RNA-seq count data. 360:1-360:14 - Rok Blagus, Lara Lusa:
Joint use of over- and under-sampling techniques and cross-validation for the development and assessment of prediction models. 363:1-363:10 - Michael A. Peabody, Thea Van Rossum, Raymond Lo, Fiona S. L. Brinkman:
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. 362:1-362:19 - Preston V. Lee, Valentin Dinu:
BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms. 364:1-364:7 - Wen Zhang, Feng Liu, Longqiang Luo, Jingxia Zhang:
Predicting drug side effects by multi-label learning and ensemble learning. 365:1-365:11 - Naresh Doni Jayavelu, Lasse Aasgaard, Nadav S. Bar:
Iterative sub-network component analysis enables reconstruction of large scale genetic networks. 366:1-366:13 - Paul Müller, Mirjam Schürmann, Jochen R. Guck:
ODTbrain: a Python library for full-view, dense diffraction tomography. 367:1-367:9 - Mark-Anthony Bray, Anne E. Carpenter:
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. 369:1-369:7 - Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, Jean-Christophe Pesquet:
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference. 368:1-368:12 - Maurits Evers, Michael Huttner, Anne Dueck, Gunter Meister, Julia C. Engelmann:
miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. 370:1-370:10 - Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch:
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems. 371:1 - Andrew E. Jaffe, Thomas Hyde, Joel Kleinman, Daniel Weinbergern, Joshua Chenoweth, Ronald McKay, Jeffrey T. Leek, Carlo Colantuoni:
Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. 372:1-372:10 - Mark R. Segal, Henrik Bengtsson:
Reconstruction of 3D genome architecture via a two-stage algorithm. 373:1-373:10 - Cécile Monat, Christine Tranchant-Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela-Bouniol, Marilyne Summo, François Sabot:
TOGGLE: toolbox for generic NGS analyses. 374:1-374:8 - Ralf Eggeling, Teemu Roos, Petri Myllymäki, Ivo Grosse:
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. 375:1-375:15 - Teri Evans, Matthew Loose:
AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts. 376:1-376:11 - Joan Maynou, Erola Pairo, Santiago Marco, Alexandre Perera:
Sequence information gain based motif analysis. 377:1-377:13 - Victor Mocioiu, Sandra Ortega-Martorell, Iván Olier, Michal Jablonski, Jana Starcuková, Paulo Lisboa, Carles Arús, Margarida Julià-Sapé:
From raw data to data-analysis for magnetic resonance spectroscopy - the missing link: jMRUI2XML. 378:1-378:11 - Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie M. P. Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens:
QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. 379:1-379:14 - David M. Kristensen, Usman Saeed, Dmitrij Frishman, Eugene V. Koonin:
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. 380:1-380:11 - James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg:
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. 381:1-381:9 - António Ribeiro, Agnieszka Golicz, Christine Hackett, Iain Milne, Gordon Stephen, David F. Marshall, Andrew J. Flavell, Micha Bayer:
An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome. 382:1-382:16 - David Edwards:
Two molecular measures of relatedness based on haplotype sharing. 383:1-383:11 - Thu-Hien To, Edwin Jacox, Vincent Ranwez, Céline Scornavacca:
A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality. 384:1-384:15 - Maria Sorokina, Claudine Médigue, David Vallenet:
A new network representation of the metabolism to detect chemical transformation modules. 385:1-385:9 - Xiao Zhu, Henry C. M. Leung, Rongjie Wang, Francis Y. L. Chin, Siu-Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang:
misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads. 386:1-386:16 - Martin Nettling, Hendrik Treutler, Jan Grau, Jens Keilwagen, Stefan Posch, Ivo Grosse:
DiffLogo: a comparative visualization of sequence motifs. 387:1-387:9 - Elena Landoni, Rosalba Miceli, Maurizio Callari, Paola Tiberio, Valentina Appierto, Valentina Angeloni, Luigi Mariani, Maria Daidone:
Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation. 388:1-388:10 - Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, Martin Mann:
antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. 389:1-389:7 - Mohammed AlQuraishi, Shengdong Tang, Xide Xia:
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. 390:1-390:19 - Bart Broeckx, Frank Coopman, Geert Verhoeven, Tim Bosmans, Ingrid Gielen, Walter Dingemanse, Jimmy Saunders, Dieter Deforce, Filip Van Nieuwerburgh:
An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors. 391:1-391:7 - Anastasiya Lapytsko, Gabriel Kollarovic, Lyubomira Ivanova, Maja Studencka, Jörg Schaber:
FoCo: a simple and robust quantification algorithm of nuclear foci. 392:1-392:13 - Mufleh Al-Shatnawi, M. Omair Ahmad, M. N. S. Swamy:
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions. 393:1-393:11 - Linda Dib, Xavier Meyer, Panu Artimo, Vassilios Ioannidis, Heinz Stockinger, Nicolas Salamin:
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree. 394:1-394:7 - Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee, Kwong-Sak Leung:
High-order dynamic Bayesian Network learning with hidden common causes for causal gene regulatory network. 395:1-395:28 - Chen Yang, Daniel Niedieker, Frederik Großerüschkamp, Melanie Horn, Andrea Tannapfel, Angela Kallenbach-Thieltges, Klaus Gerwert, Axel Mosig:
Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections. 396:1-396:14 - Michael Chiang, Sam Hallman, Amanda Cinquin, Nabora de Mochel, Adrian Paz, Shimako Kawauchi, Anne L. Calof, Ken Cho, Charless C. Fowlkes, Olivier Cinquin:
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. 397:1-397:19 - Dhany Saputra, Simon Rasmussen, Mette V. Larsen, Nizar Haddad, Maria Sperotto, Frank Aarestrup, Ole Lund, Thomas Sicheritz-Pontén:
Reads2Type: a web application for rapid microbial taxonomy identification. 398:1-398:10 - Tahsin M. Kurç, Xin Qi, Daihou Wang, Fusheng Wang, George Teodoro, Lee Cooper, Michael Nalisnik, Lin Yang, Joel H. Saltz, David J. Foran:
Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies. 399:1-399:21 - Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender, Mehmet Gültas:
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. 400:1-400:21 - Guillaume Rivière, Christophe Klopp, Nabihoudine Ibouniyamine, Arnaud Huvet, Pierre Boudry, Pascal Favrel:
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. 401:1-401:12 - Hongchu Wang, Xuehai Hu:
Accurate prediction of nuclear receptors with conjoint triad feature. 402:1-402:13 - Gengxin Li, Hongyu Zhao:
M3-S: a genotype calling method incorporating information from samples with known genotypes. 403:1-403:9 - Laval Jacquin, Tuong-Vi Cao, Cécile Grenier, Nourollah Ahmadi:
DHOEM: a statistical simulation software for simulating new markers in real SNP marker data. 404:1-404:8 - Akram Yazdani, Azam Yazdani, Eric Boerwinkle:
Rare variants analysis using penalization methods for whole genome sequence data. 405:1-405:8 - Elena Rivas, Sean R. Eddy:
Parameterizing sequence alignment with an explicit evolutionary model. 406:1-406:23 - Xiaoli Gao:
Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations. 407:1-407:14 - Filippo Del Vecchio, Francesco Gallo, Antinisca Di Marco, Valentina Mastroiaco, Pasquale Caianiello, Francesca Zazzeroni, Edoardo Alesse, Alessandra Tessitore:
Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model. 408:1-408:11 - Flavio Lichtenstein, Fernando Antoneli, Marcelo R. S. Briones:
MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets. 409:1-409:19 - Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty:
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. 410:1 - Paul Aiyetan, Stefani N. Thomas, Zhen Zhang, Hui Zhang:
MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development. 411:1-411:7 - Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch, Ovidiu Balacescu:
Unsupervised image segmentation for microarray spots with irregular contours and inner holes. 412:1-412:12 - Sini Rautio, Harri Lähdesmäki:
MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis. 413:1-413:12 - Christian Allende, Erik Sohn, Cedric Little:
Treelink: data integration, clustering and visualization of phylogenetic trees. 414:1-414:6 - Matteo Gabetta, Ivan Limongelli, Ettore Rizzo, Alberto Riva, Daniele Segagni, Riccardo Bellazzi:
BigQ: a NoSQL based framework to handle genomic variants in i2b2. 415:1-415:11 - Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce Roth, Josh Schulte, Greg B. Donarum, Ed T. Fochler, Jessica M. Hill, Alvin T. Liem, Michael R. Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard, Melanie C. Melendrez, Evan Skowronski, Phenix-Lan Quan, W. Ian Lipkin, Henry S. Gibbons, David L. Hirschberg, Gustavo F. Palacios, C. Nicole Rosenzweig:
Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. 416:1-416:12 - Suyu Mei, Hao Zhu:
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. 417:1-417:18
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