pypi: blast | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-13-202

Comparing thousands of circular genomes using the CGView Comparison Tool
Cited by: 234
Author(s): Jason R. Grant, Adriano S. Arantes, Paul Stothard
Software Mentions: 4
Published: over 14 years ago

A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli
Cited by: 18
Author(s): Robert Goldstone, David George Emslie Smith
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-015-1684-0

Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome
Cited by: 7
Author(s): Riga Wu, Qingfeng Li, Sen Meng, Peng Zhang, Dan Liang
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2180-10-65

Comparative genomics of VirR regulons in Clostridium perfringens strains
Cited by: 10
Author(s): Antonio Frandi, Alessio Mengoni, Matteo Brilli
Software Mentions: 4
Published: over 16 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: almost 9 years ago

10.1099/mic.0.034538-0

Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2
Cited by: 143
Author(s): Sharon L. Kendall, Philippa Burgess, Ricardo Balhana, Mike Withers, Annemieke Ten Bokum, J.S. Lott, Chen Gao, Iria Uhia-Castro, Neil G. Stoker
Software Mentions: 4
Published: over 16 years ago

10.1186/1471-2164-15-549

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species
Cited by: 239
Author(s): Cene Gostinčar, Robin A. Ohm, Tina Kogej, Silva Sonjak, Monika Turk, Janja Zajc, Polona Zalar, Martín Grube, Hui Sun, James Han, Aarti Sharma, Jennifer Chiniquy, Chew Yee Ngan, Anna Lipzen, Kerrie Barry, Igor V. Grigoriev, Nina Gunde‐Cimerman
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12864-020-07132-6

Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2
Cited by: 35
Author(s): Julie E. Hernández-Salmerón, Gabriel Moreno‐Hagelsieb
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000095

Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection
Cited by: 16
Author(s): Andrew C. Barnes, J. Delamare-Deboutteville, Nicholas Gudkovs, Cara L. Brosnahan, R. I. Guy Morrison, J Carson
Software Mentions: 4
Published: almost 10 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-020-02757-x

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains
Cited by: 5
Author(s): Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma‐Silva, Fábio Pinheiro
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-017-3745-z

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model
Cited by: 20
Author(s): Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon‐Mom, Perry D. Moerland, Pernette J. Verschure
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13015-016-0069-5

Bitpacking techniques for indexing genomes: I. Hash tables
Cited by: 2
Author(s): Thomas D. Wu
Software Mentions: 4
Published: over 10 years ago

10.1186/s12918-018-0566-x

KF-finder: identification of key factors from host-microbial networks in cervical cancer
Cited by: 15
Author(s): Jialu Hu, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-020-07260-z

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum
Cited by: 18
Author(s): Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen, Wuwei Ye
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000531

Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
Cited by: 20
Author(s): Bert Bogaerts, Stéphanie Nouws, Bavo Verhaegen, Sarah Denayer, Julien Van Braekel, Raf Winand, Qiang Fu, Florence Crombé, Denis Piérard, Kathleen Marchal, Nancy Roosens, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-021-01103-z

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota
Cited by: 66
Author(s): Patricia Bermudez-Martin, Jérôme A.J. Becker, Nicolas Caramello, Sebastian P. Fernandez, Renan Costa Campos, Juliette Canaguier, Susana Barbosa, Laura Martinez‐Gili, Antonis Myridakis, Marc Dumas, Aurélia Bruneau, Claire Cherbuy, Philippe Langella, Jacques Crinon, Jean Marie Launay, Joëlle Chabry, Jacques Barik, Julie Le Merrer, Nicolas Glaichenhaus, Laetitia Davidovic
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-13-670

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria
Cited by: 49
Author(s): Laura Hobley, Thomas R. Lerner, Laura E. Williams, Carey Lambert, Rob Till, David S. Milner, Sarah M. Basford, Michael J. Capeness, Andrew K. Fenton, Robert J. Atterbury, Maximilian A. T. S. Harris, R. Elizabeth Sockett
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12870-015-0663-6

Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Cited by: 40
Author(s): Amir Sherman, Mor Rubinstein, Ravit Eshed, Miri Benita, Mazal Ish-Shalom, Michal Sharabi-Schwager, Ada Rozen, David Saada, Yuval Cohen, Ron Ophir
Software Mentions: 4
Published: almost 11 years ago

10.1099/mgen.0.000312

Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids
Cited by: 13
Author(s): Thomas Vognbjerg Sydenham, Søren Overballe‐Petersen, Henrik Hasman, Hannah M. Wexler, Michael Kemp, Ulrik Stenz Justesen
Software Mentions: 4
Published: almost 7 years ago

10.1111/1751-7915.12337

Dynamic changes in microbiota and mycobiota during spontaneous ‘<scp>V</scp>ino <scp>S</scp>anto <scp>T</scp>rentino’ fermentation
Cited by: 41
Author(s): Irene Stefanini, Davide Albanese, A. Cavazza, Elena Franciosi, Carlotta De Filippo, Claudio Donati, Duccio Cavalieri
Software Mentions: 4
Published: over 10 years ago

10.1186/s13104-016-2064-9

DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses
Cited by: 40
Author(s): Marie Lisandra Zepeda Mendoza, Kristine Bohmann, Aldo Carmona Baez, M. Thomas P. Gilbert
Software Mentions: 4
Published: over 10 years ago

10.1111/1751-7915.12190

The <scp>R</scp>sm regulon of plant growth‐promoting <scp><i>P</i></scp><i>seudomonas fluorescens</i> <scp>SS</scp>101: role of small <scp>RNA</scp>s in regulation of lipopeptide biosynthesis
Cited by: 17
Author(s): Song Cui, Menno van der Voort, Judith E. van de Mortel, Karl A. Hassan, Liam D. H. Elbourne, Ian T. Paulsen, Joyce E. Loper, Jos M. Raaijmakers
Software Mentions: 4
Published: almost 12 years ago

10.1099/mgen.0.000456

Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone
Cited by: 14
Author(s): Eleonora Tassinari, Matt Bawn, Gaëtan Thilliez, Oliver J. Charity, Luke Acton, Mark Kirkwood, Liljana Petrovska, Timothy J. Dallman, Catherine M. Burgess, Neil Hall, Geraldine Duffy, Robert A. Kingsley
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12915-021-00963-z

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly
Cited by: 64
Author(s): Mahul Chakraborty, Arunachalam Ramaiah, Adriana Adolfi, Paige Halas, Bhagyashree Kaduskar, Luna Thanh Ngo, Suvratha Jayaprasad, Kiran Paul, Saurabh Whadgar, Subhashini Srinivasan, Suresh Subramani, Ethan Bier, Anthony A. James, J. J. Emerson
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000059

Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK
Cited by: 23
Author(s): Ali Al‐Shahib, Anthony Underwood, Baharak Afshar, Claire E. Turner, Theresa Lamagni, Shiranee Sriskandan, Androulla Efstratiou
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2164-15-218

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-017-4294-1

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
Cited by: 44
Author(s): Bhavya Papudeshi, John M. Haggerty, Michael P. Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano L. Thompson, Robert A. Edwards, Elizabeth A. Dinsdale
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-11-432

Bcheck: a wrapper tool for detecting RNase P RNA genes
Cited by: 24
Author(s): Dilmurat Yusuf, Manja Marz, Peter F. Stadler, Ivo L. Hofacker
Software Mentions: 4
Published: over 16 years ago

10.1186/s12864-019-6161-8

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
Cited by: 17
Author(s): Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David Konkin, Ron Knox, Yuefeng Ruan, Pierre R. Fobert
Software Mentions: 4
Published: almost 7 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/s12864-018-5183-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

10.1186/1471-2148-7-135

Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants
Cited by: 220
Author(s): Jeffrey P. Mower, Pascal Touzet, Julie S Gummow, Lynda F. Delph, Jeffrey D. Palmer
Software Mentions: 3
Published: about 19 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

10.1186/1471-2164-14-837

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

10.1186/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

10.3390/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/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

10.1186/1471-2164-11-S1-S14

Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases
Cited by: 21
Author(s): П. А. Карпов, Е. С. Надеждина, А. І. Yemets, V. G. Matusov, A. Yu. Nyporko, Nadezhda Yu Shashina, Ya. B. Blume
Software Mentions: 3
Published: over 16 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

10.1186/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

10.1186/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/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: over 7 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

10.1186/1471-2105-8-307

Protein structural similarity search by Ramachandran codes
Cited by: 45
Author(s): Wei-Cheng Lo, Po-Jung Huang, Chih Hung Chang, Ping Lyu
Software Mentions: 3
Published: about 19 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

10.1186/s12864-020-6522-3

Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments
Cited by: 13
Author(s): Federico Vita, Beatrice Giuntoli, Edoardo Bertolini, Cosimo Taiti, Elettra Marone, Chiara D’Ambrosio, Emanuela Trovato, Danilo Sciarrone, Mariosimone Zoccali, Raffaella Balestrini, Andrea Scaloni, Luigi Mondello, Stefano Mancuso, Massimo Alessio, Amedeo Alpi
Software Mentions: 3
Published: over 6 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/s12870-020-02459-4

Reducing the nicotine content of tobacco by grafting with eggplant
Cited by: 5
Author(s): Mengjuan Ren, Mengyue Zhang, Huijuan Yang, Hongzhi Shi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4448-9

The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain
Cited by: 37
Author(s): Wen Xie, Xin Yang, Chunhai Chen, Zezhong Yang, Long Guo, Dan Wang, Jinqun Huang, Hailin Zhang, Yanan Wen, Jinyang Zhao, Qingjun Wu, Shaoli Wang, Brad S. Coates, Xuguo Zhou, Youjun Zhang
Software Mentions: 3
Published: over 8 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 8 years ago

10.1186/s12870-019-2074-6

Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species
Cited by: 37
Author(s): Ying Hong, Jian Shi, Shanshan Zhang, Gesang Pingcuo, Shuo Wang, Fan Zhao, Yongning Cui, Xiuli Zeng
Software Mentions: 3
Published: almost 7 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

10.1186/1471-2164-15-262

Exome capture from saliva produces high quality genomic and metagenomic data
Cited by: 35
Author(s): Jeffrey M. Kidd, Thomas J. Sharpton, Dean Bobo, Paul J. Norman, Alicia R. Martin, Meredith L. Carpenter, Martin Sikora, Christopher R. Gignoux, Neda Nemat-Gorgani, Alexandra Adams, Moraima Guadalupe, Xiaosen Guo, Qiang Feng, Yingrui Li, Xiao Liu, Peter Parham, Eileen G. Hoal, Marcus W. Feldman, Katherine S. Pollard, Jeffrey D. Wall, Carlos D. Bustamante, Brenna M. Henn
Software Mentions: 3
Published: over 12 years ago

10.1186/s12863-017-0584-5

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
Cited by: 20
Author(s): Adugna Abdi Woldesemayat, Peter van Heusden, Bongani K. Ndimba, Alan Christoffels
Software Mentions: 3
Published: almost 9 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

10.1186/s12864-021-07447-y

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)
Cited by: 2
Author(s): Nathan Hall, Jinesh Patel, J. Scott McElroy, Leslie R. Goertzen
Software Mentions: 3
Published: over 5 years ago

10.1186/s13062-017-0195-0

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
Cited by: 12
Author(s): Adam M. Dinan, John F. Atkins, Andrew E. Firth
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-15-779

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments
Cited by: 59
Author(s): Imran Khan, Emanuel Maldonado, Vı́tor Vasconcelos, Stephen J. O’Brien, Warren E. Johnson, Agostinho Antunes
Software Mentions: 3
Published: about 12 years ago

10.3390/biology10080732

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case
Cited by: 10
Author(s): Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne‐Marie Chèvre, Patrick Wincker, Mathieu Rousseau‐Gueutin, Jean‐Marc Aury
Software Mentions: 3
Published: about 5 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/s12864-021-07467-8

Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes
Cited by: 22
Author(s): Shoubo Tian, Panling Lu, Zhaohui Zhang, Jian Wu, Hui Zhang, Haibin Shen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2574-9

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood
Cited by: 12
Author(s): Abbot O. Oghenekaro, Tommaso Raffaello, Andriy Kovalchuk, Fred O. Asiegbu
Software Mentions: 3
Published: over 10 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

10.1186/1471-2164-12-104

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

10.3390/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

10.1186/1471-2164-15-257

mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities
Cited by: 69
Author(s): Jun Ma, Cristian Coarfa, Xiang Qin, Penelope E. Bonnen, Aleksandar Milosavljevic, James Versalovic, Kjersti M. Aagaard
Software Mentions: 3
Published: over 12 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

10.3390/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

10.3390/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: over 6 years ago

10.1186/s12864-019-5984-7

An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans
Cited by: 14
Author(s): José M. C. Ribeiro, Humberto Julio Debat, Mariana Boiani, X. Ures, Sérgio Paulo Dejato da Rocha, Martı́n Breijo
Software Mentions: 3
Published: about 7 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: about 6 years ago

10.1186/s12864-017-3757-8

A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing
Cited by: 149
Author(s): Nam V. Hoang, Agnelo Furtado, Patrick J. Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P. Thirugnanasambandam, Frederik C. Botha, Robert J. Henry
Software Mentions: 3
Published: over 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

10.1111/1751-7915.12265

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

10.1186/1471-2105-10-416

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

10.1111/1751-7915.12157

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

10.1007/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

10.1186/1471-2164-15-853

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

10.1099/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

10.1099/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

10.1186/1471-2164-8-428

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

10.1099/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.0.000049

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.0.000142

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

10.1186/1471-2164-13-31

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: over 14 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

10.1099/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

10.1099/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

10.1186/1471-2164-13-517

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

10.1099/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

10.1099/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/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

10.1186/1471-2164-11-592

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: almost 16 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

10.1186/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

10.1186/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

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Papers Mentioning blast 1,819