Ecosyste.ms: Papers

10.1371/journal.pone.0179736

PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes
Cited by: 12
Author(s): Akshay Singh, Ajay Sharma, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0148374

Substantial Downregulation of Myogenic Transcripts in Skeletal Muscle of Atlantic Cod during the Spawning Period
Cited by: 1
Author(s): Kazue Nagasawa, Elena Sarropoulou, Vigdis Edvardsen, Jorge M.O. Fernandes
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0110726

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems
Cited by: 248
Author(s): Sophie S. Abby, Bertrand Néron, Hervé Ménager, Marie Touchon, Eduardo P. C. Rocha
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-5-82

Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system
Cited by: 51
Author(s): John J. Hutton, Anil G. Jegga, Sue Kong, Apoorva Gupta, Catherine L. Ebert, Sarah S. Williams, Jonathan D. Katz, Bruce J. Aronow
Software Mentions: 2
Published: about 20 years ago

10.1038/s42003-020-01370-w

Comparative ACE2 variation and primate COVID-19 risk
Cited by: 106
Author(s): Amanda D. Melin, Mareike C. Janiak, Frank Marrone, Paramjit S. Arora, James P. Higham
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0104885

A Comprehensive Reference Transcriptome Resource for the Common House Spider Parasteatoda tepidariorum
Cited by: 57
Author(s): Nico Posnien, Victor Zeng, Evelyn E. Schwager, Matthias Pechmann, Maarten Hilbrant, Joseph D. Keefe, Wim G.M. Damen, Nikola-Michael Prpíc, Alistair P. McGregor, Cassandra G. Extavour
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-018-20211-9

GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data
Cited by: 73
Author(s): Fabrício Almeida Araújo, Debmalya Barh, Artur da Costa da Luiz Silva, Luís Carlos Guimarães, Rommel Thiago Jucá Ramos
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0155327

GapBlaster—A Graphical Gap Filler for Prokaryote Genomes
Cited by: 18
Author(s): Pablo Henrique Caracciolo Gomes de Sá, Fábio Miranda, Adonney Allan de Oliveira Veras, Diego Magalhães de Melo, Siomar de Castro Soares, Kenny da Costa Pinheiro, Luís Carlos Guimarães, Vasco Azevedo, Artur M. S. Silva, Rui A. R. Ramos
Software Mentions: 2
Published: over 8 years ago

10.1016/j.dib.2020.105741

RNA-Seq transcriptome data of undifferentiated and differentiated gonads of Siberian sturgeon
Cited by: 1
Author(s): Christophe Klopp, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-22428-0

Single molecule real time sequencing in ADTKD-MUC1 allows complete assembly of the VNTR and exact positioning of causative mutations
Cited by: 35
Author(s): Andrea Wenzel, Janine Altmueller, Arif B. Ekici, Bernt Popp, Kurt Stueber, Holger Thiele, Alois Pannes, Simon Staubach, Eduardo Salido, Peter Nüernberg, Richard Reinhardt, André Reis, Patrick Rump, Franz Georg Hanisch, Matthias Wolf, Michael S. Wiesener, Bruno Huettel, Bodo B. Beck
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0216347

Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
Cited by: 28
Author(s): Christophe Guyeux, Jean‐Claude Charr, Hue T. Tran, Agnelo Furtado, Robert J. Henry, Dominique Crouzillat, Romain Guyot, Perla Hamon
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-27002-2

Enhanced carbon-sulfur cycling in the sediments of Arabian Sea oxygen minimum zone center
Cited by: 23
Author(s): Svetlana Fernandes, Aninda Mazumdar, Sabyasachi Bhattacharya, A. Peketi, Tarunendu Mapder, Ranjit Roy, Mary Ann Carvalho, Chayan Roy, P. Mahalakshmi, Rheane da Silva, P. L. Srinivasa Rao, Suman Kumar Banik, Wriddhiman Ghosh
Software Mentions: 2
Published: over 6 years ago

10.1186/s13015-020-00177-y

gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections
Cited by: 6
Author(s): Felipe A. Louza, Guilherme P. Telles, Simon Gog, Nicola Prezza, Giovanna Rosone
Software Mentions: 2
Published: about 4 years ago

10.1093/database/baz111

SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)
Cited by: 6
Author(s): Rick E. Masonbrink, Tom Maier, Arun S. Seetharam, Parijat S. Juvale, Levi Baber, Thomas J. Baum, Andrew J. Severin
Software Mentions: 2
Published: almost 6 years ago

10.1099/ijsem.0.001501

Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
Cited by: 17
Author(s): Edel Pérez‐López, Chrystel Olivier, Mauricio Luna-Rodríguez, Tim J. Dumonceaux
Software Mentions: 2
Published: almost 8 years ago

10.1099/ijs.0.048827-0

Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas
Cited by: 82
Author(s): Matthias Labrenz, Jana Grote, Kerstin Mammitzsch, Henricus T. S. Boschker, Michael Laue, Günter Jost, Sabine Glaubitz, Klaus Jürgens
Software Mentions: 2
Published: about 11 years ago

10.1093/database/baw035

ATtRACT—a database of RNA-binding proteins and associated motifs
Cited by: 184
Author(s): Girolamo Giudice, Fátima Sánchez-Cabo, Carlos Torroja, Enrique Lara‐Pezzi
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/baz160

An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms
Cited by: 3
Author(s): Mariana Reyes-Prieto, Carlos Vargas-Chávez, Mercè Llabrés, Pere Palmer, Amparo Latorre, Andrés Moya
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-018-36069-w

Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases
Cited by: 60
Author(s): Kristen A. Biernat, S.J. Pellock, Aadra P. Bhatt, Marissa M. Bivins, William G. Walton, Bryant Tran, Lianjie Wei, Michael Snider, Andrew P. Cesmat, Ashutosh Tripathy, Dorothy A. Erie, Matthew R. Redinbo
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0090234

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing
Cited by: 384
Author(s): Dylan P. Smith, Kabir G. Peay
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0043283

Deep Sequencing Reveals Complex Spurious Transcription from Transiently Transfected Plasmids
Cited by: 30
Author(s): Jana Nejepinska, Radek Malı́k, Martin Moravec, Petr Svoboda
Software Mentions: 2
Published: over 12 years ago

10.3390/diagnostics10050286

Whole Exome Sequencing with Comprehensive Gene Set Analysis Identified a Biparental-Origin Homozygous c.509G>A Mutation in PPIB Gene Clustered in Two Taiwanese Families Exhibiting Fetal Skeletal Dysplasia during Prenatal Ultrasound
Cited by: 7
Author(s): Ting‐Yu Chang, I‐Fang Chung, Wan‐Ju Wu, Shun‐Ping Chang, Wen‐Hsiang Lin, Norman Ginsberg, Gwo‐Chin Ma, Ming Chen
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.4885

Investigating the role of <i>Osiris </i>genes in <i>Drosophila sechellia </i>larval resistance to a host plant toxin
Cited by: 21
Author(s): Stephen M. Lanno, Serena Shimshak, Rubye Dimitri Peyser, Samuel C. Linde, Joseph D. Coolon
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0019816

Targeted Assembly of Short Sequence Reads
Cited by: 45
Author(s): René L. Warren, Robert A. Holt
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0091928

Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)
Cited by: 68
Author(s): Christian Koetschan, Sandra Kittelmann, Jingli Lu, Djamila Al-Halbouni, Graeme N. Jarvis, Tobias Müller, Matthias Wolf, Peter H. Janssen
Software Mentions: 2
Published: over 10 years ago

10.1002/ece3.7479

Color vision and niche partitioning in a diverse neotropical primate community in lowland Amazonian Ecuador
Cited by: 4
Author(s): Carrie C. Veilleux, Shoji Kawamura, Michæl J. Montague, Tomohide Hiwatashi, Yuka Matsushita, Eduardo Fernández-Duque, Andrés Link, Anthony Di Fiore, D. Max Snodderly
Software Mentions: 2
Published: over 3 years ago

10.1002/ece3.2502

Contrasting patterns of selection between<scp>MHC</scp>I and<scp>II</scp>across populations of Humboldt and Magellanic penguins
Cited by: 12
Author(s): Nicole Sallaberry‐Pincheira, Daniel González‐Acuña, Pamela A. Padilla, Giovana Dantas, Guillermo Luna‐Jorquera, Esteban Frere, Armando Valdés‐Velásquez, Juliana A. Vianna
Software Mentions: 2
Published: about 8 years ago

10.1002/ece3.3400

Variation in reproductive isolation across a species range
Cited by: 20
Author(s): Karen B. Barnard‐Kubow, Laura F. Galloway
Software Mentions: 2
Published: about 7 years ago

10.1007/s13205-017-0609-9

Expression of four phosphate transporter genes from Finger millet (Eleusine coracana L.) in response to mycorrhizal colonization and Pi stress
Cited by: 29
Author(s): Ramesh Namdeo Pudake, Chandra Mohan Mehta, Tapan Kumar Mohanta, Suvigya Sharma, Ajit Varma, Anil Kumar Sharma
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0050246

iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations
Cited by: 21
Author(s): Mathias Kuhring, Bernhard Y. Renard
Software Mentions: 2
Published: almost 12 years ago

10.1017/S095026881900102X

Prior exposure to immunogenic peptides found in human influenza A viruses may influence the age distribution of cases with avian influenza H5N1 and H7N9 virus infections
Cited by: 0
Author(s): Naomi Komadina, Sheena G. Sullivan, Katherine Kedzierska, Sergio M. Quiñones-Parra, Karin Leder, Jodie McVernon
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0009780

Using Deep RNA Sequencing for the Structural Annotation of the Laccaria Bicolor Mycorrhizal Transcriptome
Cited by: 32
Author(s): Peter E. Larsen, Geetika Trivedi, Avinash Sreedasyam, Vincent Lu, Gopi K. Podila, F. Collart
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-13-527

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers
Cited by: 13
Author(s): Marina de Miguel, Nuria de María, M. Ángeles Guevara, Luis Manuel Díaz, Enrique Sáez-Laguna, David Sánchez‐Gómez, Émilie Chancerel, Ismael Aranda, Carmen Collada, Christophe Plomion, José Antonio Cabezas, Marı́a Teresa Cervera
Software Mentions: 2
Published: about 12 years ago

10.1186/s13227-015-0018-2

Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones
Cited by: 14
Author(s): Stefan Siebert, Freya Goetz, Samuel H. Church, Pathikrit Bhattacharyya, Felipe Zapata, Steven H. D. Haddock, Casey W. Dunn
Software Mentions: 2
Published: over 9 years ago

10.1111/eva.12621

Hurdles in the evolutionary epidemiology of <i>Angiostrongylus cantonensis</i>: Pseudogenes, incongruence between taxonomy and DNA sequence variants, and cryptic lineages
Cited by: 14
Author(s): Sirilak Dusitsittipon, Charles D. Criscione, Sergé Morand, Chalit Komalamisra, Urusa Thaenkham
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0134382

Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum
Cited by: 111
Author(s): Rodrick J. Chiodini, Scot E. Dowd, William Henry Chamberlin, Susan Galandiuk, Brian R. Davis, Angela Glassing
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pntd.0000989

Towards a Semen Proteome of the Dengue Vector Mosquito: Protein Identification and Potential Functions
Cited by: 111
Author(s): Laura K. Sirot, Melissa C. Hardstone, Michelle E. H. Helinski, José M. C. Ribeiro, Mari Kimura, Prasit Deewatthanawong, Mariana F. Wolfner, Laura C. Harrington
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1004240

The Hmr and Lhr Hybrid Incompatibility Genes Suppress a Broad Range of Heterochromatic Repeats
Cited by: 92
Author(s): P. R. V. Satyaki, Tawny N. Cuykendall, Kevin H.-C. Wei, Nicholas J. Brideau, Ho Young Kwak, S Aruna, Patrick M. Ferree, Shuqing Ji, Daniel A. Barbash
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1000949

Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats
Cited by: 53
Author(s): Margaret R. Woodhouse, Brent S. Pedersen, Michael Freeling
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pgen.1007533

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes
Cited by: 87
Author(s): Fergal M Waldron, Graham N. Stone, Darren J. Obbard
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1008004

The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing
Cited by: 5
Author(s): Katherine Kretovich Billmyre, Anna-Lisa Doebley, Maya Spichal, Bree Heestand, Tony Bélicard, Aya Sato-Carlton, Stéphane Flibotte, Matthew C. Simon, Megan M. Gnazzo, Ahna R. Skop, Donald G. Moerman, Peter M. Carlton, Peter Sarkies, Shawn Ahmed
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1003129

Population Genomics of the Wolbachia Endosymbiont in Drosophila melanogaster
Cited by: 168
Author(s): Mark F. Richardson, Lucy A. Weinert, John J. Welch, Raquel Linheiro, Michael M. Magwire, Francis M. Jiggins, Casey M. Bergman
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-017-1620-1

DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins
Cited by: 8
Author(s): Jiafeng Yu, Xianghua Dou, Yujie Sha, Chunling Wang, Hongbo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Jihua Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-13-168

AlliumMap-A comparative genomics resource for cultivated Allium vegetables
Cited by: 38
Author(s): John McCallum, Samantha Baldwin, Masayoshi Shigyo, Yanbo Deng, Sjaak van Heusden, Meeghan Pither-Joyce, Fernand Kenel
Software Mentions: 2
Published: almost 13 years ago

10.12688/f1000research.4952.2

PAGAL - Properties and corresponding graphics of alpha helical structures in proteins
Cited by: 8
Author(s): Sandeep Chakraborty, Basuthkar J. Rao, Abhaya M. Dandekar
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-15-32

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)
Cited by: 34
Author(s): Gonghua Lin, Kun Wang, Xiao-Dong Deng, Eviatar Nevo, Fang Zhao, Jianping Su, Sheng‐Ping Guo, Tongzuo Zhang, Huabin Zhao
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1000852

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
Cited by: 57
Author(s): Stephen F. Altschul, John C. Wootton, Elena Zaslavsky, Yi‐Kuo Yu
Software Mentions: 2
Published: over 14 years ago