Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: fasta

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/fasta

Fast Adaptive Shrinkage/Thresholding Algorithm
1 version
Latest release: over 6 years ago
483 downloads last month

Papers Mentioning fasta 848

10.3389/fimmu.2020.00719
Induction of Identical IgG HIV-1 Envelope Epitope Recognition Patterns After Initial HIVIS-DNA/MVA-CMDR Immunization and a Late MVA-CMDR Boost
Cited by: 8
Author(s): Agricola Joachim, Mohamed Ahmed, Georgios Pollakis, Lisa Rogers, Verena Hoffmann, Patricia Munseri, Said Aboud, Eligius Lyamuya, Muhammad Bakari, Merlin L. Robb, Britta Wahrén, Eric Sandström, Charlotta Nilsson, Gunnel Biberfeld, Christof Geldmacher, Kathrin Held
Software Mentions: 2
Published: over 4 years ago
10.1186/1759-8753-3-2
The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
Cited by: 50
Author(s): Nicole de la Chaux, Takashi Tsuchimatsu, Kentaro Shimizu, Andreas Wagner
Software Mentions: 2
Published: almost 13 years ago
10.3389/fmicb.2016.00283
DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes
Cited by: 13
Author(s): Patrick Sobetzko, Lukas Jelonek, Marc Strickert, Wenxia Han, Alexander Goesmann, Torsten Waldminghaus
Software Mentions: 2
Published: over 8 years ago
10.3390/microorganisms9010050
Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang
Cited by: 17
Author(s): Komwit Surachat, Duangporn Kantachote, Panchalika Deachamag, Monwadee Wonglapsuwan
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2018.02675
The Probiotic Effectiveness in Preventing Experimental Colitis Is Correlated With Host Gut Microbiota
Cited by: 17
Author(s): Sharmila Suwal, Qiong Wu, Wenli Liu, Qingya Liu, Haixiang Sun, Ming Liang, Jing Gao, Bo Zhang, Yanbo Kou, Zhuanzhuan Liu, Yijun Wei, Yugang Wang, Kuiyang Zheng
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2020.00651
Analysis of a Marseillevirus Transcriptome Reveals Temporal Gene Expression Profile and Host Transcriptional Shift
Cited by: 17
Author(s): Rodrigo Araújo Lima Rodrigues, Amina Cherif Louazani, Agnello Picorelli, Graziele Pereira Oliveira, Francisco Pereira Lobo, Philippe Colson, Bernard La Scola, Jônatas Santos Abrahão
Software Mentions: 2
Published: over 4 years ago
10.3390/microorganisms8071001
Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes
Cited by: 1
Author(s): Daniel Vieira, Soraia Esteves, Carolina Rivera Santiago, Eduardo Conde-Sousa, Ticiana Fernandes, Célia Pais, Pedro Soares, Ricardo Franco-Duarte
Software Mentions: 2
Published: over 4 years ago
10.3390/microorganisms9040866
Multi-Drug Resistant Plasmids with ESBL/AmpC and mcr-5.1 in Paraguayan Poultry Farms: The Linkage of Antibiotic Resistance and Hatcheries
Cited by: 5
Author(s): Kristina Nešporová, Adam Valček, Costas C. Papagiannitsis, Iva Kutilová, Ivana Jamborová, Lenka Davidová-Geržova, Ibrahim Bitar, Jaroslav Hrabák, Ivan Literák, Monika Dolejská
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-020-59519-w
Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements
Cited by: 42
Author(s): Luz E. Ochoa, Aléssio Datovo, Carlos DoNascimiento, Fábio Fernandes Roxo, Mark H. Sabaj, Jonathan L. Chang, Bruno Francelino de Melo, Gabriel S. C. Silva, Fausto Foresti, Michael E. Alfaro, Cláudio Oliveira
Software Mentions: 2
Published: almost 5 years ago
10.1186/s40168-020-00797-x
Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”
Cited by: 28
Author(s): Olivier Pible, François Allain, Virginie Jouffret, Karen Culotta, Guylaine Miotello, Jean Armengaud
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-12-271
DNACLUST: accurate and efficient clustering of phylogenetic marker genes
Cited by: 161
Author(s): Mohammadreza Ghodsi, Bo Liu, Mihai Pop
Software Mentions: 2
Published: over 13 years ago
10.3389/fmicb.2018.01807
Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129
Cited by: 8
Author(s): Fillipe Luiz Rosa Do Carmo, Wanderson M. Silva, Guilherme Campos Tavares, Izabela Coimbra Ibraim, Bárbara Fernandes Cordeiro, Emiliano R. Oliveira, Houem Rabah, Chantal Cauty, Sara H. da Silva, Marcus Vinícius Canário Viana, Ana Carolina Barbosa Caetano, Roselane Gonçalves dos Santos, Rodrigo Dias de Oliveira Carvalho, Julien Jardin, Felipe L. Pereira, Edson Luiz Folador, Yves Le Loir, Henrique César Pereira Figueiredo, Gwénaël Jan, Vasco Azevedo
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2018.03220
Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility
Cited by: 49
Author(s): Vasudevan Dinakaran, Sammed N. Mandape, Kristina Shuba, Siddharth Pratap, Shruti S. Sakhare, Mohammad Tabatabai, Duane T. Smoot, Cherae Farmer-Dixon, Lakshmyya Kesavalu, Samuel E. Adunyah, Janet H. Southerland, Pandu R. Gangula
Software Mentions: 2
Published: almost 6 years ago
10.1186/2049-2618-1-6
CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota
Cited by: 48
Author(s): James R. White, Cynthia Maddox, Owen White, Samuel V. Angiuoli, W. Florian Fricke
Software Mentions: 2
Published: almost 12 years ago
10.3389/fmicb.2020.02066
High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure
Cited by: 9
Author(s): Abhijeet Singh, Johan A. A. Nylander, Anna Schnürer, Erik Bongcam‐Rudloff, Bettina Müller
Software Mentions: 2
Published: about 4 years ago
10.1186/s40168-018-0527-z
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX
Cited by: 50
Author(s): Christian Milani, Eoghan Casey, Gabriele Andrea Lugli, Rebecca Moore, Joanna Kaczorowska, Conor Feehily, Marta Mangifesta, Leonardo Mancabelli, Sabrina Duranti, Francesca Turroni, Francesca Bottacini, Jennifer Mahony, Paul D. Cotter, Fionnuala M. McAuliffe, Douwe van Sinderen, Marco Ventura
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2016.01553
Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality
Cited by: 16
Author(s): Matteo Mori, Miguel Ponce de León, Juli Peretó, Francisco Montero
Software Mentions: 2
Published: about 8 years ago
10.3389/fmicb.2021.670928
Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557
Cited by: 2
Author(s): Sarah L. Harthern-Flint, Jan Dolfing, Wojciech Mrozik, Paola Meynet, Lucy E. Eland, Martin Sim, Russell J. Davenport
Software Mentions: 2
Published: over 3 years ago
10.1099/mgen.0.000206
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Cited by: 264
Author(s): James A. Robertson, John H. E. Nash
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2148-7-33
Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics
Cited by: 261
Author(s): Elena Simionato, Valérie Ledent, Gemma G. Richards, Morgane Thomas‐Chollier, Pierre Kerner, David Coornaert, Bernard M. Degnan, Michel Vervoort
Software Mentions: 2
Published: over 17 years ago
10.3389/fmicb.2019.01391
Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool
Cited by: 17
Author(s): Zhila Esna Ashari, Kelly A. Brayton, Shira L. Broschat
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2015.01268
Pseudomonads Rule Degradation of Polyaromatic Hydrocarbons in Aerated Sediment
Cited by: 43
Author(s): Jiri Wald, Miluše Hroudová, Jan Jansa, Blanka Vrchotová, Tomáš Macek, Ondřej Uhlík
Software Mentions: 2
Published: about 9 years ago
10.1099/mgen.0.000035
Shetti, a simple tool to parse, manipulate and search large datasets of sequences
Cited by: 1
Author(s): Haitham Sobhy
Software Mentions: 2
Published: about 9 years ago
10.1099/mgen.0.000294
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
Cited by: 143
Author(s): Nicola De Maio, Liam P. Shaw, Alasdair T. M. Hubbard, Sophie George, Nicholas D. Sanderson, Jeremy Swann, Ryan R. Wick, Manal AbuOun, Emma Stubberfield, Sarah Hoosdally, Derrick W. Crook, Peto Tea., Anna E. Sheppard, M S Bailey, Daniel S. Read, Anjum Mf, A. Sarah Walker, Nicole Stoesser
Software Mentions: 2
Published: about 5 years ago
10.3389/fmicb.2018.02183
FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways
Cited by: 8
Author(s): Vineet Bhatt, Anwesha Mohapatra, Swadha Anand, Bhusan K. Kuntal, Sharmila S. Mande
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2017.01474
PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping
Cited by: 7
Author(s): Ming-Hsin Tsai, Yen‐Yi Liu, Von-Wun Soo
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2020.01529
A Novel Factor Essential for Unconventional Secretion of Chitinase Cts1
Cited by: 9
Author(s): Michèle Reindl, Janpeter Stock, Kai P. Hussnaetter, Aycin Genc, Andreas Brachmann, Kerstin Schipper
Software Mentions: 2
Published: over 4 years ago
10.1099/mgen.0.000192
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
Cited by: 272
Author(s): Johann Beghain, Antoine Bridier‐Nahmias, Hervé Le Nagard, Erick Denamur, Olivier Clermont
Software Mentions: 2
Published: over 6 years ago
10.1099/mgen.0.000102
Identification of Klebsiella capsule synthesis loci from whole genome data
Cited by: 279
Author(s): Kelly L. Wyres, Ryan R. Wick, Claire L. Gorrie, Adam Jenney, Rainer Follador, Nicholas R. Thomson
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12934-020-01462-6
Protein over-expression in Escherichia coli triggers adaptation analogous to antimicrobial resistance
Cited by: 8
Author(s): Jack James, Benjamin Yarnall, Andy Koranteng, Jane Gibson, Tahminur Rahman, D.A. Doyle
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12862-020-1593-y
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels
Cited by: 10
Author(s): Ying-Chen Chao, Melanie Merritt, Devin Schaefferkoetter, Tyler G. Evans
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2020.01329
Application of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae
Cited by: 17
Author(s): Roland T. Ashford, Jakub Muchowski, Mark S. Koylass, Holger C. Scholz, Adrian M. Whatmore
Software Mentions: 2
Published: over 4 years ago
10.3390/mps2030066
An Effective Protocol for Proteome Analysis of Medaka (Oryzias latipes) after Acute Exposure to Ionizing Radiation
Cited by: 4
Author(s): Yeni Natalia C. Perez-Gelvez, Shem D. Unger, Gerardo Gutiérrez-Sánchez, Robert Bridger, Olin E. Rhodes, Carl Bergmann
Software Mentions: 2
Published: over 5 years ago
10.3390/life11010040
Inferring the Phylogenetic Positions of Two Fig Wasp Subfamilies of Epichrysomallinae and Sycophaginae Using Transcriptomes and Mitochondrial Data
Cited by: 2
Author(s): Dan Zhao, Zhao-Zhe Xin, Hong-Xia Hou, Yi Zhou, Jianxia Wang, Jin‐Hua Xiao, Dawei Huang
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2015.01551
Genomic Resource of Rice Seed Associated Bacteria
Cited by: 44
Author(s): Samriti Midha, Kanika Bansal, Shikha Sharma, N. Vinod Kumar, Prabhu B. Patil, Vasvi Chaudhry
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12862-018-1246-6
The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen
Cited by: 25
Author(s): Bart van de Vossenberg, Balázs Brankovics, Hai D. T. Nguyen, M.P.E. van Gent-Pelzer, Donna S. Smith, Kasia Dadej, Jarosław Przetakiewicz, Jan Kreuze, M. Boerma, G. C. M. van Leeuwen, C. André Levesque, Theo A. J. van der Lee
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2018.03305
Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems
Cited by: 26
Author(s): Tessa Shates, Penglin Sun, Carolyn M. Malmström, Chrysalyn Dominguez, Kerry E. Mauck
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-020-77612-y
Transcriptome analysis of Xanthomonas fragariae in strawberry leaves
Cited by: 5
Author(s): Joanna Puławska, Monika Kałużna, Wojciech Warabieda, Joël F. Pothier, Michael Gétaz, J.M. van der Wolf
Software Mentions: 2
Published: almost 4 years ago
10.1093/bib/bbaa302
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting
Cited by: 5
Author(s): Stefano Grasso, Tjeerd van Rij, Jan Maarten van Dijl
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2018.01172
viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors
Cited by: 17
Author(s): Krithika Bhuvaneshwar, Lei Song, Subha Madhavan, Yuriy Gusev
Software Mentions: 2
Published: over 6 years ago
10.1186/s13058-018-1004-0
The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers
Cited by: 48
Author(s): Michael T. Barrett, Elizabeth Lenkiewicz, Smriti Malasi, Anamika Basu, Jennifer H. Yearley, Lakshmanan Annamalai, Ann E. McCullough, Heidi E. Kosiorek, Pooja Narang, Melissa A. Wilson Sayres, Meixuan Chen, Karen S. Anderson, Barbara A. Pockaj
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2105-9-141
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
Cited by: 8
Author(s): Adriano Barbosa-Silva, Venkata Satagopam, Reinhard Schneider, J. Ortega
Software Mentions: 2
Published: over 16 years ago
10.1186/s13068-015-0317-9
Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters
Cited by: 34
Author(s): Jasper Sloothaak, Dorett I Odoni, L.H. de Graaff, Vítor A. P. Martins dos Santos, Peter J. Schaap, Juan Antonio Tamayo-Ramos
Software Mentions: 2
Published: about 9 years ago
10.3389/fphys.2019.00767
Novel Lom-dh Genes Play Potential Role in Promoting Egg Diapause of Locusta migratoria L.
Cited by: 30
Author(s): Kun Hao, Xiongbing Tu, Hidayat Ullah, M.R. McNeill, Zehua Zhang
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2148-11-187
Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits
Cited by: 147
Author(s): Jenny Larsson, Johan A. A. Nylander, Birgitta Bergman
Software Mentions: 2
Published: over 13 years ago
10.3389/fpls.2020.00686
Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection
Cited by: 11
Author(s): Sen Li, Fangfang Ji, Feifan Hou, Huliang Cui, Qingqing Shi, Guoming Xing, Yiqun Weng, Xin Kang
Software Mentions: 2
Published: over 4 years ago
10.1186/s12862-021-01748-2
Patterns of variation of mutation rates of mitochondrial and nuclear genes of gastropods
Cited by: 4
Author(s): Thomas F. Duda
Software Mentions: 2
Published: almost 4 years ago
10.3389/fpls.2016.01459
The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry
Cited by: 22
Author(s): Daniela Lopes Paim Pinto, Lucio Brancadoro, Silvia Dal Santo, Gabriella De Lorenzis, Mario Pezzotti, Blake C. Meyers, Mario Enrico Pè, Erica Mica
Software Mentions: 2
Published: about 8 years ago
10.3389/fpls.2014.00296
A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs)
Cited by: 15
Author(s): Ronald M. Clouse, Nicola Carraro
Software Mentions: 2
Published: over 10 years ago
10.3389/fpls.2021.639345
Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria × ananassa)
Cited by: 16
Author(s): Youngjae Oh, Christopher R. Barbey, Saket Chandra, Jinhe Bai, Zhen Fan, Anne Plotto, Jérémy Pillet, Kevin M. Folta, Vance M. Whitaker, Seong-Hee Lee
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-83730-y
In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19
Cited by: 19
Author(s): Isabelle Phan, Sandhya Subramanian, David Kim, Michael Murphy, Deleah Pettie, Lauren Carter, Ivan Anishchenko, Lynn K. Barrett, Jonathan M. Craig, Logan Tillery, Roger Shek, Whitney E. Harrington, David M. Koelle, Anna Wald, David Veesler, Neil P. King, Jim Boonyaratanakornkit, Nina Isoherranen, Alexander L. Greninger, Keith R. Jerome, Helen Y. Chu, Bart L. Staker, Lance Stewart, Peter J. Myler, Wesley C. Van Voorhis
Software Mentions: 2
Published: over 3 years ago
10.1042/BSR20181734
A short peptide potentially promotes the healing of skin wound
Cited by: 39
Author(s): Yongli Song, Cheng-Shong Wu, Xinghe Zhang, Wenxin Bian, Naixin Liu, Saige Yin, Meifeng Yang, Mingying Luo, Jing Tang
Software Mentions: 2
Published: over 5 years ago
10.3390/biom10091271
Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation
Cited by: 7
Author(s): Giulia De Riso, Damiano F. G. Fiorillo, Annalisa Fierro, Mariella Cuomo, Lorenzo Chiariotti, Gennaro Miele, Sérgio Cocozza
Software Mentions: 2
Published: about 4 years ago
10.1186/1472-6750-9-33
Optimization of codon composition and regulatory elements for expression of human insulin like growth factor-1 in transgenic chloroplasts and evaluation of structural identity and function
Cited by: 79
Author(s): Henry Daniell, Gricel Ruiz, Béla Dénes, Laurence Sandberg, William H. R. Langridge
Software Mentions: 2
Published: almost 16 years ago
10.3389/fpls.2021.642661
Holocentric Chromosomes Probably Do Not Prevent Centromere Drive in Cyperaceae
Cited by: 13
Author(s): Marie Krátká, Jakub Šmerda, Kateřina Lojdová, Petr Bureš, František Zedek
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2105-8-S1-S6
The MEPS server for identifying protein conformational epitopes
Cited by: 22
Author(s): Tiziana Castrignanò, Paolo D’Onorio De Meo, Danilo Carrabino, Massimiliano Orsini, Matteo Floris, Anna Tramontano
Software Mentions: 2
Published: over 17 years ago
10.1186/s40659-017-0114-y
De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
Cited by: 15
Author(s): Michelle Thunders, Jo Cavanagh, Yinsheng Li
Software Mentions: 2
Published: over 7 years ago
10.3389/fpls.2018.01550
Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis
Cited by: 16
Author(s): Manijeh Mohammadi‐Dehcheshmeh, Ali Niazi‎, Mansour Ebrahimi, Mohammad Reza Tahsili, Zahra Nurollah, Reyhaneh Ebrahimi Khaksefid, Mahdi Ebrahimi, Esmaeil Ebrahimie
Software Mentions: 2
Published: about 6 years ago
10.1007/s10142-017-0545-0
Low diversity, activity, and density of transposable elements in five avian genomes
Cited by: 25
Author(s): Bo Gao, Saisai Wang, Yali Wang, Dan Shen, Song Xue, Cai Chen, Hengmi Cui, Chengyi Song
Software Mentions: 2
Published: almost 8 years ago
10.1038/s41598-021-93145-4
High-precision and cost-efficient sequencing for real-time COVID-19 surveillance
Cited by: 12
Author(s): Sung Yong Park, Gina Faraci, Pamela Ward, Jane F. Emerson, Ha Youn Lee
Software Mentions: 2
Published: over 3 years ago
10.1186/s13062-016-0159-9
IPC – Isoelectric Point Calculator
Cited by: 293
Author(s): Łukasz P. Kozłowski
Software Mentions: 2
Published: about 8 years ago
10.1534/g3.115.023119
Tying Down Loose Ends in the <i>Chlamydomonas</i> Genome: Functional Significance of Abundant Upstream Open Reading Frames
Cited by: 19
Author(s): Frederick R. Cross
Software Mentions: 2
Published: almost 9 years ago
10.6026/97320630015209
Dtar-Finder: program for drug target identification and characterization in bacteria
Cited by: 0
Author(s): Purushottam Prasad, Rati Sudha
Software Mentions: 2
Published: over 5 years ago
10.6026/97320630017266
Insights from the shotgun-based proteomics analysis of Biomphalaria glabrata
Cited by: 0
Author(s): Benson Otarigho, Mofolusho O. Falade, William Castro-Borges
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12915-021-01074-5
DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii
Cited by: 16
Author(s): Anabelle Planques, Pierre Kerner, Laure Ferry, Christoph Grunau, Eve Gazave, Michel Vervoort
Software Mentions: 2
Published: over 3 years ago
10.1093/bioinformatics/btw101
Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
Cited by: 42
Author(s): Volkan Sevi̇m, Ali Kashif Bashir, Chen-Shan Chin, Karen H. Miga
Software Mentions: 2
Published: over 8 years ago
10.1186/s12915-018-0500-0
Formation of chimeric genes with essential functions at the origin of eukaryotes
Cited by: 14
Author(s): Raphaël Méheust, Debashish Bhattacharya, Jananan S. Pathmanathan, James O. McInerney, Philippe Lopez, Éric Bapteste
Software Mentions: 2
Published: over 6 years ago
10.1534/g3.119.400552
Genomics Analysis of L-DOPA Exposure in<i>Drosophila sechellia</i>
Cited by: 8
Author(s): Stephen M. Lanno, Ivy Lam, Zachary Drum, Samuel C. Linde, Sara M. Gregory, Serena Shimshak, Mariel V. Becker, Kerry E. Brew, Aashli Budhiraja, Eliza A. Carter, Lorencia Chigweshe, Keagan P. Collins, Timothy S Earley, Hannah L. Einstein, Angela A. Fan, Sarah S. Goss, Eric R. Hagen, Sarah B. Hutcheon, Timothy T. Kim, Mackenzie A. Mitchell, Nola R. Neri, Sean E. Patterson, Gregory Ransom, Guadalupe Sánchez, Bella M. Wiener, Dacheng Zhao, Joseph D. Coolon
Software Mentions: 2
Published: almost 5 years ago
10.1100/2012/450124
Sequence Comparison Alignment-Free Approach Based on Suffix Tree and<i>L-Words</i>Frequency
Cited by: 11
Author(s): Inês Soares, Ana Goios, António Amorim
Software Mentions: 2
Published: almost 13 years ago
10.1093/bioinformatics/btz188
GToTree: a user-friendly workflow for phylogenomics
Cited by: 205
Author(s): Michael Lee
Software Mentions: 2
Published: over 5 years ago
10.1093/g3journal/jkab126
Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic
Cited by: 1
Author(s): Tetsuro Kawano-Sugaya, Koji Yatsu, Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Rina Tanaka, Makoto Kuroda
Software Mentions: 2
Published: over 3 years ago
10.1093/bioinformatics/btt047
Filtering duplicate reads from 454 pyrosequencing data
Cited by: 18
Author(s): Susanne Mignon Balzer, Ketil Malde, Markus A. Grohme, Inge Jonassen
Software Mentions: 2
Published: almost 12 years ago
10.1093/bioinformatics/bty189
scanPAV: a pipeline for extracting presence–absence variations in genome pairs
Cited by: 8
Author(s): Francesca Giordano, Maximilian R Stammnitz, Elizabeth P. Murchison, Zemin Ning
Software Mentions: 2
Published: over 6 years ago
10.1186/s13029-015-0039-1
CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments
Cited by: 2
Author(s): Carol L. Ecale Zhou
Software Mentions: 2
Published: over 9 years ago
10.1093/bioinformatics/btu010
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
Cited by: 8
Author(s): Chengxi Ye, Chiaowen Joyce Hsiao, Héctor Corrada Bravo
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2105-11-471
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations
Cited by: 41
Author(s): Amol C. Shetty, Prashanth Athri, Kajari Mondal, Vanessa L. Horner, Karyn Meltz Steinberg, Viren Patel, Tamara Caspary, David J. Cutler, Michael E. Zwick
Software Mentions: 2
Published: about 14 years ago
10.3897/BDJ.3.e7096
Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data)
Cited by: 7
Author(s): Michael Balke, Bernhard Ruthensteiner, Evie L. Warikar, Katja Neven, Lars Hendrich
Software Mentions: 2
Published: almost 9 years ago
10.3897/BDJ.8.e50630
The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases
Cited by: 3
Author(s): Reginald H.F. Young, Jiaojia Yu, Marie‐José Côté, Robert Hanner
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-9-235
Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm
Cited by: 23
Author(s): Jeremy D. DeBarry, Renyi Liu, Jeffrey L. Bennetzen
Software Mentions: 2
Published: over 16 years ago
10.3390/genes11020146
Constitutive and Plastic Gene Expression Variation Associated with Desiccation Resistance Differences in the Drosophila americana Species Group
Cited by: 6
Author(s): Jeremy S Davis, Leonie C. Moyle
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13104-020-4897-5
DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses
Cited by: 15
Author(s): Miguel Loera‐Sánchez, Bruno Studer, Roland Kölliker
Software Mentions: 2
Published: almost 5 years ago
10.3390/genes11091023
Accurately Predicting Glutarylation Sites Using Sequential Bi-Peptide-Based Evolutionary Features
Cited by: 16
Author(s): Easin Arafat, Wakil Ahmad, S.M. Shovan, Abdollah Dehzangi, Shubhashis Roy Dipta, Al Mehedi Hasan, Ghazaleh Taherzadeh, Swakkhar Shatabda, Alok Sharma
Software Mentions: 2
Published: about 4 years ago
10.3390/genes11121504
Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana
Cited by: 8
Author(s): Frederick Adzitey, Jonathan Asante, Hezekiel M. Kumalo, René B. Khan, Anou M. Somboro, Daniel G. Amoako
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13104-016-1903-z
De novo construction of a “Gene-space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources
Cited by: 7
Author(s): Christelle Aluome, Grégoire Aubert, Susete Alves Carvalho, Marie‐Christine Le Paslier, Judith Burstin, Dominique Brunel
Software Mentions: 2
Published: almost 9 years ago
10.18632/oncotarget.18603
MicroRNA profiling associated with non-small cell lung cancer: next generation sequencing detection, experimental validation, and prognostic value
Cited by: 28
Author(s): Sandra Gallach, Eloísa Jantus‐Lewintre, Silvia Calabuig‐Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
Software Mentions: 2
Published: over 7 years ago
10.1155/2016/7505268
Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python)
Cited by: 0
Author(s): Kristopher J. L. Irizarry, J. Rutllant
Software Mentions: 2
Published: over 8 years ago
10.1186/s12711-020-00597-9
Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions
Cited by: 4
Author(s): Lino C. Ramírez-Ayala, Dominique Rocha, Sebas E. Ramos-Onsins, Jordi Leno-Colorado, Mathieu Charles, Olivier Bouchez, Yoel Rodríguez-Valera, Miguel Pérez‐Enciso, Yuliaxis Ramayo-Caldas
Software Mentions: 2
Published: almost 4 years ago
10.1007/s10709-021-00113-x
Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms
Cited by: 5
Author(s): Bárbara van Asch, Luís Filipe Teixeira da Costa
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2229-9-37
Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants
Cited by: 88
Author(s): Malona V. Alinsug, Chun-Wei Yu, Keqiang Wu
Software Mentions: 2
Published: over 15 years ago
10.1186/gb-2005-6-13-r108
Cited by: 62
Author(s): Hubert Hackl, Thomas R Burkard, Alexander Sturn, Renee Rubio, Alexander Schleiffer, Sun Tian, John Quackenbush, Frank Eisenhaber, Zlatko Trajanoski
Software Mentions: 2
Published: almost 20 years ago
10.1186/gb-2006-7-1-r8
Cited by: 72
Author(s): Shoshana D. Brown, J.A. Gerlt, Jennifer L. Seffernick, Patricia C. Babbitt
Software Mentions: 2
Published: almost 19 years ago
10.1186/gb-2006-7-s1-s7
Cited by: 16
Author(s): Sarah Djebali, Franck Delaplace, Hugues Roest Crollius
Software Mentions: 2
Published: almost 19 years ago
10.1186/gb-2007-8-2-r18
Cited by: 157
Author(s): Penelope R. Haddrill, Daniel L. Halligan, Dimitris Tomaras, Brian Charlesworth
Software Mentions: 2
Published: almost 18 years ago
10.1186/1471-2105-11-173
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping
Cited by: 38
Author(s): Hsueh‐Wei Chang, Yu-Huei Cheng, Li‐Yeh Chuang, Cheng‐Hong Yang
Software Mentions: 2
Published: over 14 years ago
10.1186/s12859-015-0514-3
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments
Cited by: 96
Author(s): Koen Herten, Matthew S. Hestand, Joris Robert Vermeesch, J. K. J. Van Houdt
Software Mentions: 2
Published: over 9 years ago
10.1186/gb-2011-12-3-r30
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes
Cited by: 278
Author(s): Alessandro de Mello Varani, Patricia Siguier, Edith Gourbeyre, Vincent Charneau, Michaël Chandler
Software Mentions: 2
Published: almost 14 years ago
10.1128/AEM.00579-20
In-Depth Longitudinal Study of Listeria monocytogenes ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing
Cited by: 26
Author(s): Annette Fagerlund, Solveig Langsrud, Trond Møretrø
Software Mentions: 2
Published: over 4 years ago
10.1186/s13059-015-0701-6
A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii
Cited by: 97
Author(s): Agnes P. Chan, Granger Sutton, Jessica DePew, R. Krishnakumar, Yongwook Choi, Xiaofang Huang, Erin Beck, Derek M. Harkins, Maria Kim, Emil Lesho, Mikeljon P. Nikolich, Derrick E. Fouts
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2229-9-99
The cellulose synthase superfamily in fully sequenced plants and algae
Cited by: 141
Author(s): Yanbin Yin, Jinling Huang, Ying Xu
Software Mentions: 2
Published: over 15 years ago
10.1186/s12870-019-1889-5
Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α- and γ-gliadin gene families
Cited by: 61
Author(s): Aurélie Jouanin, Jan G. Schaart, Lesley A. Boyd, James Cockram, Fiona Leigh, Ruth Bates, Emma J. Wallington, Richard G. F. Visser, M.J.M. Smulders
Software Mentions: 2
Published: over 5 years ago