cran: fasta | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0054835

Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms
Cited by: 10
Author(s): Yuri S. Fantin, Alexey D. Neverov, Alexander V. Favorov, Maria V. Alvarez-Figueroa, Svetlana I. Braslavskaya, М. А. Гордукова, И. В. Карандашова, Konstantin V. Kuleshov, Anna I. Myznikova, M. S. Polishchuk, Denis A. Reshetov, Yana A. Voiciehovskaya, А. Миронов, Vladimir Chulanov
Software Mentions: 6
Published: over 11 years ago

10.3390/genes12010081

Non-Redundant tRNA Reference Sequences for Deep Sequencing Analysis of tRNA Abundance and Epitranscriptomic RNA Modifications
Cited by: 8
Author(s): Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2015.00277

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
Cited by: 44
Author(s): Ulisses Nunes da Rocha, Hinsby Cadillo‐Quiroz, Ulaş Karaöz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin P. Bowen, Ferrán García-Pichel, Aindrila Mukhopadhyay, Trent Northen, Eoin L. Brodie
Software Mentions: 6
Published: about 9 years ago

10.3389/fcimb.2021.609160

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells
Cited by: 27
Author(s): Ying Yin, Xiaozhao Liu, Ximiao He, Li-Quan Zhou
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: almost 4 years ago

10.1093/g3journal/jkab189

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora
Cited by: 7
Author(s): Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B Sloan
Software Mentions: 6
Published: almost 3 years ago

10.1186/1471-2164-12-619

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation
Cited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: over 12 years ago

10.7717/peerj.4013

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Cited by: 26
Author(s): Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern, Pierre Poulain
Software Mentions: 6
Published: over 6 years ago

10.3390/pathogens10091109

Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure
Cited by: 6
Author(s): Priyanka Mehta, Shanmukh Alle, Anusha Chaturvedi, Aparna Swaminathan, Sheeba Saifi, Ranjeet Maurya, Partha Chattopadhyay, Priti Devi, Ruchi Chauhan, Akshay Kanakan, Janani Srinivasa Vasudevan, Ramanathan Sethuraman, Subramanian Chidambaram, Mashrin Srivastava, Avinash Chakravarthi, Johnny Jacob, Madhuri Namagiri, Varma Konala, Sujeet Jha, U. Deva Priyakumar, P. K. Vinod, Rajesh Pandey
Software Mentions: 6
Published: over 2 years ago

10.1038/sdata.2018.192

Single-cell RNA sequencing of adult mouse testes
Cited by: 42
Author(s): Söeren Lukassen, Elisabeth Bosch, Arif B. Ekici, Andreas Winterpacht
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-016-2381-3

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
Cited by: 40
Author(s): Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque, Steve J. Charette
Software Mentions: 6
Published: over 8 years ago

10.1038/s41396-021-00895-0

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets
Cited by: 22
Author(s): Danièle De Luca, Roberta Piredda, Diana Sarno, Wiebe H. C. F. Kooistra
Software Mentions: 6
Published: over 3 years ago

10.1186/1756-0500-7-68

Simulating a population genomics data set using FlowSim
Cited by: 2
Author(s): Ketil Malde
Software Mentions: 6
Published: over 10 years ago

10.1128/AEM.01285-16

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: over 7 years ago

10.1093/bioinformatics/btz855

Improved linking of motifs to their TFs using domain information
Cited by: 1
Author(s): Nina Baumgarten, Florian Schmidt, Marcel H. Schulz
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-016-1204-5

LMAP: Lightweight Multigene Analyses in PAML
Cited by: 12
Author(s): Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 6
Published: over 7 years ago

10.1093/database/baaa082

Siberian sturgeon multi-tissue reference transcriptome database
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-020-3416-y

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Cited by: 12
Author(s): Michelle L. Treiber, Diana H. Taft, Ian F Korf, David A. Mills, Danielle G. Lemay
Software Mentions: 5
Published: about 4 years ago

10.1111/1755-0998.13257

High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae
Cited by: 19
Author(s): Simei He, Dong Xiao, Guanghui Zhang, Wei Fan, Shengchang Duan, Hong Shi, Dawei Li, Rui Li, Cuizhi Geng, Guangqiang Long, Yan Zhao, Mo Chen, Mi Yan, Jianli Yang, Yingchun Lu, Yanli Zhou, Wei Chen, Yang Dong, Shengchao Yang
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-79359-y

Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece
Cited by: 9
Author(s): Panos Bravakos, Manolis Mandalakis, Paraskevi Nomikou, Thekla I. Anastasiou, Jon Bent Kristoffersen, M. Stavroulaki, Stephanos P. Kilias, Georgios Kotoulas, Antoniοs Magoulas, Paraskevi N. Polymenakou
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-4763-1

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
Cited by: 36
Author(s): Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint‐Jean, Grégory Carrier
Software Mentions: 5
Published: almost 6 years ago

10.1186/s40064-015-1609-z

Structural homology guided alignment of cysteine rich proteins
Cited by: 16
Author(s): Thomas Shafee, Andrew Robinson, Nicole. Van Der Weerden, Marilyn A. Anderson
Software Mentions: 5
Published: over 8 years ago

10.1038/srep27722

Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Cited by: 6
Author(s): Natalie C. Fonville, Karthik Raja Velmurugan, Hongseok Tae, Zalman Vaksman, Lauren J. McIver, Harold R. Garner
Software Mentions: 5
Published: almost 8 years ago

10.1111/mpp.12764

Ribosome profiles and riboproteomes of healthy and Potato virus A‐ and Agrobacterium‐infected Nicotiana benthamiana plants
Cited by: 11
Author(s): Katri Eskelin, Markku Varjosalo, Janne J. Ravantti, Kristiina Mäkinen
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-9-420

XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
Cited by: 54
Author(s): Daniel N. Frank
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pone.0097446

Supervised Learning Classification Models for Prediction of Plant Virus Encoded RNA Silencing Suppressors
Cited by: 13
Author(s): Zeenia Jagga, Dinesh Gupta
Software Mentions: 5
Published: about 10 years ago

10.3390/antibiotics10040419

Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital
Cited by: 3
Author(s): Tiago Cabral Borelli, Gabriel Lencioni Lovate, Ana Flavia Tonelli Scaranello, Lucas F. Ribeiro, Livia S. Zaramela, Felipe Marcelo Pereira-dos-Santos, Rafael Silva‐Rocha, María‐Eugenia Guazzaroni
Software Mentions: 5
Published: about 3 years ago

10.1186/s12859-021-03981-4

cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets
Cited by: 10
Author(s): Ryan Crawford, Evan S. Snitkin
Software Mentions: 5
Published: over 3 years ago

10.1038/sdata.2019.8

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining
Cited by: 33
Author(s): Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder S. Pires, Ronnie Alves, Cecílio Fróis Caldeira, Sílvio Júnio Ramos, Guilherme Oliveira
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-66374-2

Mutations in virus-derived small RNAs
Cited by: 6
Author(s): Deepti Nigam, Katherine LaTourrette, Hernán García-Ruíz
Software Mentions: 5
Published: almost 4 years ago

10.1101/2020.12.05.409821

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures
Cited by: 6
Author(s): Martina Zafferani, Christina Haddad, Le Luo, Jesse Davila‐Calderon, Liang Yuan-Chiu, Christian Shema Mugisha, Adeline G. Monaghan, Andrew Kennedy, Joseph D. Yesselman, Robert R Gifford, Andrew W. Tai, Sebla B. Kutluay, Meiling Li, Gary Brewer, Blanton S. Tolbert, Amanda E. Hargrove
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0078316

Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes
Cited by: 15
Author(s): Lydia Smith, Arpit Tandon, Ruchir Shah, Deepak Mav, Alyson B. Scoltock, John A. Cidlowski
Software Mentions: 5
Published: over 10 years ago

10.1186/s12284-019-0322-x

Signatures of differential selection in chloroplast genome between japonica and indica
Cited by: 17
Author(s): Lin Cheng, Jungrye Nam, Sang-Ho Chu, Rungnapa Phitaktansakul, Myeong-Hyeon Min, Cheng Yuan, Ji-Min Yoo, Jee-Su Kang, Kyu‐Won Kim, Yong‐Jin Park
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0125393

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation
Cited by: 45
Author(s): Samuel Gregory, Christopher Anderson, Marta Camps Arbestain, Patrick J. Biggs, Austen R. D. Ganley, Justin M. O’Sullivan, Michael T. McManus
Software Mentions: 5
Published: about 9 years ago

10.1038/sdata.2016.131

De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
Cited by: 28
Author(s): Daniel Blande, Pauliina Halimaa, Arja Tervahauta, Mark G. M. Aarts, Sirpa Kärenlampi
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0237412

The impact of different negative training data on regulatory sequence predictions
Cited by: 3
Author(s): Louisa-Marie Krützfeldt, Max Schubach, Martin Kircher
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0057170

General Patterns of Diversity in Major Marine Microeukaryote Lineages
Cited by: 51
Author(s): Massimo C. Pernice, Ramiro Logares, Laure Guillou, Ramón Massana
Software Mentions: 5
Published: about 11 years ago

10.1186/1759-8753-5-13

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
Cited by: 129
Author(s): Marc Bailly‐Bechet, Annabelle Haudry, Emmanuelle Lerat
Software Mentions: 5
Published: about 10 years ago

10.1093/gbe/evab099

Rampant Genome-Wide Admixture across the Heliconius Radiation
Cited by: 28
Author(s): Krzysztof M. Kozak, Mathieu Joron, W. Owen McMillan, Chris D. Jiggins
Software Mentions: 5
Published: about 3 years ago

10.1186/s13104-017-2616-7

fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
Cited by: 6
Author(s): Damien M. O’Halloran
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-015-0574-4

Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease
Cited by: 42
Author(s): Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama
Software Mentions: 5
Published: about 9 years ago

10.1093/jac/dkz526

Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital
Cited by: 28
Author(s): Assaf Gordon, Hang Phan, Samuel Lipworth, Elaine Cheong, Thomas Gottlieb, Sophie George, Tim Peto, Amy J Mathers, A Sarah Walker, Derrick W. Crook, Nicole Stoesser
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0216471

NanoR: A user-friendly R package to analyze and compare nanopore sequencing data
Cited by: 17
Author(s): Davide Bolognini, Niccolò Bartalucci, Alessandra Mingrino, Alessandro M. Vannucchi, Alberto Magi
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-020-02157-2

GraphAligner: rapid and versatile sequence-to-graph alignment
Cited by: 76
Author(s): Mikko Rautiainen, Tobias Marschall
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-017-0279-1

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Cited by: 79
Author(s): Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov, Arvind Sundaram
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0152067

MaxReport: An Enhanced Proteomic Result Reporting Tool for MaxQuant
Cited by: 13
Author(s): Tao Zhou, Chuyu Li, Wene Zhao, Xinru Wang, Fuqiang Wang, Jiahao Sha
Software Mentions: 5
Published: about 8 years ago

10.1080/23802359.2021.1966334

Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format
Cited by: 0
Author(s): Joan Pons, Juan José Ensenyat, Pere Rosselló Bover, M. Serra, Francesco Nardi
Software Mentions: 5
Published: over 2 years ago

10.1371/journal.pone.0069666

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data
Cited by: 21
Author(s): Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Maria Simi, Rita Shaknovich, Fabien Campagne
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.ppat.1008717

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
Cited by: 17
Author(s): Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D. Simons, Tony L. Goldberg, Nelson Ting, Colin A. Chapman, Chris Newbold, Matthew Berriman, Adam J. Reid
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSphere.00327-18

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
Cited by: 57
Author(s): Robin R Rohwer, Joshua J. Hamilton, Ryan J. Newton, Katherine D. McMahon
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0034560

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments
Cited by: 37
Author(s): David Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A.C. Carrillo, Peter Williams, Shea N. Gardner
Software Mentions: 5
Published: about 12 years ago

10.1186/1471-2105-10-S6-S10

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
Cited by: 15
Author(s): Ernesto Picardi, Flavio Mignone, Graziano Pesole
Software Mentions: 5
Published: almost 15 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: over 9 years ago

10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes
Cited by: 11
Author(s): Carol L. Ecale Zhou, Jeffrey A. Kimbrel, Robert A. Edwards, Katelyn McNair, Brian Souza, Stephanie Malfatti
Software Mentions: 5
Published: about 3 years ago

10.3390/genes10070543

A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens
Cited by: 6
Author(s): Jinpeng An, Jinxiu Li, Ying Wang, Jing Wang, Qinghe Li, Huaijun Zhou, Xiaoxiang Hu, Yaofeng Zhao, Ning Li
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2021.660779

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia
Cited by: 4
Author(s): Mario Moreno-Pino, Juan A. Ugalde, Jorge Hernández Valdés, Susana Rodríguez-Marconi, Génesis Parada-Pozo, Nicole Trefault
Software Mentions: 5
Published: almost 3 years ago

10.1099/mgen.0.000224

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Cited by: 110
Author(s): Sergio Arredondo-Alonso, Malbert R. C. Rogers, Johanna C. Braat, Tess D. Verschuuren, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2012.00220

RNA-Seq Assembly – Are We There Yet?
Cited by: 79
Author(s): Simon Schliesky, Udo Gowik, Andreas P.M. Weber, Andrea Bräutigam
Software Mentions: 5
Published: over 12 years ago

10.1186/1471-2164-15-71

Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
Cited by: 37
Author(s): Derek Stefanik, Tristan Lubinski, Brian R. Granger, Allyson L. Byrd, Adam M. Reitzel, Lukas DeFilippo, Allison Lorenc, John R. Finnerty
Software Mentions: 5
Published: over 10 years ago

10.3390/genes10110905

MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species
Cited by: 5
Author(s): Aleš Eichmeier, Tomáš Kiss, Eliška Peňázová, Jakub Pečenka, Akila Berraf-Tebbal, Miroslav Baránek, Robert Pokluda, Jana Čechová, David Gramaje, Dariusz Grzebelus
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.559728

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds
Cited by: 21
Author(s): Mengying Wang, Alexander W. Eyre, Michael R. Thon, Yeonyee Oh, Ralph A. Dean
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1009784

R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements
Cited by: 1
Author(s): D. S. Ellis, Félix Reyes-Martín, María Rodríguez-López, Cristina Cotobal, Xi‐Ming Sun, Quentin Saintain, Daniel C. Jeffares, Samuel Marguerat, Juan Jiménez, Jürg Bähler
Software Mentions: 5
Published: over 2 years ago

10.1186/s12934-020-01489-9

Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii
Cited by: 6
Author(s): Troy R Alva, Melanie Riera, J.W. Chartron
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-12-S3-S6

ApicoAlign: an alignment and sequence search tool for apicomplexan proteins
Cited by: 5
Author(s): Jamshaid Ali, Umadevi Paila, Akash Ranjan
Software Mentions: 5
Published: over 12 years ago

10.1186/s12915-019-0734-5

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data
Cited by: 25
Author(s): Ellie E. Armstrong, Ryan W. Taylor, Danny E. Miller, Christopher B. Kaelin, Gregory S. Barsh, Elizabeth A. Hadly, Dmitri A. Petrov
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2017.00147

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
Cited by: 2
Author(s): Josef Pánek, Martin Modrák, Marek Schwarz
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2019.03014

Bacterial Exposure Mediates Developmental Plasticity and Resistance to Lethal Vibrio lentus Infection in Purple Sea Urchin (Strongylocentrotus purpuratus) Larvae
Cited by: 12
Author(s): Nicholas W Schuh, Tyler J. Carrier, Catherine S. Schrankel, Adam M. Reitzel, Andreas Heyland, Jonathan P. Rast
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-11-571

Comparing de novo assemblers for 454 transcriptome data
Cited by: 240
Author(s): Sujai Kumar, Mark Blaxter
Software Mentions: 5
Published: over 13 years ago

10.1186/s13015-019-0137-8

SNPs detection by eBWT positional clustering
Cited by: 24
Author(s): Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-015-1739-2

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil
Cited by: 20
Author(s): Bree K. Yednock, Timothy J. Sullivan, Joseph E. Neigel
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pcbi.1009300

MicrobeTrace: Retooling molecular epidemiology for rapid public health response
Cited by: 17
Author(s): Ellsworth Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, S. P. Knyazev, Roxana Cintrón, William M. Switzer
Software Mentions: 5
Published: over 2 years ago

10.1186/1471-2164-15-555

piRNAQuest: searching the piRNAome for silencers
Cited by: 49
Author(s): Arijita Sarkar, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 5
Published: almost 10 years ago

10.3389/fgene.2013.00168

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Cited by: 7
Author(s): Emily J. Richardson, Franck Escalettes, Ian Fotheringham, Robert John Wallace, Michael Watson
Software Mentions: 5
Published: over 11 years ago

10.1186/s12864-020-6661-6

Analysis of heterogeneous genomic samples using image normalization and machine learning
Cited by: 3
Author(s): Sunitha Basodi, Pelin Icer Baykal, Alexander Zelikovsky, Pavel Skums, Yi Pan
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1003457

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Cited by: 207
Author(s): Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2021.656334

A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon
Cited by: 15
Author(s): Sigmund Ramberg, Bjørn Høyheim, Tone-Kari K Østbye, Rune Andreassen
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-018-5271-z

Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain
Cited by: 23
Author(s): Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika Kariyawasam, Yamuna Deepani Siriwardana, Hideo Imamura, Nadira D. Karunaweera
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1004401

TRANSIT - A Software Tool for Himar1 TnSeq Analysis
Cited by: 158
Author(s): Michael A. DeJesus, Chaitra Ambadipudi, Richard E. Baker, Christopher M. Sassetti, Thomas R. Ioerger
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pcbi.1009308

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
Cited by: 14
Author(s): Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphaël Mourad
Software Mentions: 5
Published: almost 3 years ago

10.3389/fgene.2021.711437

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
Cited by: 23
Author(s): Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
Software Mentions: 5
Published: almost 3 years ago

10.3389/fgene.2019.00725

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics
Cited by: 4
Author(s): Caio Rafael do Nascimento Santiago, Renata de Almeida Barbosa Assis, Leandro Márcio Moreira, Luciano Antônio Digiampietri
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-15-141

Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation
Cited by: 40
Author(s): Wang Shou, Tomasz Furmanek, Harald Kryvi, Christel Krossøy, Geir K. Totland, Sindre Grotmol, Anna Wargelius
Software Mentions: 5
Published: about 10 years ago

10.12688/f1000research.28142.2

MIREyA: a computational approach to detect miRNA-directed gene activation
Cited by: 1
Author(s): A. N. Elizarova, Mumin Ozturk, Reto Guler, Yulia A. Medvedeva
Software Mentions: 5
Published: over 2 years ago

10.1371/journal.pcbi.1006731

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
Cited by: 19
Author(s): Ivar Grytten, Knut Dagestad Rand, Alexander J. Nederbragt, Geir Storvik, Ingrid K. Glad, Geir Kjetil Sandve
Software Mentions: 5
Published: about 5 years ago

10.12688/f1000research.21779.2

A role for MIR828 in pineapple fruit development
Cited by: 6
Author(s): Christopher D. Rock
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-015-0659-0

Epitopemap: a web application for integrated whole proteome epitope prediction
Cited by: 5
Author(s): DJ Farrell, Stephen V. Gordon
Software Mentions: 5
Published: almost 9 years ago

10.3389/fgene.2020.518949

tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation
Cited by: 20
Author(s): Anahi Mollà-Herman, Margarita Angelova, Maud Ginestet, Clément Carré, Christophe Antoniewski, Jean‐René Huynh
Software Mentions: 5
Published: over 3 years ago

10.1186/s12862-020-01603-w

Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly
Cited by: 6
Author(s): Dustin J. Wcisel, Jeremy Howard, Jeffrey A. Yoder, Alex Dornburg
Software Mentions: 5
Published: about 4 years ago

10.1186/s12870-016-0860-y

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors
Cited by: 16
Author(s): Saurabh Gayali, Shankar Acharya, Nilesh Vikram Lande, Ashish Pandey, Subhra Chakraborty, Niranjan Chakraborty
Software Mentions: 5
Published: almost 8 years ago

10.7717/peerj.3391

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Cited by: 15
Author(s): Dariya K. Sydykova, Claus O. Wilke
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-021-04317-y

OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow
Cited by: 12
Author(s): Jochen Bathke, Gesine Lühken
Software Mentions: 5
Published: almost 3 years ago

10.3390/pathogens3020356

Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis
Cited by: 22
Author(s): Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda
Software Mentions: 5
Published: about 10 years ago

10.7717/peerj.7484

Phylogenomic analyses confirm a novel invasive North AmericanCorbicula(Bivalvia: Cyrenidae) lineage
Cited by: 20
Author(s): Amanda E. Haponski, Diarmaid Ó Foighil
Software Mentions: 5
Published: over 4 years ago

10.1002/ece3.4981

Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America
Cited by: 37
Author(s): Philip Lavretsky, Thijs Janzen, Kevin G. McCracken
Software Mentions: 5
Published: about 5 years ago

10.1093/ve/vez060

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
Cited by: 23
Author(s): Vincent Loiseau, Elisabeth A. Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian A. Federici, Richard Cordaux, Clément Gilbert
Software Mentions: 5
Published: over 4 years ago

10.3390/v13010049

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations
Cited by: 18
Author(s): Nicholas J Dimonaco, Mazdak Salavati, Barbara Shih
Software Mentions: 5
Published: over 3 years ago

10.3390/v13020291

Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1
Cited by: 12
Author(s): Katie F. Daughenbaugh, Idan Kahnonitch, Charles C. Carey, Alexander J. McMenamin, Tanner Wiegand, Tal Erez, Naama Arkin, Brian T. Ross, Blake Wiedenheft, Asaf Sadeh, Nor Chejanovsky, Yael Mandelik, Michelle L. Flenniken
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-7-64

HotSwap for bioinformatics: A STRAP tutorial
Cited by: 8
Author(s): Christoph Gille, Peter N. Robinson
Software Mentions: 5
Published: over 18 years ago

10.1186/s40168-018-0430-7

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore
Cited by: 41
Author(s): Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M. Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel, Catherine Leblanc
Software Mentions: 5
Published: about 6 years ago

Projects: cran: fasta

Papers Mentioning fasta 848