pypi: fasta | Projects | Ecosyste.ms: Papers

10.1186/1471-2199-10-11

Identification and validation of reference genes for quantitative RT-PCR normalization in wheat
Cited by: 535
Author(s): Anna Rita Paolacci, O. A. Tanzarella, E. Porceddu, M. Ciaffi
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2199-8-67

Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR
Cited by: 414
Author(s): Ann-Britt Nygård, Claus B. Jørgensen, Susanna Cirera, Merete Fredholm
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-016-0966-0

HPG pore: an efficient and scalable framework for nanopore sequencing data
Cited by: 8
Author(s): Joaquín Tárraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquı́n Dopazo
Software Mentions: 2
Published: over 8 years ago

10.1186/s12866-017-1094-3

Genome sequencing and comparative genomics of enterohemorrhagic Escherichia coli O145:H25 and O145:H28 reveal distinct evolutionary paths and marked variations in traits associated with virulence & colonization
Cited by: 25
Author(s): Sandra C. Lorenz, Narjol González-Escalona, Michael L. Kotewicz, Markus Fischer, Julie A. Kase
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-018-0446-7

Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability
Cited by: 5
Author(s): Alena Zablotskaya, Hilde Van Esch, Kevin J. Verstrepen, Guy Froyen, Joris Robert Vermeesch
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-12-376

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database
Cited by: 23
Author(s): Nicolas Blavet, Delphine Charif, Christine Oger-Desfeux, Gabriel Marais, Alex Widmer
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-6-171

An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)
Cited by: 25
Author(s): Heidi Hagen-Larsen, Jon K. Laerdahl, Frank Panitz, Alexei A. Adzhubei, Bjørn Høyheim
Software Mentions: 2
Published: almost 19 years ago

10.1186/1471-2105-5-123

Cited by: 43
Author(s): Richard J. Edwards, Denis C. Shields
Software Mentions: 2
Published: almost 21 years ago

10.1186/1471-2105-6-93

Cited by: 119
Author(s): Scot E. Dowd, J Gomez Zaragoza, Javier Rodríguez, Melvin J. Oliver, Paxton Payton
Software Mentions: 2
Published: almost 20 years ago

10.7554/eLife.25299

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin
Cited by: 120
Author(s): Whitney L. Johnson, William T. Yewdell, Jason C. Bell, Shannon M. McNulty, Zachary Duda, Rachel J. O’Neill, Beth A. Sullivan, Aaron F. Straight
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-9-154

DNAAlignEditor: DNA alignment editor tool
Cited by: 14
Author(s): Héctor Sánchez-Villeda, Steven G. Schroeder, Sherry Flint‐Garcia, Katherine E. Guill, Mariko Yamasaki, Michael D. McMullen
Software Mentions: 2
Published: over 16 years ago

10.1186/s12864-017-4251-z

Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight
Cited by: 26
Author(s): Joanna Puławska, Monika Kałużna, Wojciech Warabieda, Artur Mikiciński
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-13-216

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
Cited by: 7
Author(s): Anna Kedzierska, Marta Casanellas
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2164-9-596

Mononucleotide repeats are asymmetrically distributed in fungal genes
Cited by: 9
Author(s): Mark W. J. van Passel, L.H. de Graaff
Software Mentions: 2
Published: almost 17 years ago

10.1186/s13073-018-0555-0

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance
Cited by: 49
Author(s): Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-6640-y

Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model
Cited by: 21
Author(s): Saidi R. Achari, Jatinder Kaur, Quang Minh Dinh, Ross Mann, Tim Sawbridge, Brett A. Summerell, Jacqueline Edwards
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-14-S5-S16

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing
Cited by: 36
Author(s): Suparna Mitra, Karin Förster-Fromme, Antje Damms-Machado, Tim Scheurenbrand, Saskia Biskup, Daniel H. Huson, Stephan C. Bischoff
Software Mentions: 2
Published: almost 12 years ago

10.1093/gigascience/gix043

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
Cited by: 72
Author(s): Alfonso Benı́tez-Páez, Yolanda Sanz
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-017-1562-7

Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides
Cited by: 24
Author(s): Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo, Eduardo Ruiz‐Pesini
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-017-1952-x

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
Cited by: 62
Author(s): Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory Bonito
Software Mentions: 2
Published: almost 7 years ago

10.1093/gigascience/giy141

The genome of the tegu lizardSalvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly
Cited by: 21
Author(s): Juliana G. Roscito, Katrin Sameith, Martin Pippel, Kees−Jan Françoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, Michael Hiller
Software Mentions: 2
Published: almost 6 years ago

10.1093/gigascience/giz006

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale
Cited by: 102
Author(s): Henrik Krehenwinkel, Aaron Pomerantz, James Henderson, Susan Kennedy, Jun Ying Lim, Varun Swamy, Juan Diego Shoobridge, Natalie Graham, Nipam H. Patel, Rosemary G. Gillespie, Stefan Prost
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-11-184

Synteny mapping between common bean and soybean reveals extensive blocks of shared loci
Cited by: 102
Author(s): Phillip E. McClean, Sujan Mamidi, Melody McConnell, Shireen Chikara, Rian Lee
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2105-8-272

A cis-regulatory logic simulator
Cited by: 1
Author(s): R. A. Zeigler, Jason Gertz, Barak A. Cohen
Software Mentions: 2
Published: over 17 years ago

10.3390/jpm9030040

Pharmacogenomic Testing: Clinical Evidence and Implementation Challenges
Cited by: 50
Author(s): Catriona Hippman, Corey Nislow
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-8-312

MaxAlign: maximizing usable data in an alignment
Cited by: 100
Author(s): Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Anders Gorm Pedersen
Software Mentions: 2
Published: about 17 years ago

10.1186/s13099-016-0103-7

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples
Cited by: 370
Author(s): Angela Glassing, Scot E. Dowd, Susan Galandiuk, Brian R. Davis, Rodrick J. Chiodini
Software Mentions: 2
Published: over 8 years ago

10.1016/j.heliyon.2019.e02530

PVCTools: parallel variation calling tools
Cited by: 1
Author(s): Jingjing Jin, Jiajun Liu, Yelin Yin, Zefeng Li, Peng Lu, Yalong Xu, Jianfeng Zhang, Peijian Cao, Dasha Hu
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00439-20

Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations
Cited by: 24
Author(s): Murilo Henrique Anzolini Cassiano, Rafael Silva‐Rocha
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00276-21

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )
Cited by: 5
Author(s): Emily R. Savoie, V. Celeste Lanclos, Michael W. Henson, Chuankai Cheng, Eric W. Getz, Shelby J Barnes, Douglas E. LaRowe, Michael S. Rappé, J. Cameron Thrash
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-11-428

Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets
Cited by: 18
Author(s): Aydın Albayrak, Hasan H. Otu, Uğur Sezerman
Software Mentions: 2
Published: over 14 years ago

10.1007/s13361-017-1633-z

Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation
Cited by: 34
Author(s): Adam Cryar, Kate Groves, Milena Quaglia
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-14-891

The early phase transcriptome of bovine monocyte-derived macrophages infected with Staphylococcus aureus in vitro
Cited by: 29
Author(s): Anna Lewandowska-Sabat, G Boman, Alison Downing, Richard Talbot, Anne K. Storset, I. Olsaker
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms20092331

Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages
Cited by: 7
Author(s): Elza Fonseca, Raquel Ruivo, André M. Machado, Francisca Conrado, Boon-Hui Tay, Byrappa Venkatesh, Miguel M. Santos, L. Filipe C. Castro
Software Mentions: 2
Published: over 5 years ago

10.1038/s41396-018-0160-7

Taxonomic diversity of fungi deposited from the atmosphere
Cited by: 52
Author(s): Cheolwoon Woo, Choa An, Siyu Xu, Sang-Heon Yi, Naomichi Yamamoto
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1005230

Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies
Cited by: 63
Author(s): Claudio Ciferri, Sumana Chandramouli, Alexander Leitner, Danilo Donnarumma, Michael A. Cianfrocco, Rachel Gerrein, Kristian Friedrich, Yukti Aggarwal, Giuseppe Palladino, Ruedi Aebersold, Nathalie Norais, Ethan C. Settembre, Andrea Carfı́
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-021-07448-x

The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria
Cited by: 16
Author(s): Liping Zeng, Katayoon Dehesh
Software Mentions: 2
Published: over 3 years ago

10.1098/rspb.2021.0119

Microarthropod contributions to fitness variation in the common moss Ceratodon purpureus
Cited by: 7
Author(s): Erin E. Shortlidge, Sarah B. Carey, Adam C. Payton, Stuart F. McDaniel, Todd N. Rosenstiel, Sarah M. Eppley
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-348

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction
Cited by: 113
Author(s): Prashant K. Srivastava, Taraka Ramji Moturu, Priyanka Pandey, Ian Thomas Baldwin, Sarvesh Pandey
Software Mentions: 2
Published: over 10 years ago

10.1186/1477-5956-10-S1-S12

An unsupervised machine learning method for assessing quality of tandem mass spectra
Cited by: 7
Author(s): Wenjun Lin, Jianxin Wang, Wenjun Zhang, Fang‐Xiang Wu
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-016-2579-4

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods
Cited by: 119
Author(s): Guillaume Martin, Franc-Christophe Baurens, Gaëtan Droc, Mathieu Rouard, Alberto Cenci, Andrzej Kilian, Alex Hastie, Jaroslav Doležel, Jean‐Marc Aury, Adriana Alberti, Françoise Carreel, Angélique D’Hont
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-2954-1

Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton
Cited by: 16
Author(s): Pawan Kumar, Ying He, Rippy Singh, Richard F. Davis, Hui Guo, Andrew H. Paterson, Daniel G. Peterson, Xinlian Shen, Robert L. Nichols, Peng W. Chee
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-12-403

The mosaicism of plasmids revealed by atypical genes detection and analysis
Cited by: 16
Author(s): Emanuele Bosi, Renato Fani, Marco Fondi
Software Mentions: 2
Published: over 13 years ago

10.1038/sdata.2016.50

A catalogue of 136 microbial draft genomes from Red Sea metagenomes
Cited by: 43
Author(s): Mohamed Fauzi Haroon, Luke R. Thompson, Donovan H. Parks, Philip Hugenholtz, Ulrich Stingl
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1618-x

Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)
Cited by: 18
Author(s): Joshua M. Miller, S. S. Moore, Paul Stothard, Xiaoping Liao, David W. Coltman
Software Mentions: 2
Published: over 9 years ago

10.1038/sdata.2017.92

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting
Cited by: 17
Author(s): Roland C. Wilhelm, Erick Cardenas, Hilary Leung, Kendra Maas, Martin Hartmann, Aria S. Hahn, Steven J. Hallam, William W. Mohn
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-7-57

Using pyrosequencing to shed light on deep mine microbial ecology
Cited by: 441
Author(s): Robert A. Edwards, Beltrán Rodriguez-Brito, Linda Wegley, Matthew Haynes, Mya Breitbart, Dean M Peterson, Martin O. Saar, Scott C. Alexander, E. Calvin Alexander, Forest Rohwer
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-12-600

De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes
Cited by: 68
Author(s): Roberto A. Barrero, Brett Chapman, Yongqiang Yang, Paula Moolhuijzen, Gabriel Keeble‐Gagnère, Nan Zhang, Qi Tang, M. Bellgard, Deyou Qiu
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-14-774

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
Cited by: 326
Author(s): Weilong Guo, Petko Fiziev, Yan Wang, Shawn J. Cokus, Xueqing Sun, Michael Q. Zhang, Pao‐Yang Chen, Matteo Pellegrini
Software Mentions: 2
Published: about 11 years ago

10.1038/srep16407

Exploring simvastatin, an antihyperlipidemic drug, as a potential topical antibacterial agent
Cited by: 91
Author(s): Shankar Thangamani, Haroon Mohammad, Mostafa F. N. Abushahba, Maha I. Hamed, Tiago J. P. Sobreira, Victoria Hedrick, Lake N. Paul, Mohamed N. Seleem
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0099366

Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei
Cited by: 31
Author(s): Rafael Silva‐Rocha, Lílian dos Santos Castro, Amanda Cristina Campos Antoniêto, María‐Eugenia Guazzaroni, Gabriela Félix Persinoti, Roberto do Nascimento Silva
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0002500

Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes
Cited by: 2
Author(s): Niall Haslam, Nava Whiteford, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Cameron Neylon
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0097629

Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies
Cited by: 278
Author(s): Michiel Op De Beeck, Bart Lievens, Pieter Busschaert, Stéphan Declerck, Jaco Vangronsveld, Jan Colpaert
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0241366

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota”
Cited by: 19
Author(s): Taiki Shiotani, Sayaka Mino, Wakana Sato, Sayo Nishikawa, Masanori Yonezawa, Stefan M. Sievert, Tomoo Sawabe
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0016986

Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial
Cited by: 82
Author(s): Mary S. Campbell, James I. Mullins, James P. Hughes, Connie Celum, Kim Wong, Dana N. Raugi, Stefanie Sorensen, Julia N. Stoddard, Hong Zhao, Wenjie Deng, Erin Kahle, Dana Panteleeff, Jared M. Baeten, Francine E. McCutchan, Jan Albert, Thomas Leitner, Anna Wald, Lawrence Corey, Jairam R. Lingappa, Hiv Transmission Study Team
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0093833

Identification of Novel Regulatory Small RNAs in Acinetobacter baumannii
Cited by: 28
Author(s): Rajnikant Sharma, Sankalp Arya, Supriya Patil, Atin Sharma, Pradeep Jain, Naveen Kumar Navani, Ranjana Pathania
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0151400

A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
Cited by: 62
Author(s): José M. C. Ribeiro, Inés Martín-Martín, Bruno Arcà, Eric Calvo
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0119851

DivStat: A User-Friendly Tool for Single Nucleotide Polymorphism Analysis of Genomic Diversity
Cited by: 3
Author(s): Inês Soares, Ana Moleirinho, G. N. P. Oliveira, António Amorim
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0246287

Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis
Cited by: 6
Author(s): Signe Tang Karlsen, Tammi Camilla Vesth, Gunnar Øregaard, Vera Kuzina Poulsen, Ole Lund, Gemma Henderson, Jacob Bælum
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0010829

W-Curve Alignments for HIV-1 Genomic Comparisons
Cited by: 2
Author(s): Douglas J. Cork, Steven Lembark, Sodsai Tovanabutra, Merlin L. Robb, Jerome H. Kim
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0147994

Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014
Cited by: 4
Author(s): Takehisa Yamamoto, Tohru Suzuki, Seiichi Ohashi, Akira Miyazaki, Toshiyuki Tsutsui
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep18757

A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe
Cited by: 15
Author(s): Tatyana Pichugina, Takeshi Sugawara, Atanas Kaykov, William Schierding, Kenta Masuda, Jun-ichi Uewaki, Ralph S. Grand, Jane R. Allison, Robert A. Martienssen, Paul Nurse, Masaru Ueno, Justin M. O’Sullivan
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0103810

Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach
Cited by: 38
Author(s): Deepak Nanjappa, Stéphane Audic, Sarah Romac, Wiebe H. C. F. Kooistra, Adriana Zingone
Software Mentions: 2
Published: over 10 years ago

10.1038/srep20842

IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity
Cited by: 140
Author(s): Yuval Avnir, Corey T. Watson, Jacob Glanville, Eric C. Peterson, Aimée St. Clair Tallarico, A. J. Bennett, Kun Qin, Ying Fu, Chiung Yu Huang, John H. Beigel, Felix Breden, Quan Zhu, Wayne A. Marasco
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-10-289

cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici
Cited by: 85
Author(s): Xiaojie Wang, Chunlei Tang, Gang Zhang, Yingchun Li, Chenfang Wang, Bo Liu, Zhibo Qu, Jie Zhao, Qingmei Han, Lili Huang, Xianming Chen, Zhensheng Kang
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0062586

Two-Gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia)
Cited by: 56
Author(s): Anna Maria Fiore-Donno, Fionn Clissmann, Marianne Meyer, Martin Schnittler, Thomas Cavalier‐Smith
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0017490

Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
Cited by: 131
Author(s): Zhifu Sun, Yan W. Asmann, Krishna R. Kalari, Brian M. Bot, Jeanette E. Eckel‐Passow, Tiffany R. Baker, Jennifer M. Carr, Irina Khrebtukova, Shujun Luo, Lu Zhang, Gary P. Schroth, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0022872

Genetic Structure of Two Protist Species (Myxogastria, Amoebozoa) Suggests Asexual Reproduction in Sexual Amoebae
Cited by: 45
Author(s): Anna Maria Fiore-Donno, Yu. K. Novozhilov, Marianne Meyer, Martin Schnittler
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0183454

Domestication reduces alternative splicing expression variations in sorghum
Cited by: 8
Author(s): Vincent Ranwez, Audrey Serra, David Pot, Nathalie Chantret
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0002946

A Semantic Web Management Model for Integrative Biomedical Informatics
Cited by: 35
Author(s): Helena F. Deus, Romesh Stanislaus, Diogo F. Veiga, Carmen Behrens, Ignacio I. Wistuba, John D. Minna, Harold R. Garner, Stephen G. Swisher, Jack A. Roth, Arlene M. Correa, Bradley M. Broom, Kevin R. Coombes, Allen Y. Chang, Lynn Harold Vogel, Jonas S. Almeida
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0196953

Genome-wide analysis of the NAC transcription factor family and their expression during the development and ripening of the Fragaria × ananassa fruits
Cited by: 40
Author(s): Enriqueta Moyano, Félix Juan Martínez Rivas, Rosario Blanco‐Portales, Francisco Javier Molina‐Hidalgo, Pablo Ric-Varas, Antonio Javier Matas-Arroyo, José L. Caballero, Juan Muñoz‐Blanco, Antonio Rodríguez-Franco
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0252414

PAN2HGENE–tool for comparative analysis and identifying new gene products
Cited by: 5
Author(s): Mônica Silva de Oliveira, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, Adonney Allan de Oliveira Veras
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-7-248

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates
Cited by: 12
Author(s): Xuming Xu, Samuel Shao Min Zhang, Colin J. Barnstable, Joyce Tombran-Tink
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0175091

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses
Cited by: 74
Author(s): Patricia Moya, Arántzazu Molins, Fernando Martínez-Alberola, Lucía Muggia, Eva Barreno
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0028008

Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake
Cited by: 62
Author(s): Ilaria Milano, Massimiliano Babbucci, Frank Panitz, Rob Ogden, Rasmus Oestergaard Nielsen, Martin I. Taylor, Sarah J. Helyar, Gary R. Carvalho, Montserrat Espiñeira, Miroslava Atanassova, Fausto Tinti, Grégory E. Maes, Tomaso Patarnello, Luca Bargelloni
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0090490

SNP-Associations and Phenotype Predictions from Hundreds of Microbial Genomes without Genome Alignments
Cited by: 18
Author(s): Barry G. Hall
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0256735

Understanding molt control switches: Transcriptomic and expression analysis of the genes involved in ecdysteroidogenesis and cholesterol uptake pathways in the Y-organ of the blue crab, Callinectes sapidus
Cited by: 6
Author(s): Émilie Legrand, Tsvetan R. Bachvaroff, Tracey B. Schock, Jessica Chung
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0167089

Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness
Cited by: 0
Author(s): Brendan A. Palmer, Liam J. Fanning
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-8-346

Characterization of oligopeptide patterns in large protein sets
Cited by: 11
Author(s): Anders Bresell, Bengt Persson
Software Mentions: 2
Published: almost 18 years ago

10.1038/srep29070

Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae)
Cited by: 59
Author(s): Mohammad Vatanparast, Prateek Shetty, Ratan Chopra, Jeff J. Doyle, N. Sathyanarayana, Ashley N. Egan
Software Mentions: 2
Published: over 8 years ago

10.1038/srep31279

A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing
Cited by: 93
Author(s): Niall O’Sullivan, Matthew D. Teasdale, Valeria Mattiangeli, Frank Maixner, Ron Pinhasi, Daniel G. Bradley, Albert Zink
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0150797

Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks
Cited by: 38
Author(s): Laurel S. Burall, Christopher J. Grim, Mark K. Mammel, Atin R. Datta
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0003515

A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
Cited by: 30
Author(s): Konrad Foerstner, Tobias Doerks, Christopher J. Creevey, Anja Doerks, Peer Bork
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0101144

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing
Cited by: 6
Author(s): Parichit Sharma, Shrikant Mantri
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0146174

G-Quadruplexes Involving Both Strands of Genomic DNA Are Highly Abundant and Colocalize with Functional Sites in the Human Genome
Cited by: 43
Author(s): Andrzej Kudlicki
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0161809

The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae
Cited by: 21
Author(s): Zhaodong Hao, Tielong Cheng, Rong Zheng, Haibin Xu, Yanwei Zhou, Meiping Li, Fushen Lu, Yini Dong, Xin Liu, Jinhui Chen, Jisen Shi
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0056726

Barcode Server: A Visualization-Based Genome Analysis System
Cited by: 0
Author(s): Feng Mao, Victor Olman, Yan Wang, Ying Xu
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0168912

PPero, a Computational Model for Plant PTS1 Type Peroxisomal Protein Prediction
Cited by: 23
Author(s): Jue Wang, Yejun Wang, Caiji Gao, Liwen Jiang, Dianjing Guo
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-14-S14-S13

SASD: the S ynthetic A lternative S plicing D atabase for identifying novel isoform from proteomics
Cited by: 8
Author(s): Fan Zhang, Renee Drabier
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0065790

Targeting the Microbiota to Address Diet-Induced Obesity: A Time Dependent Challenge
Cited by: 124
Author(s): Siobhan F. Clarke, Eileen F. Murphy, Órla O’Sullivan, R. Paul Ross, Paul W. O’Toole, Fergus Shanahan, Paul D. Cotter
Software Mentions: 2
Published: over 11 years ago

10.1038/srep43562

The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
Cited by: 13
Author(s): Liliya Doronina, Andreas T. Matzke, Gennady Churakov, Monika Stoll, Andreas Huge, Jürgen Schmitz
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0120058

In Silico Screening Based on Predictive Algorithms as a Design Tool for Exon Skipping Oligonucleotides in Duchenne Muscular Dystrophy
Cited by: 44
Author(s): Yusuke Echigoya, Vincent Mouly, Luis Garcı́a, Toshifumi Yokota, William Duddy
Software Mentions: 2
Published: over 9 years ago

10.1155/2008/412696

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation
Cited by: 151
Author(s): Luciano Carlos da Maia, Darío Abel Palmieri, Velci Queiróz de Souza, Maurício Marini Köpp, Fernando Irajá Félix de Carvalho, António Costa de Oliveira
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0030824

Polyglutamine Repeats Are Associated to Specific Sequence Biases That Are Conserved among Eukaryotes
Cited by: 29
Author(s): Matteo Ramazzotti, Élodie Monsellier, Choumouss Kamoun, Donatella Degl’Innocenti, Ronald Melki
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0140268

Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.
Cited by: 14
Author(s): Kumar Parijat Tripathi, Daniela Evangelista, Antonio Zuccaro, Mario Rosario Guarracino
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-04489-9

Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura
Cited by: 25
Author(s): Zhao-Zhe Xin, Li Yu, Dai-Zhen Zhang, Xin-Yue Chai, Zheng-Fei Wang, Huabin Zhang, Chun-Lin Zhou, Boping Tang, Qiu-Ning Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0186800

Spoligotyping and whole-genome sequencing analysis of lineage 1 strains of Mycobacterium tuberculosis in Da Nang, Vietnam
Cited by: 8
Author(s): Makoto Hijikata, Naoto Keicho, Le Van Duc, Shingo Maeda, Nguyen Thi Le Hang, Ikumi Matsushita, Seiya Kato
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0043992

Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes
Cited by: 23
Author(s): Mark Y. Stoeckle, Kevin C. R. Kerr
Software Mentions: 2
Published: about 12 years ago

10.3390/ijms20102483

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
Cited by: 17
Author(s): Veronika Kapustová, Zuzana Tulpová, Helena Toegelová, Petr Novák, Jiří Macas, Miroslava Karafiátová, Eva Hřibová, Jaroslav Doležel, Hana Šimková
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0152404

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites
Cited by: 4
Author(s): Richard M. Sharpe, Tyson Koepke, Artemus Harper, John Grimes, Marco Galli, Mio Satoh-Cruz, Ananth Kalyanaraman, Kate Evans, David Kramer, Amit Dhingra
Software Mentions: 2
Published: over 8 years ago

Projects: pypi: fasta

Papers Mentioning fasta 848