pypi: blast | Projects | Ecosyste.ms: Papers

10.1111/1755-0998.12240

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (<scp>COI</scp>) <scp>DNA</scp> barcode sequences using a naïve Bayesian classifier
Cited by: 48
Author(s): Teresita M. Porter, Joel F. Gibson, Shadi Shokralla, Donald J. Baird, G. Brian Golding, Mehrdad Hajibabaei
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2019.00448

Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida
Cited by: 40
Author(s): Sujan Timilsina, Juliana A. Pereira-Martin, Gerald V. Minsavage, Fernanda Iruegas-Bocardo, Peter Abrahamian, Neha Potnis, Bryan Kolaczkowski, Gary E. Vallad, Erica M. Goss, Jeffrey B. Jones
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.555795

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters
Cited by: 7
Author(s): Changyu Zhu, David Bass, Yutao Wang, Zhuo Shen, Weibo Song, Zhenzhen Yi
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2021.707281

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups
Cited by: 3
Author(s): Runmao Lin, Y. L. Xia, Yao Liu, Danhua Zhang, Xiang Xiao, Xianyu Niu, Linjia Jiang, Xiaolin Wang, Aiping Zheng
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2017.02384

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone
Cited by: 48
Author(s): Clara A. Fuchsman, Allan H. Devol, Jaclyn K. Saunders, Cedar McKay, Gabrielle Rocap
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2021.645353

Genome and Evolutionary Analysis of Nosema ceranae: A Microsporidian Parasite of Honey Bees
Cited by: 10
Author(s): Qiang Huang, Zhi Hao Wu, Wen Feng Li, Rui Guo, Jin Shan Xu, Xiao Qun Dang, Gang Zheng, Yan Ping Chen, Jay D. Evans
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-2142-8

Gene expression analysis at the onset of sex differentiation in turbot (Scophthalmus maximus)
Cited by: 35
Author(s): Diego Robledo, Laia Ribas, Rosa Cal, Laura Sánchez, Francesc Piferrer, Paulino Martı́nez, Ana Viñas
Software Mentions: 3
Published: about 9 years ago

10.3390/microorganisms7110551

Meta-16S rRNA Gene Phylogenetic Reconstruction Reveals the Astonishing Diversity of Cosmopolitan Myxobacteria
Cited by: 10
Author(s): Yang Liu, Qing Yao, Honghui Zhu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-015-1870-0

Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)
Cited by: 8
Author(s): Joseph Heras, Kelly McClintock, Shinichi Sunagawa, Andres Aguilar
Software Mentions: 3
Published: about 9 years ago

10.1099/mgen.0.000347

Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis
Cited by: 29
Author(s): Floriana Gona, Francesco Comandatore, Simone Battaglia, Aurora Piazza, Alberto Trovato, Giovanni Lorenzin, Paola Cichero, Anna Biancardi, Paola Nizzero, Matteo Moro, Daniela María Cirillo
Software Mentions: 3
Published: over 4 years ago

10.3389/fvets.2020.605704

New Diagnostic Assays for Differential Diagnosis Between the Two Distinct Lineages of Bovine Influenza D Viruses and Human Influenza C Viruses
Cited by: 1
Author(s): Faten A. Okda, Elizabeth C. Griffith, Ahmed Sakr, Eric Nelson, Richard J. Webby
Software Mentions: 3
Published: almost 4 years ago

10.1099/mgen.0.000352

Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones
Cited by: 30
Author(s): Catherine Ludden, Arun Gonzales Decano, Dorota Jamrozy, Derek Pickard, Dearbháile Morris, Julian Parkhill, Sharon J. Peacock, Martin Cormican, Tim Downing
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-11-592

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
Cited by: 55
Author(s): Stéphane Fénart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier Van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins, Brigitte Thomasset
Software Mentions: 3
Published: about 14 years ago

10.3389/fmicb.2015.00955

Direct sequencing of human gut virome fractions obtained by flow cytometry
Cited by: 18
Author(s): Mária Džunková, Giuseppe D’Auria, Andrés Moya
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-13-517

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis
Cited by: 16
Author(s): Óscar Dias, Andreas Gombert, Eugénio C. Ferreira, Isabel Rocha
Software Mentions: 3
Published: about 12 years ago

10.3389/fmicb.2021.673512

A Comparative Analysis on the Structure and Function of the Panax notoginseng Rhizosphere Microbiome
Cited by: 12
Author(s): Ling Kui, Baozheng Chen, Jian Chen, Rouhallah Sharifi, Dong Yang, Zhanjiang Zhang, Jun Miao
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.635772

Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles
Cited by: 5
Author(s): Eugeni Belda, Boubacar Coulibaly, Tullu Bukhari, Karin Eiglmeier, Raymond Kone, Mamadou B. Coulibaly, Soumanaba Zongo, Megan Barry, Awa Gnémé, Wamdaogo Moussa Guelbéogo, Abdoul Habib Béavogui, Sékou F. Traorè, N’Falé Sagnon, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-10-331

ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
Cited by: 29
Author(s): Frank M. You, Naxin Huo, Yong Gu, Gerard R. Lazo, Jan Dvořák, Olin D. Anderson
Software Mentions: 3
Published: about 15 years ago

10.1099/mgen.0.000144

Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence
Cited by: 75
Author(s): Roman Thibeaux, Gregorio Iraola, Ignacio Ferrés, Emilie Bierque, Dominique Girault, Marie‐Estelle Soupé‐Gilbert, Mathieu Picardeau, Cyrille Goarant
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 3 years ago

10.1099/mgen.0.000180

Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines
Cited by: 18
Author(s): Aldert Zomer, Nao Otsuka, Yukihiro Hiramatsu, Kazunari Kamachi, Naoko Nishimura, Takao Ozaki, Jan Poolman, Jeroen Geurtsen
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-12-99

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum
Cited by: 106
Author(s): Joshua P. Der, Michael S. Barker, Norman J. Wickett, Claude W. dePamphilis, Paul G. Wolf
Software Mentions: 3
Published: almost 14 years ago

10.3389/fgene.2018.00371

De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption
Cited by: 8
Author(s): Maofeng Chai, Shengnan Wang, Jie He, Wei Chen, Zelu Fan, Jia Li, Yiling Wang
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2019.00120

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr
Cited by: 14
Author(s): Laura M. Braden, S. K. Whyte, Alyson Brown, Carter Van Iderstine, Corinne Letendre, David B. Groman, J. Lewis, Sara L. Purcell, Tiago S. Hori, Mark D. Fast
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.01635

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Cited by: 49
Author(s): Marie E. Kroeger, Tom O. Delmont, A. Murat Eren, Kyle Meyer, Jiarong Guo, Kiran Yasmin Khan, Jorge L. Mazza Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clóvis Daniel Borges, James M. Tiedje, Siu Mui Tsai, Klaus Nüsslein
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2020.00374

TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon
Cited by: 36
Author(s): José M. C. Ribeiro, Ben J. Mans
Software Mentions: 3
Published: over 4 years ago

10.1111/febs.14976

Burkholderia pseudomallei <scp>d</scp> ‐alanine‐ <scp>d</scp> ‐alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target
Cited by: 3
Author(s): L. Diaz-Saez, Leah S. Torrie, Stuart P. McElroy, David W. Gray, William N. Hunter
Software Mentions: 3
Published: over 5 years ago

10.1002/2211-5463.12084

Age‐dependent transcriptional and epigenomic responses to light exposure in the honey bee brain
Cited by: 15
Author(s): Nils B. Becker, Robert Kucharski, Wolfgang Rößler, Ryszard Maleszka
Software Mentions: 3
Published: over 8 years ago

10.3389/fcimb.2020.00041

Tick-Borne Encephalitis Virus Infection Alters the Sialome of Ixodes ricinus Ticks During the Earliest Stages of Feeding
Cited by: 9
Author(s): Charles E. Hart, José M. C. Ribeiro, Mária Kazimírová, Saravanan Thangamani
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.6898

Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons
Cited by: 24
Author(s): Xavier Pochon, Patricia Wecker, Michael Stat, Véronique Berteaux‐Lecellier, Gaël Lecellier
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.4073

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
Cited by: 19
Author(s): Simon M. Dittami, Matthieu Le Corre
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: almost 17 years ago

10.1111/j.1742-4658.2009.06893.x

Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms
Cited by: 58
Author(s): Emmanuel Debrand, Yasmine El Jai, Lorraine Spence, Neil Bate, Uta Praekelt, Catrin Pritchard, Susan J. Monkley, David R. Critchley
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2105-15-61

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences
Cited by: 2
Author(s): Bart Hazes
Software Mentions: 3
Published: over 10 years ago

10.1111/pbi.13111

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant
Cited by: 177
Author(s): Enhua Xia, Fangdong Li, Wei Tong, Penghui Li, Qiong Wu, Hongxing Zhao, Ruoheng Ge, Ruopei Li, Yeyun Li, Zhengzhu Zhang, Chaoling Wei, Xiaochun Wan
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-853

Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses
Cited by: 109
Author(s): Zarqa Nawaz, Kaleem Ullah Kakar, Mumtaz Ali Saand, Qingyao Shu
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-12-104

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
Cited by: 176
Author(s): José Blanca, Joaquı́n Cañizares, Cristina Roig, Peio Ziarsolo, F. Nuez, Belén Picó
Software Mentions: 3
Published: almost 14 years ago

10.1128/AEM.02885-19

Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness
Cited by: 48
Author(s): Silvia J. Salgar-Chaparro, Kateřina Lepková, Thunyaluk Pojtanabuntoeng, Adam Darwin, Laura L. Machuca
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-015-0833-4

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Cited by: 33
Author(s): Guillaume Rivière, Christophe Klopp, Ibouniyamine Nabihoudine, Arnaud Huvet, Pierre Boudry, Pascal Favrel
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1000732

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
Cited by: 332
Author(s): Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira C. Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip SanMiguel, Jeffrey L. Bennetzen
Software Mentions: 3
Published: about 15 years ago

10.1186/s12870-018-1601-1

Transcriptomic signature reveals mechanism of flower bud distortion in witches’-broom disease of soybean (Glycine max)
Cited by: 10
Author(s): Sarika Jaiswal, P. V. Jadhav, Rahul Singh Jasrotia, P. B. Kale, Snehal Krishna Kad, M. P. Moharil, M. S. Dudhare, Jashminkumar Kheni, A. G. Deshmukh, S. S. Mane, R. S. Nandanwar, Suprasanna Penna, J. G. Manjaya, Mir Asif Iquebal, R. S. Tomar, Prashant G. Kawar, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2014.00531

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships
Cited by: 58
Author(s): Maggie C. Y. Lau, Connor Cameron, Cara Magnabosco, C. Titus Brown, Faye Schilkey, Sharon L. Grim, Sarah Hendrickson, Michael J. Pullin, Barbara Sherwood Lollar, Esta van Heerden, Thomas L. Kieft, Tullis C. Onstott
Software Mentions: 3
Published: about 10 years ago

10.1534/g3.111.001834

Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.)
Cited by: 8
Author(s): Jung Min Ha, Brian Abernathy, William M. Nelson, David Grant, Xiaolei Wu, Henry T. Nguyen, Gary Stacey, Yeisoo Yu, Rod A. Wing, Randy C. Shoemaker, Scott A. Jackson
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-019-5545-0

An insight into the sialotranscriptome and virome of Amazonian anophelines
Cited by: 21
Author(s): Vera Margarete Scarpassa, Humberto Julio Debat, Ronildo Baiatone Alencar, José Ferreira Saraiva, Eric Calvo, Bruno Arcà, José M. C. Ribeiro
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-018-2452-3

PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization
Cited by: 0
Author(s): Florian Bürger, Michele Angioni, Gianluca Russo, Martina Schad, Jim Kallarackal
Software Mentions: 2
Published: almost 6 years ago

10.1111/j.1462-2920.2010.02193.x

Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Cited by: 1,150
Author(s): Susan M. Huse, David B. Mark Welch, Hilary G. Morrison, Mitchell L. Sogin
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-11-384

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
Cited by: 167
Author(s): Sheng Guo, Yi Zheng, Je‐Gun Joung, Shiqiang Liu, Zhonghua Zhang, Oswald Crasta, Bruno W. S. Sobral, Yong Xu, Sanwen Huang, Zhangjun Fei
Software Mentions: 2
Published: over 14 years ago

10.1080/22221751.2020.1773745

Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries
Cited by: 45
Author(s): Xuemei Yang, Ning Dong, Edward Wai Chi Chan, Sheng Chen
Software Mentions: 2
Published: almost 5 years ago

10.1099/mgen.0.000497

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates
Cited by: 7
Author(s): Jo Hendrix, L. Elaine Epperson, David Durbin, Jennifer R. Honda, Michael Strong
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-15-1080

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications
Cited by: 31
Author(s): Stuart J. Lucas, Bala Anı Akpınar, Hana Šimková, Marie Kubaláková, Jaroslav Doležel, Hikmet Budak
Software Mentions: 2
Published: almost 10 years ago

10.1080/22221751.2018.1563455

Detection of human parvovirus 4 DNA in the patients with acute encephalitis syndrome during seasonal outbreaks of the disease in Gorakhpur, India
Cited by: 6
Author(s): Vidya A. Arankalle, Navin Srivastava, K. P. Kushwaha, Agnibha Sen, Ashwini Y. Ramdasi, Priyanka Patel, Sumeet Kuthe, Bangari Haldipur, Gajanan N. Sakpal, Kavita S. Lole, Nilesh Ingle
Software Mentions: 2
Published: almost 6 years ago

10.1111/j.1462-2920.2008.01667.x

The Cry48Aa-Cry49Aa binary toxin fromBacillus sphaericusexhibits highly restricted target specificity
Cited by: 37
Author(s): Gareth Wyn Jones, Margaret C. Wirth, R. G. Monnerat, Colin Berry
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-13-334

Protein interface classification by evolutionary analysis
Cited by: 126
Author(s): José M. Duarte, Adam Srebniak, Martin A. Schärer, Guido Capitani
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-014-1205-6

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes
Cited by: 39
Author(s): Jan M. Meyer, Christian Rödelsperger, Karsten Eichholz, Urban Tillmann, Allan Cembella, Angela McGaughran, Uwe John
Software Mentions: 2
Published: almost 10 years ago

10.1007/s00284-014-0629-1

The Diversity of Bacteria Isolated from Antarctic Freshwater Reservoirs Possessing the Ability to Produce Polyhydroxyalkanoates
Cited by: 27
Author(s): Sławomir Ciesielski, Dorota Górniak, Justyna Możejko, Aleksander Świątecki, Jakub Grzesiak, Marek K. Zdanowski
Software Mentions: 2
Published: over 10 years ago

10.1002/ece3.2028

Population genomics of local adaptation versus speciation in coral reef fishes ( Hypoplectrus spp, Serranidae)
Cited by: 31
Author(s): Sophie Picq, W. Owen McMillan, Oscar Puebla
Software Mentions: 2
Published: over 8 years ago

10.1099/mgen.0.000598

A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages
Cited by: 16
Author(s): Brooke R Tomlinson, Morgan E Malof, Lindsey N. Shaw
Software Mentions: 2
Published: over 3 years ago

10.1155/2019/3780245

Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm
Cited by: 1
Author(s): David N. Olivieri, Francisco Gambón-Deza
Software Mentions: 2
Published: almost 6 years ago

10.1099/mgen.0.000166

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Cited by: 162
Author(s): Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Susana Santos, Mário Ramirez, João André Carriço
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-685

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing
Cited by: 18
Author(s): Yu Liu, Mehmet Koyutürk, Sean Maxwell, Min Xiang, Marty L Veigl, Richard S. Cooper, Bamidele O. Tayo, Li Li, Thomas LaFramboise, Benlian Wang, Xiaofeng Zhu, Mark R. Chance
Software Mentions: 2
Published: almost 11 years ago

10.1016/j.csbj.2017.01.002

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis
Cited by: 14
Author(s): Jorge Duitama, Lina Kafuri, Daniel Tello, Ana Marı́a Leiva, Bernhard J. Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley J. Till, Hernán Ceballos
Software Mentions: 2
Published: almost 8 years ago

10.1002/ece3.5708

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River
Cited by: 9
Author(s): Fangyuan Cheng, Qian Wang, Pierpaolo Maisano Delser, Chenhong Li
Software Mentions: 2
Published: about 5 years ago

10.1111/1462-2920.13036

Closing the gaps on the viral photosystem‐ <scp>I</scp> psa <scp>DCAB</scp> gene organization
Cited by: 7
Author(s): Sheila Roitman, José Flores‐Uribe, Alon Philosof, Ben Knowles, Forest Rohwer, J. Cesar Ignacio‐Espinoza, Matthew B. Sullivan, Francisco M. Cornejo‐Castillo, Pablo Sánchez, Silvia G. Acinas, Chris L. Dupont, Oded Béjà
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0103160

Characterization of Hepatitis C Virus Genotypes by Direct Sequencing of HCV 5′UTR Region of Isolates from Saudi Arabia
Cited by: 13
Author(s): Medhat K. Shier, Mohammad S. El-Wetidy, Hebatallah H. Ali, Mohammad M. Al‐Qattan
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-12-164

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee
Cited by: 130
Author(s): Brian R. Johnson, Neil D. Tsutsui
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0208735

Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016
Cited by: 8
Author(s): Vaishnavi Pattabiraman, Lee S. Katz, Jessica C. Chen, Andre McCullough, Eija Trees
Software Mentions: 2
Published: almost 6 years ago

10.1099/mgen.0.000036

Recombination-mediated remodelling of host–pathogen interactions during Staphylococcus aureus niche adaptation
Cited by: 31
Author(s): Laura E. Spoor, Emily J. Richardson, Amy C. Richards, Gillian J. Wilson, Chriselle Mendonca, Ravi Gupta, Paul R. McAdam, Stephen W. Tuffs, Nikki S. Black, James P. O’Gara, Chia Y. Lee, Jukka Corander, J. Ross Fitzgerald
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-13-645

Limitations and possibilities of low cell number ChIP-seq
Cited by: 81
Author(s): Gregor D. Gilfillan, Timothy R. Hughes, Ying Sheng, Hanne Sagsveen Hjorthaug, Tobias Straub, Kristina Gervin, Jennifer R. Harris, Dag E. Undlien, Robert Lyle
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0076095

Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan “type-N” (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia
Cited by: 20
Author(s): Jan Šlapeta, Marjorie C. Linares
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-8-409

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula
Cited by: 27
Author(s): Dariusz Grzebelus, Sławomir Lasota, Tomasz Gambin, Grégory Kucherov, Anna Gambin
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0179027

Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus
Cited by: 7
Author(s): Ke-Lin Huang, Zhang Mei-li, Guangjing Ma, Huan Wu, Xiaoming Wu, Feng Ren, Xuebao Li
Software Mentions: 2
Published: over 7 years ago

10.3390/antiox10030378

Nitrosative Redox Homeostasis and Antioxidant Response Defense in Disused Vastus lateralis Muscle in Long-Term Bedrest (Toulouse Cocktail Study)
Cited by: 7
Author(s): Dieter Blottner, Daniele Capitanio, Gabor Trautmann, Sandra Furlan, Guido Gambara, Manuela Moriggi, Katharina Block, Pietro Barbacini, Enrica Torretta, Guillaume Py, Angèle Chopard, Imre Vida, Pompeo Volpe, Cecilia Gelfi, Michele Salanova
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0056093

Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
Cited by: 12
Author(s): Rosemary S. Turingan, Hans-Ulrich Thomann, Anna Zolotova, Eugene Tan, Richard F. Selden
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0000169

Vertebrate Vitellogenin Gene Duplication in Relation to the “3R Hypothesis”: Correlation to the Pelagic Egg and the Oceanic Radiation of Teleosts
Cited by: 181
Author(s): Roderick Nigel Finn, Børge André Kristoffersen
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0111655

Unique Gene Expression Profile of the Proliferating Xenopus Tadpole Tail Blastema Cells Deciphered by RNA-Sequencing Analysis
Cited by: 18
Author(s): Hiroshi Tsujioka, Takekazu Kunieda, Yuki Katou, Katsuhiko Shirahige, Takeo Kubo
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0256802

Metabolomics integrated with transcriptomics reveals the distribution of iridoid and crocin metabolic flux in Gardenia jasminoides Ellis
Cited by: 10
Author(s): Yuan Pan, Zhao Xiao, Yu Wang, Jun Tan, Da-Xia Chen
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0190938

Extension of the viral ecology in humans using viral profile hidden Markov models
Cited by: 22
Author(s): Zurab Bzhalava, Emilie Hultin, Joakim Dillner
Software Mentions: 2
Published: almost 7 years ago

10.1111/1751-7915.12316

A novel bacteriophage cocktail reduces and dispersesPseudomonas aeruginosabiofilms under static and flow conditions
Cited by: 75
Author(s): Diana R. Alves, Patricia Pérez Esteban, Witold Kot, Jessica Bean, Tom Arnot, Lars Hestbjerg Hansen, Mark C. Enright, A. Toby A. Jenkins
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0175116

Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays
Cited by: 39
Author(s): Lívia Costa de Oliveira, Tessália Diniz Luerce Saraiva, Wanderson M. Silva, Ulisses de Pádua Pereira, Bruno C. Campos, Leandro de Jesus Benevides, Flávia Souza Rocha, Henrique César Pereira Figueiredo, Vasco Azevedo, Siomar C. Soares
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0099492

A 14.7 kDa Protein from Francisella tularensis subsp. novicida (Named FTN_1133), Involved in the Response to Oxidative Stress Induced by Organic Peroxides, Is Not Endowed with Thiol-Dependent Peroxidase Activity
Cited by: 7
Author(s): Diogo de Abreu Meireles, Thiago Gerônimo Pires Alegria, Simone Alves, Carla Rani Rocha Arantes, Luís Eduardo Soares Netto
Software Mentions: 2
Published: over 10 years ago

10.1111/1751-7915.13545

Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates
Cited by: 19
Author(s): Wladimir Mardones, Carlos A. Villarroel, Kristoffer Krogerus, Sebastián M. Tapia, Kamila Urbina, Christian I. Oporto, Samuel O’Donnell, Romain Minebois, Roberto F. Nespolo, Gilles Fischer, Amparo Querol, Brian Gibson, Francisco A. Cubillos
Software Mentions: 2
Published: over 4 years ago

10.1111/1751-7915.12116

Activation and identification of five clusters for secondary metabolites in <scp>S</scp>treptomyces albus <scp>J</scp>1074
Cited by: 175
Author(s): Carlos Olano, Ignacio García, Aránzazu González, Martín González Rodríguez, Daniel Rozas, Jerónimo Rubio, Marina Sánchez‐Hidalgo, Alfredo F. Braña, Cármen Méndez, José A. Salas
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0026792

Novel Adiponectin Variants Identified in Type 2 Diabetic Patients Reveal Multimerization and Secretion Defects
Cited by: 13
Author(s): Prapaporn Jungtrakoon, Nattachet Plengvidhya, Watip Tangjittipokin, Sarin Chimnaronk, Wanisa Salaemae, Nalinee Chongjaroen, Kanjana Chanprasert, Jatuporn Sujjitjoon, Chatchawan Srisawat, Pa‐thai Yenchitsomanus
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0002103

The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
Cited by: 128
Author(s): Sara H. Thomas, Ryan D. Wagner, Adrián K. Arakaki, Jeffrey Skolnick, John R. Kirby, Lawrence J. Shimkets, Robert A. Sanford, Frank E. Löffler
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0142002

dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42
Cited by: 25
Author(s): Bin Fan, Lei Li, Yapeng Chao, Konrad U. Förstner, Jörg Vogel, Rainer Borriss, Xiao‐Qin Wu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0151574

Plant Tandem CCCH Zinc Finger Proteins Interact with ABA, Drought, and Stress Response Regulators in Processing-Bodies and Stress Granules
Cited by: 39
Author(s): Srimathi Bogamuwa, Jyan-Chyun Jang
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0194071

Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA
Cited by: 20
Author(s): Xiaofen Zhang, Guoyun Wang, Bin Chen, Heshan Du, Fenglan Zhang, Haiying Zhang, Qian Wang, Sansheng Geng
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0057459

Metagenomic Detection of Viral Pathogens in Spanish Honeybees: Co-Infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses
Cited by: 89
Author(s): Fredrik Granberg, Marina Vicente-Rubiano, Consuelo Rubio-Guerri, Oskar E. Karlsson, Deborah Kukielka, Sándor Bélak, José Manuel Sánchez-Vizcaíno
Software Mentions: 2
Published: over 11 years ago

10.1186/s12862-016-0602-7

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae
Cited by: 5
Author(s): Kwame A. Darfour‐Oduro, Hendrik‐Jan Megens, Alfred L. Roca, Martien A. M. Groenen, Lawrence B. Schook
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0192452

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3
Cited by: 29
Author(s): François P. Douillard, Diego Mora, Robyn T. Eijlander, Michiel Wels, Willem M. de Vos
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0018359

Multiple Changes in Peptide and Lipid Expression Associated with Regeneration in the Nervous System of the Medicinal Leech
Cited by: 23
Author(s): Céline Mériaux, Karim Arafah, Aurélie Tasiemski, Maxence Wisztorski, Jocelyne Bruand, Céline Boidin-Wichlacz, Annie Desmons, Delphine Debois, Olivier Laprévôte, Alain Brunelle, Terry Gaasterland, Eduardo R. Macagno, Isabelle Fournier, Michel Salzet
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0000579

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
Cited by: 72
Author(s): Christian Iseli, Giovanna Ambrosini, Philipp Bücher, C. Victor Jongeneel
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0138078

Co-Administration of Cholesterol-Lowering Probiotics and Anthraquinone from Cassia obtusifolia L. Ameliorate Non-Alcoholic Fatty Liver
Cited by: 52
Author(s): Mengji Lu, Youcai Tang, Ming Li, Ping–Chang Yang, Zhiqiang Liu, Jieli Yuan, Pengyuan Zheng
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0052302

SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies
Cited by: 24
Author(s): Eric Pante, Audrey Rohfritsch, Vanessa Becquet, Khalid Belkhir, Nicolas Bierne, Pascale Garcia
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0109831

A Transcriptome for the Study of Early Processes of Retinal Regeneration in the Adult Newt, Cynops pyrrhogaster
Cited by: 36
Author(s): Kenta Nakamura, Md. Rafiqul Islam, Miyako Takayanagi, Hirofumi Yasumuro, Wataru Inami, Ailidana Kunahong, Roman Martin Casco-Robles, Fubito Toyama, Chikafumi Chiba
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0179723

Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene
Cited by: 26
Author(s): Shivani Nayyar, Bipen Kumar Sharma, Ajinder Kaur, Anu Kalia, Gulzar S. Sanghera, K. S. Thind, Inderjit Singh Yadav, Jagdeep Singh Sandhu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0019328

Identification of Hyaloperonospora arabidopsidis Transcript Sequences Expressed during Infection Reveals Isolate-Specific Effectors
Cited by: 57
Author(s): Adriana Cabral, Joost H. M. Stassen, Michael Seidl, Jaqueline Bautor, Jane E. Parker, Guido Van den Ackerveken
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-10-295

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus
Cited by: 20
Author(s): Christian Obermeier, Bashir Hosseini, W. Friedt, Rod J. Snowdon
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0101673

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus
Cited by: 159
Author(s): Harsh Raman, Rosy Raman, Andrzej Kilian, Frank Detering, Jason Carling, Neil Coombes, Simon Diffey, Gururaj Kadkol, David Edwards, M. E. McCully, Pradeep Ruperao, Isobel A. P. Parkin, Jacqueline Batley, David J. Luckett, Neil Wratten
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-017-3570-4

Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation
Cited by: 41
Author(s): Jiaming Chen, Xiaoqiang Yang, Xiaomao Huang, Shi-Hua Duan, Chengnian Long, Jiakuan Chen, Jun Rong
Software Mentions: 2
Published: over 7 years ago

Projects: pypi: blast

Papers Mentioning blast 1,819