cran: ART | Projects | Ecosyste.ms: Papers

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: over 7 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: over 17 years ago

10.1371/journal.pcbi.1005096

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
Cited by: 10
Author(s): Qi Zheng, Elizabeth A. Grice
Software Mentions: 3
Published: about 8 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: 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: over 5 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: almost 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: about 9 years ago

10.1186/s12859-018-2319-7

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Cited by: 21
Author(s): Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: about 6 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: over 3 years ago

10.1186/s12859-020-03657-5

GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences
Cited by: 17
Author(s): Miglė Gabrielaitė, Rasmus Lykke Marvig
Software Mentions: 3
Published: over 4 years ago

10.3390/s20082208

Closed-Loop Attention Restoration Theory for Virtual Reality-Based Attentional Engagement Enhancement
Cited by: 12
Author(s): Gang Li, Shihong Zhou, Zhen Kong, Mengyuan Guo
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-017-3721-7

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples
Cited by: 19
Author(s): Jake Lin, Lenka Kramná, Reija Autio, Heikki Hyöty, Matti Nykter, Ondřej Cinek
Software Mentions: 3
Published: over 7 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: about 11 years ago

10.3390/s19112625

Mobile Code Anti-Reversing Scheme Based on Bytecode Trapping in ART
Cited by: 2
Author(s): Geonbae Na, Jun Woo Lim, Sunjun Lee, Jeong Hyun Yi
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00190-20

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
Cited by: 64
Author(s): Robert A. Petit, Timothy D. Read
Software Mentions: 3
Published: about 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: over 11 years ago

10.1186/1471-2164-13-74

GemSIM: general, error-model based simulator of next-generation sequencing data
Cited by: 141
Author(s): Kerensa McElroy, Fabio Luciani, Torsten Thomas
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-33731-1

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase
Cited by: 66
Author(s): Matthew Ezewudo, Amanda Borens, Álvaro Chiner‐Oms, Paolo Miotto, Leonid Chindelevitch, Angela M. Starks, Debra Hanna, Richard Liwski, Matteo Zignol, Christopher Gilpin, Stefan Niemann, Thomas A. Kohl, Robin M. Warren, Derrick W. Crook, Sébastien Gagneux, Sven Hoffner, Camilla Rodrigues, Iñaki Comas, David M. Engelthaler, David Alland, Leen Rigouts, Christoph Lange, Keertan Dheda, Rumina Hasan, Ruth McNerney, Daniela María Cirillo, Marco Schito, Timothy C. Rodwell, James E. Posey
Software Mentions: 3
Published: about 6 years ago

10.1007/s00429-018-1734-x

Establishing the cognitive signature of human brain networks derived from structural and functional connectivity
Cited by: 20
Author(s): JeYoung Jung, Maya Visser, Richard J. Binney, Matthew A. Lambon Ralph
Software Mentions: 3
Published: over 6 years ago

10.1038/srep19233

An evaluation of the accuracy and speed of metagenome analysis tools
Cited by: 273
Author(s): Stinus Lindgreen, Karen L. Adair, Paul P. Gardner
Software Mentions: 3
Published: almost 9 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: almost 5 years ago

10.1186/1471-2105-16-S7-S5

Heterozygous genome assembly via binary classification of homologous sequence
Cited by: 13
Author(s): Paul Bodily, Mao Fujimoto, Cameron Ortega, Nozomu Okuda, Joseph Price, Mark J. Clement, Quinn Snell
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1005619

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus
Cited by: 86
Author(s): Damien C. Tully, Colin B. Ogilvie, Rebecca Batorsky, David J. Bean, Karen A. Power, Musie Ghebremichael, Hunter E. Bedard, Adrianne D. Gladden, Aaron Seese, Molly A. Amero, Kimberly Lane, Graham McGrath, Suzane Bazner, Jake P. Tinsley, Niall J. Lennon, Matthew R. Henn, Zabrina L. Brumme, Philip J. Norris, Eric S. Rosenberg, Kenneth H. Mayer, Heiko Jessen, Sergei L. Kosakovsky Pond, Bruce D. Walker, Marcus Altfeld, Jonathan M. Carlson, Todd M. Allen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12896-018-0476-4

A highly parallel strategy for storage of digital information in living cells
Cited by: 10
Author(s): Azat Akhmetov, Andrew D. Ellington, Edward M. Marcotte
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.ppat.1008357

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak
Cited by: 18
Author(s): Maxime Godfroid, Tal Dagan, Matthias Merker, Thomas A. Kohl, Roland Diel, Florian P. Maurer, Stefan Niemann, Anne Kupczok
Software Mentions: 3
Published: about 4 years ago

10.1186/s13073-019-0699-6

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli
Cited by: 34
Author(s): Rafael Patiño-Navarrete, Isabelle Rosinski‐Chupin, Nicolas Cabanel, L. Gauthier, Julie Takissian, Jean‐Yves Madec, Monzer Hamzé, Rémy A. Bonnin, Philippe Glaser
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0125201

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data
Cited by: 55
Author(s): Lilit Nersisyan, Arsen Arakelyan
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-021-00841-x

ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data
Cited by: 29
Author(s): André E. Minoche, Ben Lundie, Greg Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schönrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger, Mark J. Cowley
Software Mentions: 3
Published: over 3 years ago

10.1073/pnas.2026289118

Dopaminergic brainstem disconnection is common to pharmacological and pathological consciousness perturbation
Cited by: 33
Author(s): Lennart R. B. Spindler, Andrea I. Luppi, R. Adapa, Michael Craig, Peter Coppola, Alexander R.D. Peattie, Anne Manktelow, Paola Finoia, Barbara J. Sahakian, Guy B. Williams, Judith Allanson, John D. Pickard, David Menon, Emmanuel A. Stamatakis
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-017-1537-8

GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data
Cited by: 64
Author(s): Simona De Summa, Giovanni Malerba, Rosamaria Pinto, Antonio Mori, Vladan Mijatovic, Stefania Tommasi
Software Mentions: 3
Published: over 7 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: about 5 years ago

10.1371/journal.pgen.1007279

Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens
Cited by: 74
Author(s): Lyndal Henden, Stuart Lee, Ivo Müeller, Alyssa E. Barry, Melanie Bahlo
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-15-40

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data
Cited by: 53
Author(s): Swetansu Pattnaik, Saurabh Gupta, Rao Av, Binay Panda
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13073-015-0167-x

JAFFA: High sensitivity transcriptome-focused fusion gene detection
Cited by: 130
Author(s): N. Davidson, Ian J. Majewski, Alicia Oshlack
Software Mentions: 3
Published: over 9 years ago

10.3390/ijerph17114175

Comparison between Communicated and Calculated Exposure Estimates Obtained through Three Modeling Tools
Cited by: 1
Author(s): Andrea Spinazzè, Francesca Borghi, Daniele Magni, Costanza Rovida, Monica Locatelli, Andrea Cattaneo, Domenico Maria Cavallo
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/bts408

Accurate estimation of short read mapping quality for next-generation genome sequencing
Cited by: 30
Author(s): Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise
Software Mentions: 2
Published: about 12 years ago

10.1186/s13059-019-1872-3

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression
Cited by: 17
Author(s): Kujin Tang, Jie Ren, Fengzhu Sun
Software Mentions: 2
Published: almost 5 years ago

10.1093/bioinformatics/btx021

PALADIN: protein alignment for functional profiling whole metagenome shotgun data
Cited by: 34
Author(s): Anthony Westbrook, Jordan Ramsdell, Taruna Schuelke, Louisa Normington, R. Daniel Bergeron, W. Kelley Thomas, Matthew D. MacManes
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-017-1827-1

VAliBS: a visual aligner for bisulfite sequences
Cited by: 2
Author(s): Min Li, Peijun Huang, Xiaodong Yan, Jianxin Wang, Yi Pan, Fang‐Xiang Wu
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1632-4

Skmer: assembly-free and alignment-free sample identification using genome skims
Cited by: 75
Author(s): Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-16-S5-S8

Re-alignment of the unmapped reads with base quality score
Cited by: 13
Author(s): Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li, Yi Pan
Software Mentions: 2
Published: over 9 years ago

10.1093/bioinformatics/bty630

Simulating Illumina metagenomic data with InSilicoSeq
Cited by: 116
Author(s): Hadrien Gourlé, Oskar Karlsson Lindsjö, Juliette Hayer, Erik Bongcam‐Rudloff
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-020-3445-6

Joining Illumina paired-end reads for classifying phylogenetic marker sequences
Cited by: 10
Author(s): Tsunglin Liu, Chen-Yu Chen, An Chen-Deng, Yi Lin Chen, Jiu Yao Wang, Yung I. Hou, Min Lin
Software Mentions: 2
Published: over 4 years ago

10.1016/j.bcp.2020.114404

Modulation of recognition memory performance by light and its relationship with cortical EEG theta and gamma activities
Cited by: 9
Author(s): Sibah Hasan, Tam Ske., Russell G. Foster, Vladyslav V. Vyazovskiy, David M. Bannerman, Stuart N. Peirson
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-15-182

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
Cited by: 991
Author(s): Hongshan Jiang, Rong Lei, Shou‐Wei Ding, Shuifang Zhu
Software Mentions: 2
Published: over 10 years ago

10.1002/gepi.22362

On the application, reporting, and sharing of in silico simulations for genetic studies
Cited by: 3
Author(s): Kaleigh Riggs, Huann‐Sheng Chen, Melissa Rotunno, Bing Li, Naoko I. Simonds, Leah E. Mechanic, Bo Peng
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-015-0502-7

SCNVSim: somatic copy number variation and structure variation simulator
Cited by: 29
Author(s): Maochun Qin, Biao Liu, Jeffrey M. Conroy, Carl Morrison, Qiang Hu, Yijun Cheng, Mitsuko Murakami, Adekunle Odunsi, Candace S. Johnson, Lei Wei, Song Liu, Jianmin Wang
Software Mentions: 2
Published: over 9 years ago

10.1136/bcr-2020-238554

Body integrity identity disorder using augmented reality: a symptom reduction study
Cited by: 10
Author(s): Collin Turbyne, Pelle de Koning, Jasper B. Zantvoord, Damiaan Denys
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes10080561

SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data
Cited by: 8
Author(s): Luca Ferretti, Chandana Tennakoon, Adrian Silesian, Graham Freimanis andPaolo Ribeca
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-017-1213-3

A comparative evaluation of genome assembly reconciliation tools
Cited by: 47
Author(s): Hind Alhakami, Hamid Mirebrahim, Stefano Lonardi
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04058-y

Instance-based error correction for short reads of disease-associated genes
Cited by: 1
Author(s): Xuan Zhang, Yuansheng Liu, Zu-Guo Yu, Michael Blumenstein, György Hutvágner, Jinyan Li
Software Mentions: 2
Published: over 3 years ago

10.3389/fpsyg.2020.01560

Mindfulness-Based Restoration Skills Training (ReST) in a Natural Setting Compared to Conventional Mindfulness Training: Psychological Functioning After a Five-Week Course
Cited by: 9
Author(s): Freddie Lymeus, Marie Ahrling, Josef Apelman, Cecilia de Mander Florin, Cecilia Nilsson, Janina Vincenti, Agnes Zetterberg, Per Lindberg, Terry Hartig
Software Mentions: 2
Published: over 4 years ago

10.1186/1756-0500-7-40

XS: a FASTQ read simulator
Cited by: 20
Author(s): Diogo Pratas, Armando J. Pinho, João M. O. S. Rodrigues
Software Mentions: 2
Published: almost 11 years ago

10.3389/fpsyt.2019.00156

Effects of Childhood Maltreatment on Social Cognition and Brain Functional Connectivity in Borderline Personality Disorder Patients
Cited by: 20
Author(s): Xóchitl Duque-Alarcón, Ruth Alcalá-Lozano, Eduardo A. Garza‐Villarreal, Francisco Pellicer
Software Mentions: 2
Published: over 5 years ago

10.3389/fpsyg.2015.00471

Is the preference of natural versus man-made scenes driven by bottom–up processing of the visual features of nature?
Cited by: 63
Author(s): Omid Kardan, Emre Demiralp, Michael C. Hout, Mary Carol R. Hunter, Hossein Karimi, Taylor Hanayik, Grigori Yourganov, John Jonides, Marc G. Berman
Software Mentions: 2
Published: over 9 years ago

10.3389/fnsys.2012.00066

ADHD classification by a texture analysis of anatomical brain MRI data
Cited by: 54
Author(s): Che‐Wei Chang, Chien-Chang Ho, Jyh-Horng Chen
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12888-018-1612-3

Prevention of violent revictimization in depressed patients with an add-on internet-based emotion regulation training (iERT): study protocol for a multicenter randomized controlled trial
Cited by: 10
Author(s): Carolien Christ, Marleen M. de Waal, Digna J. F. van Schaik, Martijn Kikkert, Matthijs Blankers, Claudi Bockting, Aartjan Beekman, Jack Dekker
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnins.2021.670287

DeepNavNet: Automated Landmark Localization for Neuronavigation
Cited by: 4
Author(s): Christine A. Edwards, Abhinav Goyal, Aaron E. Rusheen, Abbas Z. Kouzani, Kendall H. Lee
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2432-7

Assessing the impact of exact reads on reducing the error rate of read mapping
Cited by: 2
Author(s): Farzaneh Salari, Fatemeh Zare-Mirakabad, Mehdi Sadeghi, Hassan Rokni‐Zadeh
Software Mentions: 2
Published: about 6 years ago

10.3389/fninf.2016.00020

VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis
Cited by: 58
Author(s): Sulantha Mathotaarachchi, Seqian Wang, Monica Shin, Tharick A. Pascoal, Min Su Kang, Thomas Beaudry, Vladimir S. Fonov, Serge Gauthier, Aurélie Labbe, Pedro Rosa‐Neto
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-019-3204-8

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework
Cited by: 2
Author(s): Guo Liang Gan, Elijah Willie, Cédric Chauve, Leonid Chindelevitch
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1006413

MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
Cited by: 41
Author(s): Christos Vlachos, Robert Kofler
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-13-239

SNP calling by sequencing pooled samples
Cited by: 61
Author(s): Emanuele Raineri, Luca Ferretti, Anna Esteve‐Codina, Bruno Nevado, Simon Heath, Miguel Pérez‐Enciso
Software Mentions: 2
Published: about 12 years ago

10.3389/fnhum.2018.00465

Connectivity of the Human Number Form Area Reveals Development of a Cortical Network for Mathematics
Cited by: 11
Author(s): Federico Nemmi, Margot A. Schel, Torkel Klingberg
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1003709

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis
Cited by: 53
Author(s): Andrew E. Teschendorff, Xiaoping Li, Helena Carén, Steven M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen
Software Mentions: 2
Published: over 10 years ago

10.3389/fimmu.2021.626616

Bispecific Antibodies: From Research to Clinical Application
Cited by: 106
Author(s): Jiabing Ma, Yicheng Mo, Menglin Tang, Junjie Shen, Yanan Qi, Wenxu Zhao, Yi You Huang, Yanmin Xu, Cheng Qian
Software Mentions: 2
Published: over 3 years ago

10.3389/fnhum.2017.00364

Transcranial Electric Stimulation Can Impair Gains during Working Memory Training and Affects the Resting State Connectivity
Cited by: 18
Author(s): Annie Möller, Federico Nemmi, Kim Karlsson, Torkel Klingberg
Software Mentions: 2
Published: over 7 years ago

10.1186/s13015-015-0052-6

GAML: genome assembly by maximum likelihood
Cited by: 8
Author(s): Vladimír Boža, Broňa Brejová, Tomáš Vinař
Software Mentions: 2
Published: over 9 years ago

10.3389/fnhum.2020.00204

Differential Functional Connectivity in Anterior and Posterior Hippocampus Supporting the Development of Memory Formation
Cited by: 28
Author(s): Lingfei Tang, Patrick Pruitt, Qijing Yu, Roya Homayouni, Ana M. Daugherty, Jessica S. Damoiseaux, Noa Ofen
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.119.400853

Synaptonemal Complex-DeficientDrosophila melanogasterFemales Exhibit Rare DSB Repair Events, Recurrent Copy-Number Variation, and an Increased Rate ofde NovoTransposable Element Movement
Cited by: 7
Author(s): Danny E. Miller
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1008949

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
Cited by: 0
Author(s): Thomas K. F. Wong, Teng Li, Louis Ranjard, Steven Wu, Jeet Sukumaran, Allen G. Rodrigo
Software Mentions: 2
Published: about 3 years ago

10.3389/fendo.2019.00917

Validation of ART Calculator for Predicting the Number of Metaphase II Oocytes Required for Obtaining at Least One Euploid Blastocyst for Transfer in Couples Undergoing in vitro Fertilization/Intracytoplasmic Sperm Injection
Cited by: 23
Author(s): Sandro C. Esteves, Hakan Yaralı́, Filippo Maria Ubaldi, José Ferreira de Carvalho, Fabiola C. Bento, Alberto Vaiarelli, Danilo Cimadomo, Irem Yarali Ozbek, Mehtap Polat, Gürkan Bozdağ, Laura Rienzi, Carlo Alviggi
Software Mentions: 2
Published: almost 5 years ago

10.7717/peerj.11717

On the use of sequence-quality information in OTU clustering
Cited by: 2
Author(s): Robert Müller, Markus E. Nebel
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-020-07125-5

Towards a better understanding of the low recall of insertion variants with short-read based variant callers
Cited by: 12
Author(s): Wesley Delage, Julien Thévenon, Claire Lemaitre
Software Mentions: 2
Published: about 4 years ago

10.3389/fnagi.2021.721171

Amyloid-Beta Influences Memory via Functional Connectivity During Memory Retrieval in Alzheimer's Disease
Cited by: 3
Author(s): Binyin Li, Miao Zhang, Ikbeom Jang, Guanyu Ye, Liche Zhou, Guoping He, Xiaozhu Lin, Hongping Meng, Xin‐Yun Huang, Wangxi Hai, Shengdi Chen, Jun Li
Software Mentions: 2
Published: about 3 years ago

10.3389/fgene.2020.603093

Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data
Cited by: 0
Author(s): Huijing Zhao, Shuang Wang, Xiguo Yuan
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-15-918

Census-based rapid and accurate metagenome taxonomic profiling
Cited by: 17
Author(s): Amirhossein Shamsaddini, Yang Pan, William Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy E. Zanne, Raja Mazumder
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-016-3154-8

High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes
Cited by: 22
Author(s): Sebastian Hutchinson, Lucy Glover, David Horn
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.3729

Challenging a bioinformatic tool’s ability to detect microbial contaminants usingin silicowhole genome sequencing data
Cited by: 8
Author(s): Nathan D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin
Software Mentions: 2
Published: about 7 years ago

10.1016/j.csbj.2017.07.002

Scalability and Validation of Big Data Bioinformatics Software
Cited by: 34
Author(s): Andrian Yang, Michael Troup, Joshua W. K. Ho
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2019.01051

Detecting Weak Signals by Combining Small P-Values in Genetic Association Studies
Cited by: 5
Author(s): Olga A. Vsevolozhskaya, Fengjiao Hu, Dmitri V. Zaykin
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-016-3213-1

In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer
Cited by: 42
Author(s): Kiatichai Faksri, Eryu Xia, Jun Tan, Yik-Ying Teo, Rick Twee‐Hee Ong
Software Mentions: 2
Published: about 8 years ago

10.3390/v12070758

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses
Cited by: 2
Author(s): Keylie M. Gibson, Margaret C. Steiner, Uzma Rentia, Matthew L. Bendall, Marcos Pérez‐Losada, Keith A. Crandall
Software Mentions: 2
Published: over 4 years ago

10.1093/texcom/tgaa033

Associations between Amygdala-Prefrontal Functional Connectivity and Age Depend on Neighborhood Socioeconomic Status
Cited by: 15
Author(s): Bruce Ramphal, Mariah DeSerisy, David Pagliaccio, Elizabeth Raffanello, Virginia Rauh, Gregory Tau, Jonathan Posner, Rachel Marsh, Amy E. Margolis
Software Mentions: 2
Published: almost 5 years ago

10.3390/v7030939

Differential Expression of HERV-K (HML-2) Proviruses in Cells and Virions of the Teratocarcinoma Cell Line Tera-1
Cited by: 54
Author(s): Neeru Bhardwaj, Meagan Montesion, Farrah Roy, John M. Coffin
Software Mentions: 2
Published: over 9 years ago

10.3390/pharmaceutics3020229

Fluorescence Molecular Tomography: Principles and Potential for Pharmaceutical Research
Cited by: 121
Author(s): Florian Stuker, Jorge Ripoll, Markus Rudin
Software Mentions: 2
Published: over 13 years ago

10.1093/ve/veaa099

GRACy: A tool for analysing human cytomegalovirus sequence data
Cited by: 4
Author(s): Salvatore Camiolo, Nicolás M. Suárez, Antonia Chalka, Cristina Venturini, Judith Breuer, Andrew J. Davison
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-11-499

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites
Cited by: 73
Author(s): Paul Hunt, Axel Martinelli, Katarzyna Modrzynska, Sofia Trindade Borges, Alison M. Creasey, Louise Rodrigues, Dario Beraldi, Laurence Loewe, R.H. Fawcett, Sujai Kumar, Marian Thomson, Urmi Trivedi, Thomas D. Otto, Arnab Pain, Mark Blaxter, Pedro Vitor Lemos Cravo
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12864-017-3713-7

Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements
Cited by: 46
Author(s): Frédéric Guèrin, Olivier Arnaiz, Nicole Boggetto, Cyril Denby Wilkes, Éric Meyer, Linda Sperling, Sandra Duharcourt
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-15-S9-S13

Ensemble analysis of adaptive compressed genome sequencing strategies
Cited by: 0
Author(s): Zeinab Taghavi
Software Mentions: 2
Published: about 10 years ago

10.1093/texcom/tgab038

Cerebellar and Cortical Correlates of Internal and External Speech Error Monitoring
Cited by: 5
Author(s): Elin Runnqvist, Valérie Chanoine, Kristof Strijkers, Chotiga Pattamadilok, Mireille Bonnard, Bruno Nazarian, Julien Sein, Jean-Luc Anton, Lydia Dorokhova, Pascal Belin, F.‐Xavier Alario
Software Mentions: 2
Published: almost 4 years ago

10.1186/s41235-020-00247-0

Resting-state posterior alpha power changes with prolonged exposure in a natural environment
Cited by: 10
Author(s): Rachel J. Hopman, Sara LoTemplio, Emily Scott, Ty L. McKinney, David L. Strayer
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-016-1278-0

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
Cited by: 74
Author(s): Jiwoong Kim, Min Soo Kim, Andrew Y. Koh, Yang Xie, Xiaowei Zhan
Software Mentions: 2
Published: about 8 years ago

10.1155/2012/530305

Retinal Damage in Multiple Sclerosis Disease Subtypes Measured by High-Resolution Optical Coherence Tomography
Cited by: 89
Author(s): Timm Oberwahrenbrock, Sven Schippling, Marius Ringelstein, Falko Kaufhold, Hanna Zimmermann, Nazmiye Keser, Kim Lea Young, Jens Harmel, Hans‐Peter Hartung, Roland Martin, Friedemann Paul, Orhan Aktaş, Alexander U. Brandt
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0075448

NeSSM: A Next-Generation Sequencing Simulator for Metagenomics
Cited by: 56
Author(s): Ben Jia, Xuan Liu, Kaiye Cai, Zhiqiang Hu, Liangxiao Ma, Chaochun Wei
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0251252

Measuring and explaining inequality of continuous care for people living with HIV receiving antiretroviral therapy in Kunming, China
Cited by: 4
Author(s): Yongmei Jin, Sawitri Assanangkornchai, Yingrong Du, Jun Li, Jingsong Bai, Yongrui Yang
Software Mentions: 2
Published: over 3 years ago

Projects: cran: ART

Papers Mentioning ART 580