pypi: blast | Projects | Ecosyste.ms: Papers

10.1111/mec.15168

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation
Cited by: 34
Author(s): Jasper R L Depotter, Xiaoqian Shi-Kunne, Hélène Missonnier, Tingli Liu, Luigi Faino, Grardy C. M. van den Berg, Thomas A. Wood, Baolong Zhang, Alban Jacques, Michael Seidl, B.P.H.J. Thomma
Software Mentions: 3
Published: about 7 years ago

10.1111/jam.12516

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration
Cited by: 78
Author(s): Isabel Douterelo, Rebecca Sharpe, Joby Boxall
Software Mentions: 3
Published: over 12 years ago

10.1038/s41437-021-00438-5

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish
Cited by: 7
Author(s): Axel Jensen, Mette Lillie, Kristofer Bergström, Per Larsson, Jacob Höglund
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-10-416

DescFold: A web server for protein fold recognition
Cited by: 31
Author(s): Renxiang Yan, Jing-Na Si, Chuan Wang, Ziding Zhang
Software Mentions: 3
Published: almost 17 years ago

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 12 years ago

10.1038/s41438-020-00424-8

Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz
Cited by: 24
Author(s): Jian Zhang, Huwei Yuan, Yujuan Li, Yanhong Chen, Guoyuan Liu, Meixia Ye, Chunmei Yu, Bolin Lian, Fei Zhong, Yuna Jiang, Junfeng Xu
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41597-020-0480-0

An improved high-quality genome assembly and annotation of Tibetan hulless barley
Cited by: 23
Author(s): Xingquan Zeng, Tong Xu, Zhihao Ling, Yulin Wang, Xiangfeng Li, Shuqing Xu, Qijun Xu, Zha Sang, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzhai Yu, Hongjun Yuan, Nyima Tashi
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giy075

Binning enables efficient host genome reconstruction in cnidarian holobionts
Cited by: 15
Author(s): Juan Sebastián Celis, Daniel Wibberg, Catalina Ramírez‐Portilla, Oliver Rupp, Alexander Sczyrba, Anderson M. Winkler, Jörn Kalinowski, Thomas Wilke
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-837

Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1
Cited by: 81
Author(s): Nikolai V. Ravin, Michael A. Eldarov, Vitaly V. Kadnikov, Alexey V. Beletsky, Jessica Schneider, Eugenia S. Mardanova, Elena M. Smekalova, Maria I. Zvereva, О. А. Донцова, Andrey V. Mardanov, K. G. Skryabin
Software Mentions: 3
Published: almost 13 years ago

10.3390/microorganisms9051006

Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates
Cited by: 6
Author(s): Merima Alispahic, Lukas Endler, Michael Heß, Claudia Heß
Software Mentions: 3
Published: over 5 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: almost 7 years ago

10.3390/microorganisms7100444

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes
Cited by: 40
Author(s): Dipti Deo, Dimple Davray, Ram Kulkarni
Software Mentions: 3
Published: about 7 years ago

10.3390/microorganisms8101621

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis
Cited by: 16
Author(s): Guillaume Dubrulle, Adeline Picot, Stéphanie Madec, Matthieu Le Corre, Audrey Pawtowski, Riccardo Baroncelli, Michel Zivy, Thierry Balliau, Gaétan Le Floch, Flora Pensec
Software Mentions: 3
Published: about 6 years ago

10.1186/2047-217X-2-10

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Cited by: 584
Author(s): Keith Bradnam, Joseph Fass, A. A. Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert, Jarrod Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T. Roderick Docking, Richard Durbin, Dent Earl, Scott J. Emrich, P.I. Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph Hiatt, Isaac Ho, Jason T. Howard, Martin Hunt, Shaun D. Jackman, David B. Jaffe, Erich D. Jarvis, Huaiyang Jiang, С. В. Казаков, Paul J. Kersey, Jacob O. Kitzman, James Knight, Sergey Koren, Tak Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D. MacManes, Nicolas Maillet, Sergey Melnikov, Delphine Naquin, Zemin Ning, Thomas D. Otto, Benedict Paten, Octávio S. Paulo, Adam M. Phillippy, Francisco Pina‐Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J. Ribeiro, Stephen Richards, Daniel S. Rokhsar, J. Graham Ruby, Simone Scalabrin, Michael C. Schatz, David C. Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I. Shaw, Jay Shendure, Yujian Shi, Jared T. Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Bruno Miguel Vieira, Jun Wang, Kim C. Worley, Shuangye Yin, Siu Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian F Korf
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-018-5183-y

Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues
Cited by: 4
Author(s): Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu, Dan Xie
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-021-02904-y

QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps
Cited by: 22
Author(s): Qiang Lian, Qihua Fu, Yong Xu, Zhicheng Hu, Jing Zheng, Aiai Zhang, Yue He, Changsheng Wang, Chuanqiang Xu, Benxue Chen, Jordi García-Más, Guangwei Zhao, Huaisong Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-016-1090-1

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Cited by: 119
Author(s): Federico Abascal, André Corvelo, Fernando Cruz, José Luis Villanueva‐Cañas, Anna Vlasova, Marina Marcet‐Houben, Begoña Martínez‐Cruz, Jade Yu Cheng, Pablo Prieto, Vı́ctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frías, Paolo Ribeca, Salvador Capella-Gutiérrez, José Manuel Vázquez Rodríguez, Francisco Câmara, Ernesto Lowy, Luca Cozzuto, Ionas Erb, Michael L. Tress, José Manuel Rodriguez, Jorge Ruiz-Orera, Ferrán Reverter, Mireia Casas-Marcé, Laura García-España Soriano, Javier R. Arango, Sophia Derdak, Beatriz Galán, Julie Blanc, Marta Gut, Belén Lorente-Galdós, Marta Andrés-Nieto, Carlos López‐Otín, Alfonso Valencia, Ivo Gut, José Luis Garcı́a, Roderic Guigó, William J. Murphy, Aurora Ruiz‐Herrera, Tomàs Marquès-Bonet, Guglielmo Roma, Cédric Notredame, Thomas Mailund, Mar Albà, Toni Gabaldón, Tyler Alioto, José A. Godoy
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12870-020-02461-w

Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset
Cited by: 14
Author(s): Yunsheng Wang, Fude Nie, Muhammad Qasim Shahid, Faheem Shehzad Baloch
Software Mentions: 3
Published: over 6 years ago

10.1099/mic.0.000861

Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100
Cited by: 11
Author(s): Laura E. Williams, Nicole Cullen, Joseph A. DeGiorgis, Karla J Martinez, Justina Mellone, Molly Oser, Jing Wang, Ying Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1186/gb-2012-13-2-r14

Chromatin structure changes around satellite repeats on the Schistosoma mansoni female sex chromosome suggest a possible mechanism for sex chromosome emergence
Cited by: 30
Author(s): Julie M. J. Lepesant, Céline Cosseau, Jérôme Boissier, Michael Freitag, Julien Portela, Déborah Climent, Cécile Perrin, Adhemar Zerlotini, Christoph Grunau
Software Mentions: 3
Published: almost 15 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 6 years ago

10.1186/s12870-019-1672-7

Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume
Cited by: 35
Author(s): Xinxin Wu, Ting Shi, Shahid Iqbal, Yong Zhang, Lin Liu, Zhihong Gao
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2007-8-11-r242

Quantification of ortholog losses in insects and vertebrates
Cited by: 60
Author(s): Stefan Wyder, Evgenia V. Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M. Zdobnov
Software Mentions: 3
Published: almost 20 years ago

10.1186/s12859-019-3261-z

Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
Cited by: 12
Author(s): Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li, Xinchun Lin
Software Mentions: 3
Published: almost 7 years ago

10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 15 years ago

10.3389/fmicb.2017.01812

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets
Cited by: 21
Author(s): Shijuan Yan, Cui Zhu, Ting Yu, Wenjie Huang, Jianfeng Huang, Qian Kong, Jiandang Shi, Zhongjian Chen, Qinjian Liu, Shaolei Wang, Zongyong Jiang, Zhuang Chen
Software Mentions: 3
Published: about 9 years ago

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: about 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 7 years ago

10.3390/ani11071924

Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse
Cited by: 0
Author(s): Wooseok Lee, Seyoung Mun, Song‐Yi Choi, Do Hoon Oh, Yong Soo Park, Kyudong Han
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-016-0883-6

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Cited by: 156
Author(s): Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Ángel Hernández‐Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, George J. Pappas, Soledad Saburido-Álvarez, Darek Kedra, Irene González González, Luca Cozzuto, Jèssica Gómez-Garrido, María A. Aguilar-Morón, Núria Andreu, O. Mario Aguilar, Jordi García-Más, Maik Zehnsdorf, Martı́n Vázquez, Alfonso Delgado‐Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana Pereira Vianello-Brondani, José Luis Garcı́a, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cédric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó
Software Mentions: 3
Published: over 10 years ago

10.1093/gigascience/giaa148

Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
Cited by: 29
Author(s): Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuß, Lars Riff Jensen, C. J. Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: almost 7 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 8 years ago

10.1186/s12915-020-00822-3

Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps
Cited by: 22
Author(s): Fabrice Legeai, Bernardo F. Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca B. Dikow, Claire Lemaitre, Véronique Jouan, Marc Ravallec, Jean‐Michel Drezen, Denis Tagu, Frédéric Baudat, Gábor Gyapay, Xin Zhou, Shanlin Liu, Bruce A. Webb, Seán G. Brady, Anne Nathalie Volkoff
Software Mentions: 3
Published: over 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: almost 12 years ago

10.1186/s12866-020-01877-6

Proteomic analysis of Rickettsia akari proposes a 44 kDa-OMP as a potential biomarker for Rickettsialpox diagnosis
Cited by: 5
Author(s): František Csicsay, Gabriela Flores‐Ramírez, Fernando Zúñiga-Navarrete, Mária Bartošová, Alena Fučíková, Petr Pajer, Jiří Dresler, Ľudovít Škultéty, Marco Antonio Quevedo-Diaz
Software Mentions: 3
Published: over 6 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 5 years ago

10.1186/s12859-015-0633-x

PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides
Cited by: 24
Author(s): S. M. Ashiqul Islam, Tanvir Sajed, Christopher Michel Kearney, Erich J. Baker
Software Mentions: 3
Published: over 11 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: over 7 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 11 years ago

10.1186/1471-2350-7-18

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions
Cited by: 24
Author(s): Raihan K. Uddin, Yang Zhang, Victoria Mok Siu, Yao Shan Fan, Richard O’Reilly, Jay Rao, Shiva M. Singh
Software Mentions: 3
Published: over 20 years ago

10.1186/s12864-018-4675-0

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Cited by: 31
Author(s): Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Sharon Benjamini, Shoval Miyara, M. Ruzal, Manfred Grabherr, Nima Rafati, Anna Maja Molin, Ken Pendavis, Shane C. Burgess, Leif Andersson, Miriam Friedman‐Einat
Software Mentions: 3
Published: over 8 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 5 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 5 years ago

10.1186/1471-2164-13-31

Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes
Cited by: 8
Author(s): Kristopher J. L. Irizarry, S. B. Malladi, Xiangming Gao, Katherine Mitsouras, Lynda Melendez, Patricia A Burris, Jeffrey A. Brockman, Samer Al-Murrani
Software Mentions: 3
Published: almost 15 years ago

10.1099/mgen.0.000049

Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates of Staphylococcus aureus
Cited by: 4
Author(s): Debra Smith, Matthew K. Siggins, Magdalena Gierula, Bruno Pichon, Claire E. Turner, Nicola N. Lynskey, Mia Mosavie, Angela Kearns, Robert J. Edwards, Shiranee Sriskandan
Software Mentions: 3
Published: over 10 years ago

10.1099/mgen.0.000231

SynerClust: a highly scalable, synteny-aware orthologue clustering tool
Cited by: 12
Author(s): C Georgescu, Abigail L. Manson, Alexander D. Griggs, Christopher A. Desjardins, Alejandro Pironti, Ilan Wapinski, Thomas Abeel, Brian J. Haas, Ashlee M. Earl
Software Mentions: 3
Published: almost 8 years ago

10.1099/mgen.0.000187

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny
Cited by: 8
Author(s): Katelyn Brandt, Rodolphe Barrangou
Software Mentions: 3
Published: over 8 years ago

10.1099/mgen.0.000142

Vibrio cholerae genomic diversity within and between patients
Cited by: 24
Author(s): Inès Levade, Yves Terrat, Jean-Baptiste Leducq, Ana A. Weil, Leslie M. Mayo-Smith, Fahima Chowdhury, Ashraful Islam Khan, Jacques Boncy, Josiane Buteau, Louise C. Ivers, Edward T. Ryan, Richelle C. Charles, Stephen B. Calderwood, Firdausi Qadri, Jason B. Harris, Regina C. LaRocque, B. Jesse Shapiro
Software Mentions: 3
Published: almost 9 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 6 years ago

10.1099/mgen.0.000307

Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia
Cited by: 6
Author(s): Tamieka A. Fraser, Mikaela G. Bell, Patrick N A Harris, S. C. Bell, Haakon Bergh, Thuy‐Khanh Nguyen, Timothy J. Kidd, Graeme R. Nimmo, Derek S. Sarovich, Erin P. Price
Software Mentions: 3
Published: about 7 years ago

10.1099/mgen.0.000080

Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems
Cited by: 34
Author(s): Eleanor Jameson, Andrew C. Doxey, Ruth L. Airs, Kevin J. Purdy, J. Colin Murrell, Yin Chen
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-019-5815-x

Transcriptome Analysis of Gene Families Involved in Chemosensory Function in Spodoptera littoralis (Lepidoptera: Noctuidae)
Cited by: 53
Author(s): William B. Walker, Amit Roy, Peter Anderson, Fredrik Schlyter, Bill S. Hansson, Mattias C. Larsson
Software Mentions: 3
Published: over 7 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: over 6 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: almost 11 years ago

10.1099/mgen.0.000188

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
Cited by: 32
Author(s): Arnold Bainomugisa, Tânia Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben J. Marais, Lachlan Coin
Software Mentions: 3
Published: over 8 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 11 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 9 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 8 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 9 years ago

10.1007/s00248-015-0568-9

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences
Cited by: 37
Author(s): Sandra Pucciarelli, Raghul Rajan Devaraj, Alessio Mancini, Patrizia Ballarini, Michele Castelli, Martina Schrallhammer, Giulio Petroni, Cristina Miceli
Software Mentions: 3
Published: over 11 years ago

10.1111/1751-7915.12157

Compositional profile of α / β‐hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil‐contaminated sites
Cited by: 14
Author(s): Diego Javier Jiménez, Francisco Dini‐Andreote, Júlia Ronzella Ottoni, Valéria Maia de Oliveira, Jan Dirk van Elsas, Fernando Dini Andreote
Software Mentions: 3
Published: about 12 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 16 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 17 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 5 years ago

10.1186/s13072-021-00397-5

Dynamics of cattle sperm sncRNAs during maturation, from testis to ejaculated sperm
Cited by: 21
Author(s): Eli Sellem, Sylvain Marthey, Andrea Rau, Luc Jouneau, A. Bonnet, Chrystelle Le Danvic, Benoît Guyonnet, Hélène Kiefer, Hélène Jammes, Laurent Schibler
Software Mentions: 3
Published: over 5 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 14 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 7 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 17 years ago

10.1371/journal.pone.0125964

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species
Cited by: 34
Author(s): S. P. Singh, Suresh Chand, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0212514

Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification
Cited by: 11
Author(s): Dengqun Liao, Juan Zhu, Zhang Menghuan, Peng Sun, Jianhe Wei, Jianjun Qi
Software Mentions: 3
Published: over 7 years ago

10.1186/s12883-020-02040-4

Mild cognitive impairment in novel SPG11 mutation-related sporadic hereditary spastic paraplegia with thin corpus callosum: case series
Cited by: 4
Author(s): Chuan Li, Qi Yan, Feng-ju Duan, Chao Zhao, Zhuo Zhang, Ying Du, Wei Zhang
Software Mentions: 3
Published: almost 6 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 6 years ago

10.1371/journal.pone.0173974

Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus
Cited by: 35
Author(s): Wei Chi, Yu Gao, Qing Hu, Wei Guo, Dapeng Li
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0210116

Evidence of CD1d pathway of lipid antigen presentation in mouse primary lung epithelial cells and its up-regulation upon Mycobacterium bovis BCG infection
Cited by: 15
Author(s): Zaigham Abbas Rizvi, Niti Puri, Rajiv K. Saxena
Software Mentions: 3
Published: almost 8 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: over 15 years ago

10.1371/journal.pone.0131292

An Insight into the Sialome of the Lone Star Tick, Amblyomma americanum, with a Glimpse on Its Time Dependent Gene Expression
Cited by: 95
Author(s): Shahid Karim, José M. C. Ribeiro
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: about 14 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 10 years ago

10.1371/journal.pone.0246915

Experimental and molecular predictions of the adjuvanticity of snail mucin on hepatitis B vaccine in albino mice
Cited by: 2
Author(s): Parker Elijah Joshua, Cynthia Ogochukwu Nwauzor, Damian Chukwu Odimegwu, Uzochukwu Gospel Ukachukwu, Rita Onyekachukwu Asomadu, Timothy Prince Chidike Ezeorba
Software Mentions: 3
Published: over 5 years ago

10.3390/md18010061

Differential Expression of Nicotine Acetylcholine Receptors Associates with Human Breast Cancer and Mediates Antitumor Activity of αO-Conotoxin GeXIVA
Cited by: 17
Author(s): Zhigang Sun, Manqi Zhangsun, Shuai Dong, Liu Yiqiao, Qian Jiang, Dongting Zhangsun, Sulan Luo
Software Mentions: 3
Published: almost 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 19 years ago

10.3390/md19060286

An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces
Cited by: 2
Author(s): Ricardo Valencia, Valentina González, Agustina Undabarrena, Leonardo Zamora-Leiva, Juan A. Ugalde, Beatríz Cámara
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0036234

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]
Cited by: 140
Author(s): Tao Xiang, Yinghong Gu, Haiyan Wang, Wen Zheng, Xiao Li, Chuan-Wu Zhao, Yizheng Zhang
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0026495

New Inflammation-Related Biomarkers during Malaria Infection
Cited by: 44
Author(s): Fikregabrail Aberra Kassa, Marina Tiemi Shio, Marie-Josée Bellemare, Babacar Faye, Momar Ndao, Martin Olivier
Software Mentions: 3
Published: about 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 12 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 12 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: over 15 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 8 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 6 years ago

10.3390/life11020129

Population Genomics Insights into the First Wave of COVID-19
Cited by: 14
Author(s): Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, Pavlos Pavlidis
Software Mentions: 3
Published: over 5 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 11 years ago

10.1186/s12870-014-0333-0

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants
Cited by: 64
Author(s): Patrick Favre, Laure Bapaume, Eligio Bossolini, Mauro Delorenzi, Laurent Falquet, Didier Reinhardt
Software Mentions: 3
Published: almost 12 years ago

10.1186/1754-6834-6-72

Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation
Cited by: 79
Author(s): Tao Xiang, Yang Fang, Yao Xiao, Yanling Jin, Xinrong Ma, Yun Zhao, Kai He, Hai Zhao, Haiyan Wang
Software Mentions: 3
Published: over 13 years ago

10.1111/1751-7915.12265

Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway
Cited by: 18
Author(s): André Pick, Jochen Schmid, Volker Sieber
Software Mentions: 3
Published: over 11 years ago

10.1186/s12870-020-02634-7

The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development
Cited by: 12
Author(s): Dandan Wang, Zhaodong Hao, Xiaofei Long, Zhanjun Wang, Xianrui Zheng, Daiquan Ye, Peng Ye, Weihuang Wu, Xiangyang Hu, Guibin Wang, Renhua Zheng, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: almost 6 years ago

10.1093/gigascience/gix040

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Cited by: 52
Author(s): Peter R. Sternes, Danna Lee, Dariusz R. Kutyna, Anthony R. Borneman
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0235153

A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy
Cited by: 5
Author(s): Sheng Hung Juan, Teng Ruei Chen, Wei-Cheng Lo
Software Mentions: 3
Published: over 6 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 5 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 14 years ago

Projects: pypi: blast

Enhanced Analysis

Science Score: 65/100

Bonuses:

Penalties:

Papers Mentioning blast 1,819