cran: ART | Projects | Ecosyste.ms: Papers

10.12688/f1000research.51477.2

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
Cited by: 2
Author(s): Ann Mc Cartney, Medhat Mahmoud, Michael D. Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K. Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M. Khayat, Maximillian G. Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jimin Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. Sedlazeck
Software Mentions: 14
Published: over 2 years ago

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: over 7 years ago

10.7554/eLife.65088

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Cited by: 604
Author(s): Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Léonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Vallès-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Software Mentions: 10
Published: about 3 years ago

10.1016/j.csbj.2018.01.003

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Cited by: 184
Author(s): Chang Xu
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: over 6 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: over 9 years ago

10.1186/s40168-017-0339-6

Metagenomic characterization of ambulances across the USA
Cited by: 29
Author(s): Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E. Mason
Software Mentions: 8
Published: over 6 years ago

10.1186/s13059-019-1755-7

Benchmarking of alignment-free sequence comparison methods
Cited by: 134
Author(s): Andrzej Zieleziński, Hani Z. Girgis, Guillaume Bernard, Chris-André Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S. Waterman, Matteo Comin, Sung‐Hou Kim, Susana Vinga, Jonas S. Almeida, Cheong Xin Chan, Benjamin James, Fengzhu Sun, Burkhard Morgenstern, Wojciech M. Karłowski
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12864-021-07898-3

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events
Cited by: 4
Author(s): Ümit Akköse, Veysel Oğulcan Kaya, Laura A. Lindsey-Boltz, Zeynep Karagöz, Adam D. Brown, Peter A. Larsen, Anne D. Yoder, Aziz Sancar, Ogün Adebali
Software Mentions: 8
Published: almost 3 years ago

10.3390/brainsci11060735

Statistical and Machine Learning Link Selection Methods for Brain Functional Networks: Review and Comparison
Cited by: 3
Author(s): Ilinka Ivanoska, Kire Trivodaliev, Slobodan Kalajdziski, Massimiliano Zanin
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pcbi.1006158

Comment on "A comprehensive overview and evaluation of circular RNA detection tools"
Cited by: 14
Author(s): Chia-Ying Chen, Trees‐Juen Chuang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-017-4429-4

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains
Cited by: 27
Author(s): Luis A. Amador, Aline Primot, Édouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
Software Mentions: 7
Published: over 6 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: about 4 years ago

10.1186/s13059-021-02265-7

ReSeq simulates realistic Illumina high-throughput sequencing data
Cited by: 7
Author(s): Stephan Schmeing, Mark D. Robinson
Software Mentions: 7
Published: about 3 years ago

10.1038/s41597-020-0458-y

Epigenomic profiling of neuroblastoma cell lines
Cited by: 23
Author(s): Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Software Mentions: 6
Published: about 4 years ago

10.3389/fbioe.2021.612893

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering
Cited by: 4
Author(s): Somtirtha Roy, Tijana Radivojević, Mark Forrer, Jose Manuel Martí, Vamshi Jonnalagadda, Tyler W. H. Backman, William Morrell, Hector Plahar, Joonhoon Kim, Nathan J. Hillson, Héctor García Martín
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-019-2961-8

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Cited by: 11
Author(s): Leandro Gabriel Roser, Fernán Agüero, Daniel O. Sánchez
Software Mentions: 6
Published: almost 5 years ago

10.1093/gigascience/giz022

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data
Cited by: 41
Author(s): Mark Ziemann, Antony Kaspi, Assam El‐Osta
Software Mentions: 6
Published: about 5 years ago

10.1098/rsbl.2016.0407

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies
Cited by: 64
Author(s): Camille Sessegolo, Nelly Burlet, Annabelle Haudry
Software Mentions: 6
Published: almost 8 years ago

10.3389/fnbot.2020.00036

A Path Toward Explainable AI and Autonomous Adaptive Intelligence: Deep Learning, Adaptive Resonance, and Models of Perception, Emotion, and Action
Cited by: 36
Author(s): Stephen Grossberg
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms22116052

Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species
Cited by: 18
Author(s): Eugenia E. Montiel, Francisco Panzera, Teresa Palomeque, Pedro Lorite, Sebastián Pita
Software Mentions: 6
Published: almost 3 years ago

10.1186/s13059-017-1367-z

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
Cited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: over 6 years ago

10.1186/s13059-021-02423-x

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Cited by: 58
Author(s): Daniel Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclán, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley, Anthony T. Papenfuss
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pone.0118867

A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig
Cited by: 22
Author(s): Erica Bianco, Bruno Nevado, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-021-04128-1

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis
Cited by: 4
Author(s): José Francisco Sánchez-Herrero, Raquel Pluvinet, Antonio Luna de Haro, Lauro Sumoy
Software Mentions: 6
Published: about 3 years ago

10.1186/1471-2105-14-320

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
Cited by: 40
Author(s): David Sturgill, John H. Malone, Xia Sun, Harold E. Smith, Léonard Rabinow, Marie-Laure Samson, Brian Oliver
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pcbi.1005420

A comprehensive overview and evaluation of circular RNA detection tools
Cited by: 285
Author(s): Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
Software Mentions: 6
Published: almost 7 years ago

10.1093/gigascience/giab065

SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples
Cited by: 4
Author(s): Lanying Wei, Martin Dugas, Sarah Sandmann
Software Mentions: 5
Published: over 2 years ago

10.1002/ajpa.24293

Exploring directional and fluctuating asymmetry in the human palate during growth
Cited by: 8
Author(s): Gregorio Oxilia, Jessica C. Menghi Sartorio, Eugenio Bortolini, Giulia Zampirolo, Andrea Papini, Marco Boggioni, Sergio Martini, Filippo Marciani, Simona Arrighi, Carla Figus, Giulia Marciani, Matteo Romandini, Sara Silvestrini, Maria Elena Pedrosi, Tommaso Mori, Alessandro Riga, Ottmar Kullmer, Rachel Sarig, Luca Fiorenza, Melchiore Giganti, Rita Sorrentino, Maria Giovanna Belcastro, Jacopo Moggi‐Cecchi, Stefano Benazzi
Software Mentions: 5
Published: about 3 years ago

10.1093/gigascience/giaa054

Fcirc: A comprehensive pipeline for the exploration of fusion linear and circular RNAs
Cited by: 5
Author(s): Zhaoqing Cai, Hongzhang Xue, Yue Xu, Jens Köhler, Xiaoyu Cheng, Yanjun Dai, Jie Zheng, Haiyun Wang
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0220436

Affect regulation training reduces symptom severity in depression – A randomized controlled trial
Cited by: 28
Author(s): Matthias Berking, Eva Eichler, Maike Luhmann, Alice Diedrich, Wolfgang Hiller, Winfried Rief
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00003-15

Open-Source Sequence Clustering Methods Improve the State Of the Art
Cited by: 139
Author(s): Evguenia Kopylova, José A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Zhou Hong, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pgen.1008502

Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay
Cited by: 26
Author(s): Kevin H.-C. Wei, Doris Bachtrog
Software Mentions: 5
Published: over 4 years ago

10.3389/fcimb.2021.612656

Higher-Order Chromatin Structures of Chromosomally Integrated HHV-6A Predict Integration Sites
Cited by: 2
Author(s): Michael Mariani, Cosima Zimmerman, Princess D. Rodriguez, Ellie Hasenohr, Giulia Aimola, Diana L. Gerrard, Alyssa Richman, Andrea Dest, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 5
Published: about 3 years ago

10.1093/ve/vex023

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data
Cited by: 17
Author(s): Cindy G. Santander, Philippe Gambron, Emanuele Marchi, Timokratis Karamitros, Aris Katzourakis, Gkikas Magiorkinis
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-87564-6

The ANTsX ecosystem for quantitative biological and medical imaging
Cited by: 56
Author(s): Nicholas J. Tustison, Philip A. Cook, Andrew J. Holbrook, Hans J. Johnson, John Muschelli, Gabriel A. Devenyi, Jeffrey T. Duda, Sandhitsu R. Das, Nicholas Cullen, Daniel L. Gillen, Michael A. Yassa, James L. Stone, James C. Gee, Brian Avants
Software Mentions: 5
Published: about 3 years ago

10.1093/bioinformatics/btw088

fqtools: an efficient software suite for modern FASTQ file manipulation
Cited by: 21
Author(s): Alastair Droop
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.10501

Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data
Cited by: 3
Author(s): Eliot Cline, Nuttachat Wisittipanit, Tossapon Boongoen, Ekachai Chukeatirote, D. Struss, A. Eungwanichayapant
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02474-0

Gramtools enables multiscale variation analysis with genome graphs
Cited by: 13
Author(s): Brice Letcher, Martin Hunt, Zamin Iqbal
Software Mentions: 5
Published: over 2 years ago

10.1186/s13059-017-1309-9

DESMAN: a new tool for de novo extraction of strains from metagenomes
Cited by: 149
Author(s): Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren
Software Mentions: 5
Published: over 6 years ago

10.3389/fnins.2013.00055

Optimized Design and Analysis of Sparse-Sampling fMRI Experiments
Cited by: 65
Author(s): Tyler K. Perrachione, Samik Ghosh
Software Mentions: 5
Published: over 11 years ago

10.1186/s12859-021-04154-z

Tamock: simulation of habitat-specific benchmark data in metagenomics
Cited by: 0
Author(s): Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei
Software Mentions: 5
Published: about 3 years ago

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-017-1196-0

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
Cited by: 88
Author(s): Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wei Wang, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sébastien Gagneux, Clifton E. Barry, Qian Gao
Software Mentions: 5
Published: about 7 years ago

10.1099/mgen.0.000271

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
Cited by: 5
Author(s): Charles H. D. Williamson, Nathan E. Stone, Amalee E. Nunnally, Heidie Hornstra, David M. Wagner, Chandler C. Roe, Adam J. Vazquez, Nivedita Nandurkar, Jacob Vinocur, Joel Terriquez, John D. Gillece, Jason Travis, Darrin Lemmer, Paul Keim, Jason W. Sahl
Software Mentions: 5
Published: almost 5 years ago

10.1038/srep26447

MetaTrans: an open-source pipeline for metatranscriptomics
Cited by: 84
Author(s): Xavier Martínez, Marta Pozuelo, Victoria Pascal, David Campos, Marta Gut, Fernando Azpiroz, Francisco Guarner, Chaysavanh Manichanh
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12859-020-03838-2

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference
Cited by: 3
Author(s): Robert J. Moore, Michael Barnathan, Brian Fristensky, Yán Li, Greg Knowles, Paul Gardner-Stephen, Angelo Bueti, Peter Anderson, Jianguang Qin, Andrew S. Ball
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-017-1772-z

Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum
Cited by: 13
Author(s): Daniel Amsel, Andreas Vilcinskas, André Billion
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2020.01701

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences
Cited by: 17
Author(s): John P. Bannantine, Cyril Condé, Darrell O. Bayles, Maxime Branger, Franck Biet
Software Mentions: 4
Published: almost 4 years ago

10.3389/fnhum.2017.00578

COMT Val158Met Polymorphism Exerts Sex-Dependent Effects on fMRI Measures of Brain Function
Cited by: 16
Author(s): Amanda Elton, Christopher T. Smith, Michael H. Parrish, Charlotte A. Boettiger
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2018.00537

SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data
Cited by: 4
Author(s): Prashanthi Dharanipragada, Sampreeth Reddy Seelam, Nita Parekh
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000418

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Cited by: 16
Author(s): Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene R. Bowers, David M. Engelthaler, Apurva Narechania, Darrin Lemmer, Júlio Croda, Jason R Andrews
Software Mentions: 4
Published: almost 4 years ago

10.3389/fcimb.2021.671926

Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity
Cited by: 3
Author(s): Keah V. Higgins, Lauren N. Woodie, Haley Hallowell, Michael W. Greene, Elizabeth Hiltbold Schwartz
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12859-020-03611-5

DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples
Cited by: 1
Author(s): Julie Hurel, Sophie Schbath, Stéphanie Bougeard, Mathieu Rolland, Mauro Petrillo, Fabrice Touzain
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13062-018-0225-6

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards
Cited by: 9
Author(s): Samuel M. Gerner, Thomas Rattei, Alexandra B. Graf
Software Mentions: 4
Published: over 5 years ago

10.1093/cercor/bhaa133

Overarching Principles and Dimensions of the Functional Organization in the Inferior Parietal Cortex
Cited by: 19
Author(s): Gina F. Humphreys, Rebecca L. Jackson, Matthew A. Lambon Ralph
Software Mentions: 4
Published: almost 4 years ago

10.3390/s19224935

SNAPS: Sensor Analytics Point Solutions for Detection and Decision Support Systems
Cited by: 17
Author(s): Eric S. McLamore, Shoumen Datta, Victoria L. Morgan, Nicholas D. Cavallaro, Gregory A. Kiker, Daniel M. Jenkins, Yonghua Rong, Carmen Gomes, Jonathan C. Claussen, Diana Vanegas, Evangelyn C. Alocilja
Software Mentions: 4
Published: over 4 years ago

10.1186/s40246-016-0068-0

A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis
Cited by: 18
Author(s): Isaac Akogwu, Nan Wang, Chaoyang Zhang, Ping Gong
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.cognition.2017.01.001

Cognitive representation of “musical fractals”: Processing hierarchy and recursion in the auditory domain
Cited by: 21
Author(s): Maurício Martins, Bruno Gingras, Estela Puig‐Waldmueller, W. Tecumseh Fitch
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pntd.0007332

Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil
Cited by: 19
Author(s): Laís Ceschini Machado, Mariana C. Morais-Sobral, Túlio de Lima Campos, Mylena Ribeiro Pereira, Maria de Fátima Pessoa Militão de Albuquerque, Clément Gilbert, Rafael Freitas Oliveira Franca, Gabriel Luz Wallau
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0049110

Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
Cited by: 48
Author(s): Matthew Frampton, Richard S. Houlston
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pcbi.1008904

High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING
Cited by: 15
Author(s): Wesley M. Marin, Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan A. Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, Jill A. Hollenbach
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12859-017-1911-6

Reference-guided de novo assembly approach improves genome reconstruction for related species
Cited by: 73
Author(s): Heidi E. L. Lischer, Kentaro Shimizu
Software Mentions: 4
Published: over 6 years ago

10.1093/gigascience/giz096

To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)
Cited by: 24
Author(s): Muhammad Zohaib Anwar, Anders Lanzén, Toke Bang‐Andreasen, Carsten Suhr Jacobsen
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-017-1690-0

Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities
Cited by: 48
Author(s): Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman, David N. Fredricks
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-021-02483-z

Trycycler: consensus long-read assemblies for bacterial genomes
Cited by: 128
Author(s): Ryan R. Wick, Louise M. Judd, Louise Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Software Mentions: 4
Published: over 2 years ago

10.7717/peerj.2571

The single-species metagenome: subtyping<i>Staphylococcus aureus</i>core genome sequences from shotgun metagenomic data
Cited by: 8
Author(s): Sandeep J. Joseph, Ben Li, Robert A. Petit, Zhaohui S. Qin, Lyndsey A. Darrow, Timothy D. Read
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-016-1279-z

Impact of post-alignment processing in variant discovery from whole exome data
Cited by: 28
Author(s): Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L. Slager
Software Mentions: 4
Published: over 7 years ago

10.1186/1756-0500-7-533

FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets
Cited by: 35
Author(s): Anna Shcherbina
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.2619

The PARA-suite: PAR-CLIP specific sequence read simulation and processing
Cited by: 8
Author(s): Andreas Kloetgen, Arndt Borkhardt, Jessica I. Hoell, Alice C. McHardy
Software Mentions: 4
Published: over 7 years ago

10.1093/bib/bby121

Homeolog expression quantification methods for allopolyploids
Cited by: 24
Author(s): Tony Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro Shimizu, Jun Sese
Software Mentions: 4
Published: over 5 years ago

10.12688/wellcomeopenres.9892.2

COMPASS: Continuous Open Mouse Phenotyping of Activity and Sleep Status
Cited by: 41
Author(s): L. M. Brown, Sibah Hasan, Russell G. Foster, Stuart N. Peirson
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.3406

MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
Cited by: 25
Author(s): Koji Ishiya, Shintaroh Ueda
Software Mentions: 3
Published: almost 7 years ago

10.3389/fnins.2016.00515

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging
Cited by: 132
Author(s): José Miguel Soares, Ricardo Magalhães, Pedro Silva Moreira, Alexandre Vieira de Sousa, Edward Ganz, Adriana Sampaio, Victor Alves, Paulo Marques, Nuno Sousa
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.01683

Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data
Cited by: 20
Author(s): Donghyeok Seol, So Yun Jhang, Hyaekang Kim, Seyoung Kim, Hyo‐Sun Kwak, Soon Han Kim, Woojung Lee, Sewook Park, Heebal Kim, Seoae Cho, Woori Kwak
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-020-3414-0

NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
Cited by: 5
Author(s): Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2016.00469

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Cited by: 13
Author(s): Ankit Gupta, Sanjiv Kumar, Vishnu P. K. Prasoodanan, K. Harish, Ashok Sharma, Vineet K. Sharma
Software Mentions: 3
Published: about 8 years ago

10.3389/fphys.2020.524833

Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a “Two Hit” Stressor Model
Cited by: 10
Author(s): Christine L. Foxx, Jared D. Heinze, Antonio González, Fernando Vargas, Michael V. Baratta, Ahmed Elsayed, Jessica R. Stewart, Kelsey M. Loupy, Mathew R. Arnold, Michael C. Flux, Saydie A Sago, Philip H. Siebler, Lauren N. Milton, Margaret W. Lieb, James E. Hassell, David Glenn Smith, Kyo A K Lee, Sandra A. Appiah, Evan J. Schaefer, Morgan Panitchpakdi, Nicole Sikora, Kelly C. Weldon, Christopher E. Stamper, Dominic Schmidt, David A Duggan, Yosan M Mengesha, Mikale Ogbaselassie, Kadi T. Nguyen, Chloé A. Gates, K’Loni S. Schnabel, Linh Tran, Joslynn D Jones, Martha Hotz Vitaterna, Fred W. Turek, Monika Fleshner, Pieter C. Dorrestein, Rob Knight, Kenneth P. Wright, Christopher A. Lowry
Software Mentions: 3
Published: over 3 years ago

10.1186/s13100-019-0192-1

Tools and best practices for retrotransposon analysis using high-throughput sequencing data
Cited by: 51
Author(s): Aurélie Teissandier, Nicolas Servant, Emmanuel Barillot, Déborah Bourc’his
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-015-0105-6

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering
Cited by: 72
Author(s): Oscar Franzén, Jianzhong Hu, Xiulong Bao, Steven H. Itzkowitz, Inga Peter, Ali Kashif Bashir
Software Mentions: 3
Published: over 8 years ago

10.3389/fncom.2019.00036

The Embodied Brain of SOVEREIGN2: From Space-Variant Conscious Percepts During Visual Search and Navigation to Learning Invariant Object Categories and Cognitive-Emotional Plans for Acquiring Valued Goals
Cited by: 8
Author(s): Stephen Grossberg
Software Mentions: 3
Published: almost 5 years ago

10.3758/s13414-019-01789-2

The resonant brain: How attentive conscious seeing regulates action sequences that interact with attentive cognitive learning, recognition, and prediction
Cited by: 13
Author(s): Stephen Grossberg
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-021-03955-6

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
Cited by: 2
Author(s): Ana Maria Martins Alves Vasconcelos, Maria Beatriz Carmo, Beatriz Quintino Ferreira, Inês Viegas, Margarida Gama‐Carvalho, António E. N. Ferreira, Andreia J. Amaral
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-021-01019-8

Reduced metagenome sequencing for strain-resolution taxonomic profiles
Cited by: 12
Author(s): Lars Snipen, Inga-Leena Angell, Torbjørn Rognes, Knut Rudi
Software Mentions: 3
Published: about 3 years ago

10.1099/mgen.0.000261

Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP
Cited by: 32
Author(s): Dai Yoshimura, Rei Kajitani, Yasuhiro Gotoh, Katsuyuki Katahira, Miki Okuno, Tetsuya Hayashi, Takehiko Itoh
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-017-1784-8

Evaluation of the impact of Illumina error correction tools on de novo genome assembly
Cited by: 45
Author(s): Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.4892

BLAST-based validation of metagenomic sequence assignments
Cited by: 13
Author(s): Adam L. Bazinet, Brian D. Ondov, Daniel Sommer, Shashikala Ratnayake
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00335

Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads
Cited by: 10
Author(s): Ehsan Motazedi, Chris Maliepaard, Richard Finkers, R.G.F. Visser, Dick de Ridder
Software Mentions: 3
Published: about 5 years ago

10.3389/fphys.2020.583082

Sulprostone-Induced Gastric Dysrhythmia in the Ferret: Conventional and Advanced Analytical Approaches
Cited by: 1
Author(s): Zhonghua Lu, Yu Zhou, Longlong Tu, Sze Wa Chan, Man P. Ngan, Dexuan Cui, Julia Y.H. Liu, Ianto Bosheng Huang, Jeng Sum Charmaine Kung, Chung Man Jessica Hui, John A. Rudd
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0222271

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples
Cited by: 79
Author(s): Ardi Tampuu, Zurab Bzhalava, Joakim Dillner, Rául Vicente
Software Mentions: 3
Published: over 4 years ago

10.3390/brainsci10020115

Random Forest Classification of Alcohol Use Disorder Using fMRI Functional Connectivity, Neuropsychological Functioning, and Impulsivity Measures
Cited by: 24
Author(s): Chella Kamarajan, Babak A. Ardekani, Ashwini K. Pandey, Sivan Kinreich, Gayathri Pandey, David B. Chorlian, Jacquelyn L. Meyers, Jian Zhang, Elaine Bermudez, Arthur T. Stimus, Bernice Porjesz
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0076935

Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq
Cited by: 36
Author(s): Ivan Borozan, Stuart Watt, Vincent Ferretti
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-017-1592-1

TreeToReads - a pipeline for simulating raw reads from phylogenies
Cited by: 14
Author(s): Emily Jane McTavish, James B. Pettengill, Steven R. Davis, Hugh Rand, Errol Strain, Marc W. Allard, Ruth Timme
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0086869

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Cited by: 46
Author(s): Yong-Chao Liu, Bernt Popp, Bertil Schmidt
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-020-03665-5

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Cited by: 11
Author(s): Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0061737

Simultaneous Analysis and Quality Assurance for Diffusion Tensor Imaging
Cited by: 59
Author(s): Carolyn B. Lauzon, Andrew J. Asman, Michael L. Esparza, Scott S. Burns, Qiuyun Fan, Yurui Gao, Adam W. Anderson, Nicole Davis, Laurie E. Cutting, Bennett A. Landman
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-12-73

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies
Cited by: 33
Author(s): Minxiao Wang, Song Sun, Chaolun Li, Xin Shen
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2105-8-288

TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy
Cited by: 262
Author(s): Cédric MessaoudiI, Thomas Boudier, C.O.S. Sorzano, Sergio Marco
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pone.0159029

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis
Cited by: 33
Author(s): Mingyu Gan, Qingyun Liu, Chongguang Yang, Qian Gao, Tāo Luò
Software Mentions: 3
Published: almost 8 years ago

Projects: cran: ART

Papers Mentioning ART 580