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ORCIDBMC Bioinformatics, Volume 19
Volume 19, Number 1, December 2018
- Anna Marco-Ramell, Magali Palau-Rodriguez, Ania Alay
, Sara Tulipani, Mireia Urpi-Sarda, Alex Sánchez-Pla, Cristina Andres-Lacueva:
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. 1:1-1:11 - Min Shi, David M. Umbach, Alison S. Wise, Clarice R. Weinberg:
Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect. 2:1-2:10 - Peng Guo, Bo Zhu, Hong Niu, Zezhao Wang, Yonghu Liang, Yan Chen, Lupei Zhang, Hemin Ni, Yong Guo, El Hamidi A. Hay, Xue Gao, Huijiang Gao, Xiaolin Wu, Lingyang Xu, Junya Li:
Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis. 3:1-3:11 - Jader M. Caldonazzo Garbelini, André Yoshiaki Kashiwabara, Danilo Sipoli Sanches:
Sequence motif finder using memetic algorithm. 4:1-4:13 - Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet:
Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform. 5:1-5:10 - Qin Zhu, Stephen A. Fisher, Hannah Dueck, Sarah Middleton, Mugdha Khaladkar, Junhyong Kim:
PIVOT: platform for interactive analysis and visualization of transcriptomics data. 6:1-6:8 - Miguel Ángel Rodríguez-García, Robert Hoehndorf:
Inferring ontology graph structures using OWL reasoning. 7:1-7:9 - Qi-Lei Zou, Xiao-Ping You, Jian-Long Li, Wing Kam Fung, Ji-Yuan Zhou:
A powerful parent-of-origin effects test for qualitative traits on X chromosome in general pedigrees. 8:1-8:9 - Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes:
Thresher: determining the number of clusters while removing outliers. 9:1-9:15 - Yichen Zheng, Axel Janke:
Gene flow analysis method, the D-statistic, is robust in a wide parameter space. 10:1-10:19 - Derek S. Chiu, Aline Talhouk:
diceR: an R package for class discovery using an ensemble driven approach. 11:1-11:4 - Marek Palkowski, Wlodzimierz Bielecki:
Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding. 12:1-12:12 - Audrey Legendre, Eric Angel, Fariza Tahi:
Bi-objective integer programming for RNA secondary structure prediction with pseudoknots. 13:1-13:15 - Yanhua Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu, Peng Chen:
Protein-protein interface hot spots prediction based on a hybrid feature selection strategy. 14:1-14:16 - Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen, Burkhard Rost:
LocText: relation extraction of protein localizations to assist database curation. 15:1-15:11 - Shifu Chen, Tanxiao Huang, Tiexiang Wen, Hong Li, Mingyan Xu, Jia Gu:
MutScan: fast detection and visualization of target mutations by scanning FASTQ data. 16:1-16:11 - Michail Tsagris, Vincenzo Lagani, Ioannis Tsamardinos:
Feature selection for high-dimensional temporal data. 17:1-17:14 - R. Michael Sivley, Jonathan H. Sheehan, Jonathan A. Kropski, Joy D. Cogan, Timothy S. Blackwell, John A. Phillips, William S. Bush, Jens Meiler, John A. Capra:
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. 18:1-18:10 - Chenyue W. Hu, Hanyang Li, Amina A. Qutub:
Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications. 19:1-19:11 - Thomas C. A. Hitch, Christopher J. Creevey:
Spherical: an iterative workflow for assembling metagenomic datasets. 20:1-20:8 - Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Won-Ho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan, Jaewoo Kang:
Deep learning of mutation-gene-drug relations from the literature. 21:1-21:13 - Badri Adhikari, Jianlin Cheng:
CONFOLD2: improved contact-driven ab initio protein structure modeling. 22:1-22:5 - Guido Zampieri, Dinh Tran-Van, Michele Donini, Nicolò Navarin, Fabio Aiolli, Alessandro Sperduti, Giorgio Valle:
Scuba: scalable kernel-based gene prioritization. 23:1-23:12 - Roman Prytuliak, Friedhelm Pfeiffer, Bianca Habermann:
SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data. 24:1-24:19 - Daniel Koile, Marta Cordoba, Maximiliano de Sousa Serro, Marcelo Andres Kauffman, Patricio Yankilevich:
GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases. 25:1-25:6 - Dang Liu, Martin Hunt, Isheng J Tsai:
Inferring synteny between genome assemblies: a systematic evaluation. 26:1-26:13 - Ana Julia Velez Rueda, Alexander Miguel Monzon, Sebastián M. Ardanaz, Luis E. Iglesias, Gustavo D. Parisi:
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. 27:1-27:10 - Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros:
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. 28:1-28:9 - Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures. 29:1-29:8 - Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su, Chunlei Wu:
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. 30:1-30:7 - David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons, Kyoung-Jae Won:
Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus. 31:1-31:12 - Eliot C. Bush, Anne E. Clark, Carissa A. DeRanek, Alexander Eng, Juliet Forman, Kevin N. Heath, Alexander B. Lee, Daniel M. Stoebel, Zunyan Wang, Matthew Wilber, Helen Wu:
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria. 32:1-32:11 - Billy Chiu, Sampo Pyysalo, Ivan Vulic, Anna Korhonen:
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. 33:1-33:13 - Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman:
Semantic annotation of consumer health questions. 34:1-34:28 - Sebastian Daberdaku, Carlo Ferrari:
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. 35:1-35:23 - Marco Di Salvo, Eva Pinatel, Adelfia Talà, Marco Fondi, Clelia Peano, Pietro Alifano:
G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs. 36:1-36:11 - Jie Zhou, Bo-quan Fu:
The research on gene-disease association based on text-mining of PubMed. 37:1-37:8 - Monika Mozere, Mehmet Tekman, Jameela Kari, Detlef Bockenhauer, Robert Kleta, Horia Stanescu:
OVAS: an open-source variant analysis suite with inheritance modelling. 46:1-46:10 - Yaogong Zhang, Jiahui Liu, Xiaohu Liu, Xin Fan, YuXiang Hong, Yuan Wang, Yalou Huang, Maoqiang Xie:
Prioritizing disease genes with an improved dual label propagation framework. 47:1-47:12 - Jeremy R. Wang, James Holt, Leonard McMillan, Corbin D. Jones:
FMLRC: Hybrid long read error correction using an FM-index. 50:1-50:11 - Christopher S. Anderson, Patrick R. McCall, Harry A. Stern, Hongmei Yang, David J. Topham:
Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation. 51:1-51:11 - Mario Latendresse, Peter D. Karp:
Evaluation of reaction gap-filling accuracy by randomization. 53:1-53:13 - Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn:
Oasis 2: improved online analysis of small RNA-seq data. 54:1-54:10 - Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I. Nakaya, Vinicius Maracaja-Coutinho:
StructRNAfinder: an automated pipeline and web server for RNA families prediction. 55:1-55:7 - Pedro S. T. Russo, Gustavo R. Ferreira, Lucas E. Cardozo, Matheus C. Bürger, Raúl Arias-Carrasco, Sandra R. Maruyama, Thiago D. C. Hirata, Diógenes S. Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João S. Silva, Vinicius Maracaja-Coutinho, Helder I. Nakaya:
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. 56:1-56:13 - Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad D. Huff, Lynn Jorde, Martin G. Reese, Mark Yandell:
The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. 57:1-57:13 - Oliviero Carugo:
How large B-factors can be in protein crystal structures. 61:1-61:9 - Faliu Yi, Lin Yang, Shidan Wang, Lei Guo, Chenglong Huang, Yang Xie, Guanghua Xiao:
Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks. 64:1-64:9 - Muluye E. Liku, Elizabeth-Ann Legere, Alan M. Moses:
NoLogo: a new statistical model highlights the diversity and suggests new classes of Crm1-dependent nuclear export signals. 65:1-65:15 - César Domínguez, Jónathan Heras, Eloy J. Mata, Vico Pascual:
DecoFungi: a web application for automatic characterisation of dye decolorisation in fungal strains. 66:1-66:4 - Diego Garrido-Martín, Florencio Pazos:
Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. 67:1-67:9 - Andrey Ziyatdinov, Miquel Vázquez-Santiago, Helena Brunel, Angel Martinez-Perez, Hugues Aschard, José Manuel Soria:
lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals. 68:1-68:5 - Amna Klich, Catherine Mercier, Laurent Gerfault, Pierre Grangeat, Corinne Beaulieu, Elodie Degout-Charmette, Tanguy Fortin, Pierre Mahé, Jean-François Giovannelli, Jean-Philippe Charrier, Audrey Giremus, Delphine Maucort-Boulch, Pascal Roy:
Variance component analysis to assess protein quantification in biomarker validation: application to selected reaction monitoring-mass spectrometry. 73:1-73:12 - Weibo Wang, Wei Sun, Wei Wang, Jin Szatkiewicz:
A randomized approach to speed up the analysis of large-scale read-count data in the application of CNV detection. 74:1-74:11 - Yözen Hernández, Rocky Bernstein, Pedro E. Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Wei-Gang Qiu:
BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. 76:1-76:7 - Samuel J. Yang, Marc Berndl, D. Michael Ando, Mariya Barch, Arunachalam Narayanaswamy, Eric Christiansen, Stephan Hoyer, Chris Roat, Jane Hung, Curtis T. Rueden, Asim Shankar, Steven Finkbeiner, Philip Nelson:
Assessing microscope image focus quality with deep learning. 77:1-77:9 - Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher, Peggy Sekula:
Control procedures and estimators of the false discovery rate and their application in low-dimensional settings: an empirical investigation. 78:1-78:10 - Skylar W. Marvel, Kimberly To, Fabian A. Grimm, Fred A. Wright, Ivan Rusyn, David M. Reif:
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models. 80:1-80:7 - Jalal K. Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z. Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P. McElroy, Kevin R. Coombes, Ewy A Mathé:
IntLIM: integration using linear models of metabolomics and gene expression data. 81:1-81:12 - Luan Lin, Wilson H. McKerrow, Bryce Richards, Chukiat Phonsom, Charles E. Lawrence:
Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory. 82:1-82:10 - Armen Abnousi, Shira L. Broschat, Ananth Kalyanaraman:
Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing. 83:1-83:18 - Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
Natural language processing in text mining for structural modeling of protein complexes. 84:1-84:10 - Crhisllane Rafaele dos Santos Vasconcelos, Tulio de Lima Campos, Antônio M. Rezende:
Building protein-protein interaction networks for Leishmania species through protein structural information. 85:1-85:13 - Shuxiang Ruan, Gary D. Stormo:
Comparison of discriminative motif optimization using matrix and DNA shape-based models. 86:1-86:8 - W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias:
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data. 87:1-87:23 - Bin Zou, Victor H. F. Lee, Hong Yan:
Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis. 88:1-88:13 - Rajiv Gandhi Govindaraj, Michal Brylinski:
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. 91:1-91:17 - Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu:
Fast and efficient short read mapping based on a succinct hash index. 92:1-92:14 - Jesse M. Zhang, Jue Fan, H. Christina Fan, David Rosenfeld, David N. C. Tse:
An interpretable framework for clustering single-cell RNA-Seq datasets. 93:1-93:12 - Hans-Michael Müller, Kimberly Van Auken, Yuling Li, Paul W. Sternberg:
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. 94:1-94:16 - Gen Li, Dereje Jima, Fred A. Wright, Andrew B. Nobel:
HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues. 95:1-95:11 - Shu Yang, Junwen Wang, Raymond T. Ng:
Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution. 96:1-96:12 - Michael Kluge, Caroline C. Friedel:
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data. 97:1-97:13 - Thomas Kovac, Tom Haber, Frank Van Reeth, Niel Hens:
Heterogeneous computing for epidemiological model fitting and simulation. 101:1-101:11 - Xilun Xiang, Haiguang Liu:
IDPM: an online database for ion distribution in protein molecules. 102:1-102:12 - Lei Huang, Li Liao, Cathy H. Wu:
Completing sparse and disconnected protein-protein network by deep learning. 103:1-103:12 - Katrijn Van Deun, Elise A. V. Crompvoets, Eva Ceulemans:
Obtaining insights from high-dimensional data: sparse principal covariates regression. 104:1-104:13 - Ingo Bulla, Benoît Aliaga, Virginia Lacal, Jan Bulla, Christoph Grunau, Cristian Chaparro:
Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types. 105:1-105:13 - Christine Sinoquet:
A method combining a random forest-based technique with the modeling of linkage disequilibrium through latent variables, to run multilocus genome-wide association studies. 106:1-106:24 - Kun Liang, Chuanlong Du, Hankun You, Dan Nettleton:
A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets. 107:1-107:11 - Angel Mojarro, Julie Hachey, Gary Ruvkun, Maria T. Zuber, Christopher E. Carr:
CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing. 108:1-108:4 - Peihua Chen, Chuandi Pan:
Diabetes classification model based on boosting algorithms. 109:1-109:9 - Douglas G. Howe:
A statistical approach to identify, monitor, and manage incomplete curated data sets. 110:1-110:12 - Kevin Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen:
BS-Seeker3: ultrafast pipeline for bisulfite sequencing. 111:1-111:4 - Anurag Verma, Yukiko Bradford, Scott M. Dudek, Anastasia Lucas, Shefali S. Verma, Sarah A. Pendergrass, Marylyn D. Ritchie:
A simulation study investigating power estimates in phenome-wide association studies. 120:1-120:8 - Braden Katzman, Doris Tang, Anthony Santella, Zhirong Bao:
AceTree: a major update and case study in the long term maintenance of open-source scientific software. 121:1-121:7 - Clemens L. Weiß, Marina Pais, Liliana M. Cano, Sophien Kamoun, Hernán A. Burbano:
nQuire: a statistical framework for ploidy estimation using next generation sequencing. 122:1-122:8 - Katarína Furmanová, Jan Byska, M. Eduard Gröller, Ivan Viola, Jan J. Palecek, Barbora Kozlíková:
COZOID: contact zone identifier for visual analysis of protein-protein interactions. 125:1-125:17 - M. Heath Farris, Andrew R. Scott, Pamela A. Texter, Marta Bartlett, Patricia Coleman, David Masters:
TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing. 126:1-126:13 - Thomas Thorne:
Approximate inference of gene regulatory network models from RNA-Seq time series data. 127:1-127:12 - Nishith Kumar, Md. Aminul Hoque, Masahiro Sugimoto:
Robust volcano plot: identification of differential metabolites in the presence of outliers. 128:1-128:11 - Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman K. Halgamuge:
A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. 129:1-129:18 - Ali Oghabian, Dario Greco, Mikko J. Frilander:
IntEREst: intron-exon retention estimator. 130:1-130:10 - Senthil B. Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel L. Vera, Jonathan H. Dennis, Hank W. Bass, Jinfeng Zhang:
iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. 131:1-131:15 - Jonathan Mercier, Adrien Josso, Claudine Médigue, David Vallenet:
GROOLS: reactive graph reasoning for genome annotation through biological processes. 132:1-132:12 - M. Sivade Dumousseau, Maximilian Koch, Anjali Shrivastava, Diego Alonso-López, Javier De Las Rivas, Noemi del-Toro, Colin W. Combe, Birgit H. M. Meldal, Joshua Heimbach, Juri Rappsilber, Julie M. Sullivan, Yo Yehudi, Sandra E. Orchard:
JAMI: a Java library for molecular interactions and data interoperability. 133:1-133:9 - M. Sivade Dumousseau, Diego Alonso-López, Mais G. Ammari, Glyn Bradley, Nancy H. Campbell, Arnaud Céol, Gianni Cesareni, Colin W. Combe, Javier De Las Rivas, Noemi del-Toro, Joshua Heimbach, Henning Hermjakob, Igor Jurisica, Maximilian Koch, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit H. M. Meldal, Gos Micklem, Simona Panni, Pablo Porras, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwínski, Anjali Shrivastava, Julie M. Sullivan, Nicolas Thierry-Mieg, Yo Yehudi, Kim Van Roey, Sandra E. Orchard:
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. 134:1-134:8 - MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, Xiaole Shirley Liu, Henry W. Long:
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. 135:1-135:14 - Makbule Gulcin Ozsoy, Tansel Özyer, Faruk Polat, Reda Alhajj:
Realizing drug repositioning by adapting a recommendation system to handle the process. 136:1-136:14 - Vincent Picaud, Jean-François Giovannelli, Caroline Truntzer, Jean-Philippe Charrier, Audrey Giremus, Pierre Grangeat, Catherine Mercier:
Linear MALDI-ToF simultaneous spectrum deconvolution and baseline removal. 123:1-123:20 - Yoshihiro Noguchi, Anri Ueno, Manami Otsubo, Hayato Katsuno, Ikuto Sugita, Yuta Kanematsu, Aki Yoshida, Hiroki Esaki, Tomoya Tachi, Hitomi Teramachi:
A simple method for exploring adverse drug events in patients with different primary diseases using spontaneous reporting system. 124:1-124:7 - Martin Modrák, Jirí Vohradský:
Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. 137:1-137:9 - Matthew D. King, Thomas Long, Daniel L. Pfalmer, Timothy L. Andersen, Owen M. McDougal:
SPIDR: small-molecule peptide-influenced drug repurposing. 138:1-138:11 - Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer, Yan W. Asmann:
Identification of missing variants by combining multiple analytic pipelines. 139:1-139:12 - Haochen Zhao, Linai Kuang, Lei Wang, Pengyao Ping, Zhanwei Xuan, Tingrui Pei, Zhelun Wu:
Prediction of microRNA-disease associations based on distance correlation set. 141:1-141:14 - Ajayrama Kumaraswamy, Kazuki Kai, Hiroyuki Ai, Hidetoshi Ikeno, Thomas Wachtler:
Spatial registration of neuron morphologies based on maximization of volume overlap. 143:1-143:16 - Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras, Ioanna Chouvarda:
IRProfiler - a software toolbox for high throughput immune receptor profiling. 144:1-144:11 - Zhentang Li, Yi Wang, Fei Wang:
A study on fast calling variants from next-generation sequencing data using decision tree. 145:1-145:14 - Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong:
Identification of residue pairing in interacting β-strands from a predicted residue contact map. 146:1-146:19 - Johanna Bertl, Qianyun Guo, Malene Juul, Søren Besenbacher, Morten Muhlig Nielsen, Henrik Hornshøj, Jakob Skou Pedersen, Asger Hobolth:
A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data. 147:1-147:15 - Hoai-Nam Nguyen, Vincent Paveau, Cyril Cauchois, Charles Kervrann:
ATMAD: robust image analysis for Automatic Tissue MicroArray De-arraying. 148:1-148:23 - Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak, Marasri Ruengjitchatchawalya:
SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database. 149:1-149:10 - Egon A. Ozer:
ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. 150:1-150:12 - Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre:
SECIMTools: a suite of metabolomics data analysis tools. 151:1-151:11 - Antoine Buetti-Dinh, Ran Friedman:
Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6. 155:1-155:13 - Rasmus Krempel, Pranav Kulkarni, Annie Yim, Ulrich Lang, Bianca Habermann, Peter Frommolt:
Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB). 156:1-156:10 - Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger, Carsten Denkert:
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data. 157:1-157:4 - Nenad S. Mitic, Sasa N. Malkov, Jovana J. Kovacevic, Gordana Pavlovic-Lazetic, Milos V. Beljanski:
Structural disorder of plasmid-encoded proteins in Bacteria and Archaea. 158:1-158:18 - Brigitte T. Hofmeister, Robert J. Schmitz:
Enhanced JBrowse plugins for epigenomics data visualization. 159:1-159:6 - Kishore J. Doshi, Raja Reddy Kuppili, Siddharth Gurdasani, Navneet Venkatakrishnan, Amit Saxena, Kakoli Bose:
PDZscape: a comprehensive PDZ-protein database. 160:1-160:6 - Jiongmin Zhang, Ke Jia, Jinmeng Jia, Ying Qian:
An improved approach to infer protein-protein interaction based on a hierarchical vector space model. 161:1-161:14 - Maxwell Shapiro, Stephen R. Meier, Thomas MacCarthy:
The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. 163:1-163:9 - Fabrizio Menardo, Chloé Loiseau, Daniela Brites, Mireia Coscolla, Sebastian M. Gygli, Liliana K. Rutaihwa, Andrej Trauner, Christian Beisel, Sonia Borrell, Sebastien Gagneux:
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. 164:1-164:8 - Jie Lin, Jing Wei, Donald A. Adjeroh, Bing-Hua Jiang, Yue Jiang:
SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform. 165:1-165:11 - Deborah Galpert, Alberto Fernández, Francisco Herrera, Agostinho Antunes, Reinaldo Molina Ruiz, Guillermín Agüero-Chapín:
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. 166:1-166:17 - Taushif Khan, Shailesh Kumar Panday, Indira Ghosh:
ProLego: tool for extracting and visualizing topological modules in protein structures. 167:1-167:6 - Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga:
Ensemble outlier detection and gene selection in triple-negative breast cancer data. 168:1-168:15 - Chia-Pin Kang, Hung-Chi Tu, Tzu-Fun Fu, Jhe-Ming Wu, Po-Hsun Chu, Darby Tien-Hao Chang:
An automatic method to calculate heart rate from zebrafish larval cardiac videos. 169:1-169:10 - Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min, Sungroh Yoon:
Correction to: HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment. 170:1 - Claudia de Molina, Estefania Serrano, Francisco Javier García Blas, Jesús Carretero, Manuel Desco, Mónica Abella:
GPU-accelerated iterative reconstruction for limited-data tomography in CBCT systems. 171:1-171:7 - Guilherme P. Telles, Graziela S. Araújo, Maria Emília Telles Walter, Marcelo M. Brigido, Nalvo F. Almeida:
Live neighbor-joining. 172:1-172:13 - Kevin Faust, Quin Xie, Dominick Han, Kartikay Goyle, Zoya I. Volynskaya, Ugljesa Djuric, Phedias Diamandis:
Visualizing histopathologic deep learning classification and anomaly detection using nonlinear feature space dimensionality reduction. 173:1-173:15 - Xuan Li, Yuejiao Fu, Xiaogang Wang, Weiliang Qiu:
Robust joint score tests in the application of DNA methylation data analysis. 174:1-174:11 - Samuel T. Westreich, Michelle L. Treiber, David A. Mills, Ian Korf, Danielle G. Lemay:
SAMSA2: a standalone metatranscriptome analysis pipeline. 175:1-175:11 - Gamal K. O. Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen:
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. 176:1-176:11 - Ze-Gang Wei, Shao-Wu Zhang:
NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model. 177:1-177:9 - Mark D. Temple:
A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens. 179:1-179:7 - Li Fang, Jiang Hu, Depeng Wang, Kai Wang:
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data. 180:1-180:11 - Dan Li, Mary Qu Yang:
Correction to: Identification and characterization of conserved lncRNAs in human and rat brain. 181:1 - Katherine Eason, Gift Nyamundanda, Anguraj Sadanandam:
polyClustR: defining communities of reconciled cancer subtypes with biological and prognostic significance. 182:1-182:11 - Gurnoor Singh, Arnold Kuzniar, Erik M. van Mulligen, Anand Gavai, Christian W. Bachem, Richard G. F. Visser, Richard Finkers:
QTLTableMiner++: semantic mining of QTL tables in scientific articles. 183:1-183:11 - Yiming Wu, Yanan Liu, Yueming Wang, Yan Shi, Xudong Zhao:
JCDSA: a joint covariate detection tool for survival analysis on tumor expression profiles. 187:1-187:8 - Jens Keilwagen, Frank Hartung, Michael Paulini, Sven Twardziok, Jan Grau:
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. 189:1-189:12 - Hans Christian Wittich, Marco Seeland, Jana Wäldchen, Michael Rzanny, Patrick Mäder:
Recommending plant taxa for supporting on-site species identification. 190:1-190:17 - Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr:
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. 191:1-191:8 - Tom Hartmann, Matthias Bernt, Martin Middendorf:
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. 192:1-192:10 - Shengtian Sang, Zhihao Yang, Lei Wang, Xiaoxia Liu, Hongfei Lin, Jian Wang:
SemaTyP: a knowledge graph based literature mining method for drug discovery. 193:1-193:11 - Mark R. Segal, Henrik Bengtsson:
Improved accuracy assessment for 3D genome reconstructions. 196:1-196:9 - Laura Frølich, Tobias Søren Andersen, Morten Mørup:
Rigorous optimisation of multilinear discriminant analysis with Tucker and PARAFAC structures. 197:1-197:15 - Yifeng Li, Wenqiang Shi, Wyeth W. Wasserman:
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. 202:1-202:14 - Herman De Beukelaer, Guy F. Davenport, Veerle Fack:
Core Hunter 3: flexible core subset selection. 203:1-203:12 - Min Han, Yifan Song, Jiaqiang Qian, Dengming Ming:
Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database. 204:1-204:12 - Jianing Xi, Minghui Wang, Ao Li:
Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network. 214:1-214:14 - Lingtao Su, Guixia Liu, Tian Bai, Xiangyu Meng, Qingshan Ma:
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. 215:1-215:12 - Jongin Lee, Daehwan Lee, Mikang Sim, Daehong Kwon, Juyeon Kim, Younhee Ko, Jaebum Kim:
mySyntenyPortal: an application package to construct websites for synteny block analysis. 216:1-216:7 - Ankit Jambusaria, Jeff Klomp, Zhigang Hong, Shahin Rafii, Yang Dai, Asrar B. Malik, Jalees Rehman:
A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks. 217:1-217:15 - Mohammad Hadigol, Hossein Khiabanian:
MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications. 219:1-219:13 - Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa, Daniel J. Garry:
DrImpute: imputing dropout events in single cell RNA sequencing data. 220:1-220:10 - Joon-Yong Lee, Grant M. Fujimoto, Ryan Wilson, H. Steven Wiley, Samuel H. Payne:
Blazing Signature Filter: a library for fast pairwise similarity comparisons. 221:1-221:12 - Tara N. Furstenau, Jill H. Cocking, Jason W. Sahl, Viacheslav Fofanov:
Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. 222:1-222:13 - Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, Hélène Touzet, Martin Figeac:
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. 223:1-223:10 - Marcos Díaz-Gay, Maria Vila-Casadesús, Sebastià Franch-Expósito, Eva Hernández-Illán, Juan José Lozano, Sergi Castellví-Bel:
Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples. 224:1-224:6 - Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie K. Yeager, Robert E. Akins:
Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy. 225:1-225:10 - Jean-François Gibrat:
A short note on dynamic programming in a band. 226:1-226:5 - Qiang Yu, Dingbang Wei, Hongwei Huo:
SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets. 228:1-228:16 - C. F. Gao, X. Y. Wu:
Feature extraction method for proteins based on Markov tripeptide by compressive sensing. 229:1-229:10 - Qiuming Luo, Chao Guo, Yijun Zhang, Ye Cai, Gang Liu:
Algorithms designed for compressed-gene-data transformation among gene banks with different references. 230:1-230:12 - Clément Chatelain, Guillermo Durán, Vincent Thuillier, Franck Augé:
Performance of epistasis detection methods in semi-simulated GWAS. 231:1-231:17 - Shuonan Chen, Jessica Cara Mar:
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. 232:1-232:21 - Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu:
Predicting drug-disease associations by using similarity constrained matrix factorization. 233:1-233:12 - Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanç Birol, René L. Warren:
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. 234:1-234:10 - Renata De Paris, Christian Vahl Quevedo, Duncan D. Ruiz, Furia Gargano, Osmar Norberto de Souza:
A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model. 235:1-235:16 - Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan Ijzermans, Peter Paul L. O. Coene, Jan Willem T. Dekker, David D. E. Zimmerman, Geert W. M. Tetteroo, Wouter J. Vles, Wietske W. Vrijland, Rolf Torenbeek, Mike Kliffen, J. H. Carel Meijer, Anneke A. vd Wurff, John W. M. Martens, Anieta M. Sieuwerts:
Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons. 236:1-236:13 - Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma, Xiaowei Zhao:
Detecting Succinylation sites from protein sequences using ensemble support vector machine. 237:1-237:9 - Carlos García-Pérez, Xianwu Guo, Juan García Navarro, Diego Alonso Gómez Aguilar, Edgar E. Lara-Ramírez:
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus. 238:1-238:9 - Maria Luisa Matey-Hernandez, Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Mikkel Heide Schierup, Søren Brunak:
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. 239:1-239:12 - Kristiina Ausmees, Aji John, Salman Zubair Toor, Andreas Hellander, Carl Nettelblad:
BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data. 240:1-240:11 - Muxin Gu, Michael Buckley:
Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting. 241:1-241:9 - Yuanfang Ren, Aisharjya Sarkar, Tamer Kahveci:
ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. 242:1-242:17 - Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarík, Vladimir Benes, Vojtech Bystrý, Sarka Pospisilova:
ToTem: a tool for variant calling pipeline optimization. 243:1-243:9 - Dimitri Kagaris, Alireza Khamesipour, Constantin T. Yiannoutsos:
AUCTSP: an improved biomarker gene pair class predictor. 244:1-244:13 - Rafael V. Veiga, Helio J. C. Barbosa, Heder S. Bernardino, Joao Marcos de Freitas, Caroline A. Feitosa, Sheila M. A. Matos, Neuza M. Alcantara-Neves, Maurício Lima Barreto:
Multiobjective grammar-based genetic programming applied to the study of asthma and allergy epidemiology. 245:1-245:16 - Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger G. Sutton, Derrick E. Fouts:
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes. 246:1-246:6 - Georg Stricker, Mathilde Galinier, Julien Gagneur:
GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes. 247:1-247:9 - John A. Bachman, Benjamin M. Gyori, Peter K. Sorger:
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. 248:1-248:14 - Hitoshi Iuchi, Masahiro Sugimoto, Masaru Tomita:
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data. 249:1-249:11 - Makbule Gulcin Ozsoy, Tansel Özyer, Faruk Polat, Reda Alhajj:
Correction to: Realizing drug repositioning by adapting a recommendation system to handle the process. 250:1 - Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni:
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. 252:1-252:19 - Carl G. de Boer, Aviv Regev:
BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. 253:1-253:13 - Tadi Venkata Sivakumar, Anirban Bhaduri, Rajasekhara Reddy Duvvuru Muni, Jin Hwan Park, Tae Yong Kim:
SimCAL: a flexible tool to compute biochemical reaction similarity. 254:1-254:9 - Henning Lenz, Anke Hein, Volker Knoop:
Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. 255:1-255:18 - Maxwell Shapiro, Stephen R. Meier, Thomas MacCarthy:
Correction to: The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. 256:1-256:2 - Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen, Lars Paulin:
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. 257:1-257:6 - Simone Dinarelli, Marco Girasole, Giovanni Longo:
FC_analysis: a tool for investigating atomic force microscopy maps of force curves. 258:1-258:12 - Geert Heyman, Ivan Vulic, Marie-Francine Moens:
A deep learning approach to bilingual lexicon induction in the biomedical domain. 259:1-259:15 - Teng Zhang, Shao-Wu Zhang, Lin Zhang, Jia Meng:
trumpet: transcriptome-guided quality assessment of m6A-seq data. 260:1-260:11 - Haojing Shao, Devika Ganesamoorthy, Tania P. S. Duarte, Minh Duc Cao, Clive J. Hoggart, Lachlan J. M. Coin:
npInv: accurate detection and genotyping of inversions using long read sub-alignment. 261:1-261:13 - Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran, W. Evan Johnson:
Alternative empirical Bayes models for adjusting for batch effects in genomic studies. 262:1-262:15 - Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie, Hua Han:
Effective automated pipeline for 3D reconstruction of synapses based on deep learning. 263:1-263:18 - Ryohei Eguchi, Mohammad Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya, Md. Altaf-Ul-Amin:
An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease. 264:1-264:12 - Abhik Seal, David J. Wild:
Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links. 265:1-265:10 - Yasunobu Okamura, Kengo Kinoshita:
Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data. 266:1-266:9 - Devika Ganesamoorthy, Minh Duc Cao, Tania P. S. Duarte, Wenhan Chen, Lachlan James M. Coin:
GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. 267:1-267:14 - Syed Ahmad Chan Bukhari, Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein:
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. 268:1-268:6 - Lana Yeganova, Sun Kim, Grigory Balasanov, W. John Wilbur:
Discovering themes in biomedical literature using a projection-based algorithm. 269:1-269:12 - Raphaël Couronné, Philipp Probst, Anne-Laure Boulesteix:
Random forest versus logistic regression: a large-scale benchmark experiment. 270:1-270:14 - Saurabh Baheti, Xiaojia Tang, Daniel R. O'Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher, Krishna R. Kalari:
HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. 271:1-271:11 - Kazunori D. Yamada, Kengo Kinoshita:
De novo profile generation based on sequence context specificity with the long short-term memory network. 272:1-272:11 - Wiktor Kusmirek, Robert Nowak:
De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application. 273:1-273:10 - Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson:
Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods. 274:1-274:15 - Yin Lu, Alexander S. Baras, Marc K. Halushka:
miRge 2.0 for comprehensive analysis of microRNA sequencing data. 275:1-275:12 - Alicja Pluciennik, Michal Stolarczyk, Maria Bzówka, Agata Raczynska, Tomasz Magdziarz, Artur Góra:
BALCONY: an R package for MSA and functional compartments of protein variability analysis. 300:1-300:8 - Costa Bachas, Jasmina Hodzic, Johannes C. van der Mijn, Chantal Stoepker, Henk M. W. Verheul, Rob M. F. Wolthuis, Emanuela Felley-Bosco, Wessel N. van Wieringen, Victor W. van Beusechem, Ruud H. Brakenhoff, Renée X. de Menezes:
Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection. 301:1-301:12 - Felix Francis, Michael D. Dumas, Scott B. Davis, Randall J. Wisser:
Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries. 302:1-302:8 - Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Kam, German E. Novakovsky, Jasper Wong, Dylan Aïssi, Li Yao:
bioSyntax: syntax highlighting for computational biology. 303:1-303:6 - Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk:
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. 304:1-304:11 - Rongquan Wang, Guixia Liu, Caixia Wang, Lingtao Su, Liyan Sun:
Predicting overlapping protein complexes based on core-attachment and a local modularity structure. 305:1-305:15 - Jingjing He, Ting Fang, Zizheng Zhang, Bei Huang, Xiaolei Zhu, Yi Xiong:
PseUI: Pseudouridine sites identification based on RNA sequence information. 306:1-306:11 - Philip T. L. C. Clausen, Frank Aarestrup, Ole Lund:
Rapid and precise alignment of raw reads against redundant databases with KMA. 307:1-307:8 - Marek Ostaszewski, Emmanuel Kieffer, Grégoire Danoy, Reinhard Schneider, Pascal Bouvry:
Clustering approaches for visual knowledge exploration in molecular interaction networks. 308:1-308:15 - Adeola M. Rotimi, Rian Pierneef, Oleg N. Reva:
Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools. 309:1-309:11 - Hani Z. Girgis, Alfredo Velasco II, Zachary E. Reyes:
HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures. 310:1-310:18 - Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier:
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs. 311:1-311:10 - Kevin Vanneste, Linda Garlant, Sylvia Broeders, Steven Van Gucht, Nancy Roosens:
Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study. 312:1-312:18 - Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot, Jean-Philippe Vert:
Effective normalization for copy number variation in Hi-C data. 313:1-313:16 - Caroline Bazzoli, Sophie Lambert-Lacroix:
Classification based on extensions of LS-PLS using logistic regression: application to clinical and multiple genomic data. 314:1-314:13 - Hao Sun, Yiting Shen, Guangwen Luo, Yuepiao Cai, Zheng Xiang:
An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example. 315:1-315:11 - Mario A. Flores, Ivan Ovcharenko:
Enhancer reprogramming in mammalian genomes. 316:1-316:10 - Itziar Irigoien, Concepción Arenas:
Identification of differentially expressed genes by means of outlier detection. 317:1-317:20 - Danilo Dessì, Jacopo Cirrone, Diego Reforgiato Recupero, Dennis E. Shasha:
SuperNoder: a tool to discover over-represented modular structures in networks. 318:1-318:12 - Mazen Alobaidi, Khalid Mahmood Malik, Susan Sabra:
Linked open data-based framework for automatic biomedical ontology generation. 319:1-319:13 - Sandhya P. Tiwari, Florence Tama, Osamu Miyashita:
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. 320:1-320:14 - Robert Müller, Markus E. Nebel:
GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach. 321:1-321:14 - Simon Klau, Vindi Jurinovic, Roman Hornung, Tobias Herold, Anne-Laure Boulesteix:
Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data. 322:1-322:14 - Matthew M. Parks, Benjamin J. Raphael, Charles E. Lawrence:
Using controls to limit false discovery in the era of big data. 323:1-323:8 - Luc Villandré, Aurélie Labbe, Bluma Brenner, Michel Roger, David A. Stephens:
DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference. 324:1-324:16 - Takeyuki Tamura:
Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. 325:1-325:9 - Rohit Kongari, Manoj Rajaure, Jesse Cahill, Eric Rasche, Eleni Mijalis, Joel Berry, Ry Young:
Phage spanins: diversity, topological dynamics and gene convergence. 326:1-326:26 - Weizhuang Zhou, Russ B. Altman:
Data-driven human transcriptomic modules determined by independent component analysis. 327:1-327:25 - Wei Zheng, Hongfei Lin, Xiaoxia Liu, Bo Xu:
A document level neural model integrated domain knowledge for chemical-induced disease relations. 328:1-328:12 - Xiangdong Zhou, Keith C. C. Chan:
Detecting gene-gene interactions for complex quantitative traits using generalized fuzzy classification. 329:1-329:13 - Chenchen Ma, Tieming Ji:
Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously. 330:1-330:10 - Massimo Maiolo, Xiaolei Zhang, Manuel Gil, Maria Anisimova:
Progressive multiple sequence alignment with indel evolution. 331:1-331:8 - Xiaoxia Liu, Zhihao Yang, Shengtian Sang, Ziwei Zhou, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Bo Xu:
Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks. 332:1-332:14 - Alperen Dalkiran, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan:
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. 334:1-334:13 - Jie-Huei Wang, Yi-Hau Chen:
Overlapping group screening for detection of gene-gene interactions: application to gene expression profiles with survival trait. 335:1-335:14 - Zurab Bzhalava, Ardi Tampuu, Piotr Bala, Raul Vicente, Joakim Dillner:
Machine Learning for detection of viral sequences in human metagenomic datasets. 336:1-336:11 - William F. Hooper, Benjamin D. Walcott, Xing Wang, Christopher Bystroff:
Fast design of arbitrary length loops in proteins using InteractiveRosetta. 337:1-337:9 - Nicolás Stocchi, María Victoria Revuelta, Priscila Ailín Lanza Castronuovo, D. Mariano A. Vera, Arjen ten Have:
Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins. 338:1-338:16 - Christopher I Cooper, Delia Yao, Dorota H. Sendorek, Takafumi N. Yamaguchi, Christine P'ng, Kathleen E. Houlahan, Cristian Caloian, Michael Fraser, Kyle Ellrott, Adam A. Margolin, Robert G. Bristow, Joshua M. Stuart, Paul C. Boutros:
Valection: design optimization for validation and verification studies. 339:1-339:11 - Siavash Sheikhizadeh, Dick de Ridder, M. Eric Schranz, Sandra Smit:
Efficient inference of homologs in large eukaryotic pan-proteomes. 340:1-340:11 - Connor Sweetnam, Simone Mocellin, Michael Krauthammer, Nathaniel Knopf, Robert Baertsch, Jeff Shrager:
Prototyping a precision oncology 3.0 rapid learning platform. 341:1-341:19 - Francesco Sambo, Francesca Finotello, Enrico Lavezzo, Giacomo Baruzzo, Giulia Masi, Elektra Peta, Marco Falda, Stefano Toppo, Luisa Barzon, Barbara Di Camillo:
Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene. 343:1-343:10 - Tian-Jian Luo, Changle Zhou, Fei Chao:
Exploring spatial-frequency-sequential relationships for motor imagery classification with recurrent neural network. 344:1-344:18 - Johannes M. Freudenberg, Ian Dunham, Philippe Sanseau, Deepak K. Rajpal:
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands. 345:1-345:11 - Patrick Kunzmann, Kay Hamacher:
Biotite: a unifying open source computational biology framework in Python. 346:1-346:8 - Pierre Mahé, Maud Tournoud:
Predicting bacterial resistance from whole-genome sequences using k-mers and stability selection. 383:1-383:11 - Ruth Alexandra Stoney, Jean-Marc Schwartz, David L. Robertson, Goran Nenadic:
Using set theory to reduce redundancy in pathway sets. 386:1-386:11 - Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul A. Rejto, Jadwiga R. Bienkowska, James Hardwick, Tao Xie:
TNER: a novel background error suppression method for mutation detection in circulating tumor DNA. 387:1-387:7 - Thomas K. F. Wong, Louis Ranjard, Yu Lin, Allen G. Rodrigo:
HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. 389:1-389:11 - Rolf Hühne, Viktor Kessler, Axel Fürstberger, Silke D. Kühlwein, Matthias Platzer, Jürgen Sühnel, Ludwig Lausser, Hans A. Kestler:
3D Network exploration and visualisation for lifespan data. 390:1-390:19 - Mai Oudah, Andreas Henschel:
Taxonomy-aware feature engineering for microbiome classification. 227:1-227:13 - Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond:
phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. 276:1-276:5 - Victor A. O. Carmelo, Lisette J. A. Kogelman, Majbritt Busk Madsen, Haja N. Kadarmideen:
WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases. 277:1-277:7 - Alan Medlar, Liisa Holm:
TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases. 278:1-278:9 - John C. Stansfield, Kellen Garrison Cresswell, Vladimir I. Vladimirov, Mikhail G. Dozmorov:
HiCcompare: an R-package for joint normalization and comparison of HI-C datasets. 279:1-279:10 - Shanliang Zhong, Jinyan Wang, Qian Zhang, Hanzi Xu, Jifeng Feng:
CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers. 292:1-292:5 - Buzhong Zhang, Jinyan Li, Qiang Lü:
Prediction of 8-state protein secondary structures by a novel deep learning architecture. 293:1-293:13 - Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternaehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Celia M. T. Greenwood, Patricia P. Silveira, Michael J. Meaney, Kieran J. O'Donnell:
PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores. 295:1-295:9 - Maria Luisa Amaral, Galina A. Erikson, Maxim N. Shokhirev:
BART: bioinformatics array research tool. 296:1-296:6 - Renato R. M. Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira, Ronnie Alves:
PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. 297:1-297:10 - Kendrick Cetina, José Miguel Buenaposada, Luis Baumela:
Multi-class segmentation of neuronal structures in electron microscopy images. 298:1-298:13 - Luqman Hakim Abdul Hadi, Quy Xiao Xuan Lin, Tri Tran Minh, Marie Loh, Hong Kiat Ng, Agus Salim, Richie Soong, Touati Benoukraf:
miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set. 299:1-299:8 - Shu-Ju Lin, Tzu-Pin Lu, Qi-You Yu, Chuhsing Kate Hsiao:
Probabilistic prioritization of candidate pathway association with pathway score. 391:1-391:10 - Deisy Morselli Gysi, André Voigt, Tiago de Miranda Fragoso, Eivind Almaas, Katja Nowick:
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. 392:1-392:16 - Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Benjamin P. Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Jörg Bohlmann, Steven J. M. Jones, Inanç Birol:
Tigmint: correcting assembly errors using linked reads from large molecules. 393:1-393:10 - Peizhuo Wang, Lin Gao, Yuxuan Hu, Feng Li:
Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. 394:1-394:13 - Shenghui Liu, Chunrui Xu, Yusen Zhang, Jiaguo Liu, Bin Yu, Xiaoping Liu, Matthias Dehmer:
Feature selection of gene expression data for Cancer classification using double RBF-kernels. 396:1-396:14 - Michael A. Zeller, Tavis K. Anderson, Rasna W Walia, Amy L. Vincent, Phillip C. Gauger:
ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of Influenza A virus in swine. 397:1-397:10 - Guilherme Silva da Pereira, Antonio Augusto F. Garcia, Gabriel Rodrigues Alves Margarido:
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. 398:1-398:10 - Jaesik Kwak, Joonhong Park:
What we can see from very small size sample of metagenomic sequences. 399:1-399:13 - Michal R. Grzadkowski, Dorota H. Sendorek, Christine P'ng, Vincent Huang, Paul C. Boutros:
A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models. 400:1-400:9 - Xin-Ping Xie, Yu-Feng Xie, Yi-Tong Liu, Hong-Qiang Wang:
Adaptively capturing the heterogeneity of expression for cancer biomarker identification. 401:1-401:12 - Erno Lindfors, Jesse C. J. van Dam, Carolyn M. C. Lam, Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez:
SyNDI: synchronous network data integration framework. 403:1-403:15 - Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons, Melissa J. Davis:
Single sample scoring of molecular phenotypes. 404:1-404:10 - Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clément Jonquet:
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes. 405:1-405:26 - Farzaneh Salari, Fatemeh Zare-Mirakabad, Mehdi Sadeghi, Hassan Rokni-Zadeh:
Assessing the impact of exact reads on reducing the error rate of read mapping. 406:1-406:15 - Teresa Maria Rosaria Noviello, Antonella Di Liddo, Giovanna M. M. Ventola, Antonietta Spagnuolo, Salvatore D'Aniello, Michele Ceccarelli, Luigi Cerulo:
Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics. 407:1-407:12 - Konstantina Dimitrakopoulou, Elisabeth Wik, Lars A. Akslen, Inge Jonassen:
Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples. 408:1-408:17 - Jialu Hu, Yiqun Gao, Junhao He, Yan Zheng, Xuequn Shang:
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks. 422:1-422:6 - Alyssa Baccarella, Claire R. Williams, Jay Z. Parrish, Charles C. Kim:
Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance. 423:1-423:12 - Hyoyoung Choo-Wosoba, Paul S. Albert, Bin Zhu:
hsegHMM: hidden Markov model-based allele-specific copy number alteration analysis accounting for hypersegmentation. 424:1-424:14 - Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas:
Learning protein binding affinity using privileged information. 425:1-425:12 - Yang Shen, Nard Kubben, Julián Candia, Alexandre V. Morozov, Tom Misteli, Wolfgang Losert:
RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'. 427:1-427:12 - Sonisilpa Mohapatra, James C. Weisshaar:
Modified Pearson correlation coefficient for two-color imaging in spherocylindrical cells. 428:1-428:14 - Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud M. Meerzaman:
Comparing the performance of selected variant callers using synthetic data and genome segmentation. 429:1-429:11 - Ivan P. Gorlov, Claudio W. Pikielny, Hildreth R. Frost, Stephanie C. Her, Michael D. Cole, Samuel D. Strohbehn, David Wallace-Bradley, Marek Kimmel, Olga Y. Gorlova, Christopher I. Amos:
Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. 430:1-430:14 - Pablo Mier, Antonio J. Pérez-Pulido, Miguel A. Andrade-Navarro:
Automated selection of homologs to track the evolutionary history of proteins. 431:1-431:9 - Hector Sanz, Clarissa Valim, Esteban Vegas, Josep M. Oller, Ferran Reverter:
SVM-RFE: selection and visualization of the most relevant features through non-linear kernels. 432:1-432:18 - Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni:
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. 444:1-444:21 - Taekeon Lee, Youngmi Yoon:
Drug repositioning using drug-disease vectors based on an integrated network. 446:1-446:12 - Manuel Zahariev, Wen Chen, Cobus M. Visagie, C. André Lévesque:
Cluster oligonucleotide signatures for rapid identification by sequencing. 395:1-395:14 - Hui Xiao, Krzysztof Bartoszek, Pietro Lio':
Multi-omic analysis of signalling factors in inflammatory comorbidities. 439:1-439:18 - Sinan Abo Alchamlat, Frédéric Farnir:
Aggregation of experts: an application in the field of "interactomics" (detection of interactions on the basis of genomic data). 445:1-445:15 - Florian Burger, Michele Angioni, Gianluca Russo, Martina Schad, Jim Kallarackal:
PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization. 447:1-447:10 - Yi Li, Xiaoyu Liu, Yanyun Ma, Yi Wang, Weichen Zhou, Meng Hao, Zhenghong Yuan, Jie Liu, Momiao Xiong, Yin Yao Shugart, Jiucun Wang, Li Jin:
knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable. 448:1-448:12 - Swapna Thorve, Mandy L. Wilson, Bryan L. Lewis, Samarth Swarup, Anil Kumar S. Vullikanti, Madhav V. Marathe:
EpiViewer: an epidemiological application for exploring time series data. 449:1-449:10 - Yi-Pin Lai, Thomas R. Ioerger:
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility. 450:1-450:15 - A. J. Fernández-Rodríguez, Luis de Santiago, María Elena López Guillén, José Manuel Rodríguez Ascariz, Juan Manuel Miguel-Jiménez, Luciano Boquete:
Coding Prony's method in MATLAB and applying it to biomedical signal filtering. 451:1-451:14 - Ruochi Zhang, Ruixue Zhao, Xinyang Zhao, Di Wu, Weiwei Zheng, Xin Feng, Fengfeng Zhou:
pyHIVE, a health-related image visualization and engineering system using Python. 452:1-452:6 - Efthymia Chantzi, Malin Jarvius, Mia Niklasson, Anna Segerman, Mats G. Gustafsson:
COMBImage: a modular parallel processing framework for pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies. 453:1-453:19 - Paul Guilhamon, Mathieu Lupien:
SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations. 454:1-454:5 - Quanya Liu, Peng Chen, Bing Wang, Jun Zhang, Jinyan Li:
dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions. 455:1-455:7 - Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno:
Correction to: cuRnet: an R package for graph traversing on GPU. 456:1 - Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O'Connor, Michael R. Crusoe, Don Armstrong, Shaun Aron, Fourie Joubert, Azza E. Ahmed, Mamana Mbiyavanga, Peter van Heusden, Lerato E. Magosi, Jennie Zermeno, Liudmila S. Mainzer, Faisal M. Fadlelmola, C. Victor Jongeneel, Nicola J. Mulder:
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics. 457:1-457:13 - Ruoting Yang, Daniel Watson, Joshua Williams, Raina Kumar, Ross Campbell, Uma Mudunuri, Rasha Hammamieh, Marti Jett:
PanoromiX: a time-course network medicine platform integrating molecular assays and pathophenotypic data. 458:1-458:6 - Florent Guinot, Marie Szafranski, Christophe Ambroise, Franck Samson:
Learning the optimal scale for GWAS through hierarchical SNP aggregation. 459:1-459:14 - Michael J. Roach, Simon A. Schmidt, Anthony R. Borneman:
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. 460:1-460:10 - Gerard C. P. Schaafsma, Mauno Vihinen:
Representativeness of variation benchmark datasets. 461:1-461:19 - Peter Sona, Jong Hui Hong, Sunho Lee, Byong Joon Kim, Woon-Young Hong, Jongcheol Jung, Han-Na Kim, Hyung-Lae Kim, David Christopher, Laurent Herviou, Young Hwan Im, Kwee-Yum Lee, Tae Soon Kim, Jongsun Jung:
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis. 462:1-462:10 - Shirley Fritz, Andriamiharimamy Rajaonison, Olivier Chabrol, Didier Raoult, Jean-Marc Rolain, Vicky Merhej:
Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect. 463:1-463:10 - Facundo Orts, Arjen ten Have:
Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi. 464:1-464:15 - Yuanfang Ren, Ahmet Ay, Tamer Kahveci:
Shortest path counting in probabilistic biological networks. 465:1-465:19 - Emil Karlsen, Christian Schulz, Eivind Almaas:
Automated generation of genome-scale metabolic draft reconstructions based on KEGG. 467:1-467:11 - Kyle Boone, Kyle V. Camarda, Paulette Spencer, Candan Tamerler:
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries. 469:1-469:10 - Lacramioara Dranca, Lopez de Abetxuko Ruiz de Mendarozketa, Alfredo Goñi, Arantza Illarramendi, Irene Navalpotro Gomez, Manuel Delgado Alvarado, Maria C. Rodriguez-Oroz:
Using Kinect to classify Parkinson's disease stages related to severity of gait impairment. 471:1-471:15 - Seokjun Soe, Yoonjae Park, Heejoon Chae:
BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data. 472:1-472:9 - Kushal K. Dey, Dongyue Xie, Matthew Stephens:
A new sequence logo plot to highlight enrichment and depletion. 473:1-473:9 - Qian Li, Janelle R. Noel-MacDonnell, Devin C. Koestler, Ellen L. Goode, Brooke L. Fridley:
Subject level clustering using a negative binomial model for small transcriptomic studies. 474:1-474:10 - Helen N. Catanese, Kelly A. Brayton, Assefaw H. Gebremedhin:
A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen. 475:1-475:18 - Francesco Musacchia, Andrea Ciolfi, Margherita Mutarelli, Alessandro Bruselles, Raffaele Castello, Michele Pinelli, Swaraj Basu, Sandro Banfi, Giorgio Casari, Marco Tartaglia, Vincenzo Nigro:
VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database. 477:1-477:14 - Ariel W. Chan, Amy L. Williams, Jean-Luc Jannink:
A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data. 478:1-478:14 - H. Robert Frost, Christopher I. Amos:
A multi-omics approach for identifying important pathways and genes in human cancer. 479:1-479:14 - Hyunwoo Kim, Sunggeun Han, Jung-Ho Um, Kyongseok Park:
Accelerating a cross-correlation score function to search modifications using a single GPU. 480:1-480:5 - Mikhail Pomaznoy, Brendan Ha, Bjoern Peters:
GOnet: a tool for interactive Gene Ontology analysis. 470:1-470:8 - Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve:
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. 481:1-481:9 - Jie Hao, Youngsoon Kim, Tae-Kyung Kim, Mingon Kang:
PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data. 510:1-510:13 - Bojan Mihaljevic, Pedro Larrañaga, Ruth Benavides-Piccione, Sean L. Hill, Javier DeFelipe, Concha Bielza:
Towards a supervised classification of neocortical interneuron morphologies. 511:1-511:22 - Xingang Jia, Qiuhong Han, Zuhong Lu:
Analyzing the similarity of samples and genes by MG-PCC algorithm, t-SNE-SS and t-SNE-SG maps. 512:1-512:13 - S. M. Salleh, Gianluca Mazzoni, Peter Løvendahl, Haja N. Kadarmideen:
Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency. 513:1-513:15 - Paolo Boldi, Marco Frasca, Dario Malchiodi:
Correction to: Evaluating the impact of topological protein features on the negative examples selection. 530:1 - Lennart F. Johansson, Hendrik A. de Weerd, Eddy N. de Boer, Freerk van Dijk, Gerard J. te Meerman, Rolf Sijmons, Birgit Sikkema-Raddatz, Morris A. Swertz:
NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. BMC Bioinform. 19(1): 531:1-531:5 (2018) - Joshua B. Singer, Emma C. Thomson, John McLauchlan, Joseph Hughes, Robert J. Gifford:
GLUE: a flexible software system for virus sequence data. 532:1-532:18 - Rezvan Ehsani, Finn Drabløs:
Measures of co-expression for improved function prediction of long non-coding RNAs. 533:1-533:12 - Steven X. Ge, Eun Wo Son, Runan Yao:
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. 534:1-534:24 - Bo Xu, Kun Li, Wei Zheng, Xiaoxia Liu, Yijia Zhang, Zhehuan Zhao, Zengyou He:
Protein complexes identification based on go attributed network embedding. 535:1-535:10 - John M. Gaspar:
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors. 536:1-536:9 - Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau, Frederik Vercauteren:
Towards practical privacy-preserving genome-wide association study. 537:1-537:12 - Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Oscar Yanes, Alexandre Perera-Lluna:
FELLA: an R package to enrich metabolomics data. 538:1-538:9 - Stephen T. A. Rush, Dirk Repsilber:
Capturing context-specific regulation in molecular interaction networks. 539:1-539:14 - Jingting Xu, Shimeng Liu, Ping Yin, Serdar Bulun, Yang Dai:
MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data. 540:1-540:12 - Asan Agibetov, Kathrin Blagec, Hong Xu, Matthias Samwald:
Fast and scalable neural embedding models for biomedical sentence classification. 541:1-541:9 - Gue-Ho Hwang, Jeongbin Park, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Eunchong Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim, Sangsu Bae:
Web-based design and analysis tools for CRISPR base editing. 542:1-542:7 - Reza Rezazadegan, Christian M. Reidys:
Degeneracy and genetic assimilation in RNA evolution. 543:1-543:17 - Dejian Zhao, Deyou Zheng:
SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis. 544:1-544:13 - Phan Nguyen, Rosemary Braun:
Time-lagged Ordered Lasso for network inference. 545:1-545:15 - Michael Schmidt, Kay Hamacher:
hoDCA: higher order direct-coupling analysis. 546:1-546:5
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