pypi: blast | Projects | Ecosyste.ms: Papers

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

10.3389/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 6 years ago

10.1038/s42003-021-02559-3

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 5 years ago

10.1038/srep39749

An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus
Cited by: 13
Author(s): James A. Cotton, Sascha Steinbiss, Toshiro Yokoi, Isheng Jason Tsai, Taisei Kikuchi
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.csbj.2020.11.013

HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae
Cited by: 13
Author(s): Sundeep Chaitanya Vedithi, Sony Malhotra, Marcin J. Skwark, Asma Munir, Marta Acebrón-García-de-Eulate, Vaishali P. Waman, Ali Alsulami, David B. Ascher, Tom L. Blundell
Software Mentions: 3
Published: almost 7 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 6 years ago

10.1371/journal.pone.0079612

Comparative Transcriptome Analysis of Salivary Glands of Two Populations of Rice Brown Planthopper, Nilaparvata lugens, That Differ in Virulence
Cited by: 74
Author(s): Rui Ji, Haixin Yu, Qiang Fu, Hongdan Chen, Wenfeng Ye, Shaohui Li, Yonggen Lou
Software Mentions: 3
Published: almost 13 years ago

10.1111/jcmm.14154

Absence of PARP‐1 affects Cxcl12 expression by increasing DNA demethylation
Cited by: 7
Author(s): Anja Tolić, Nevena Grdović, Svetlana Dinić, Jovana Rajić, Miloš Đorđević, Marija Sinadinović, Jelena Arambašić Jovanović, Mirjana Mihailović, Goran Poznanović, Aleksandra Uskoković, Melita Vidaković
Software Mentions: 3
Published: over 7 years ago

10.1099/vir.0.043182-0

Application of next-generation sequencing technologies in virology
Cited by: 223
Author(s): Alan Radford, Dave Chapman, Lucas Dixon, Julian Chantrey, Alistair C. Darby, Neil Hall
Software Mentions: 3
Published: about 14 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

10.1111/1751-7915.12157

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/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

10.1186/1471-2105-8-307

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

10.1371/journal.pone.0073514

Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet
Cited by: 59
Author(s): Hui Bai, Yinghao Cao, J. Z. Quan, Lü Dong, Zhiyong Li, Yanbin Zhu, Lihuang Zhu, Zimei Dong, Dayong Li
Software Mentions: 3
Published: about 13 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

10.1371/journal.pone.0145053

Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans
Cited by: 57
Author(s): Aijaz Ahmad, Mohmmad Younus Wani, Amber Khan, Nikhat Manzoor, Julitha Molepo
Software Mentions: 3
Published: almost 11 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

10.1186/1471-2164-15-257

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

10.1371/journal.pone.0041645

Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Cited by: 36
Author(s): Qinghua Nie, Erin Sandford, Xiquan Zhang, Lisa K. Nolan, Susan J. Lamont
Software Mentions: 3
Published: about 14 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

10.1371/journal.pone.0146283

Multiple and Diverse vsp and vlp Sequences in Borrelia miyamotoi, a Hard Tick-Borne Zoonotic Pathogen
Cited by: 34
Author(s): Alan G. Barbour
Software Mentions: 3
Published: over 10 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

10.1186/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/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/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/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

10.1371/journal.pntd.0006786

Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats
Cited by: 32
Author(s): Daniel J. Becker, Laura M. Bergner, Alexandra B. Bentz, Richard Orton, Sonia Altizer, Daniel G. Streicker
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pntd.0002728

Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans
Cited by: 63
Author(s): Corey L. Brelsfoard, George Tsiamis, Marco Falchetto, Ludvik M. Gomulski, Erich Loza Telleria, Uzma Alam, Vangelis Doudoumis, Francesca Scolari, Joshua B. Benoit, Martin Swain, Peter Takáč, Anna R. Malacrida, Kostas Bourtzis, Serap Aksoy
Software Mentions: 3
Published: over 12 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

10.1371/journal.pgen.1009541

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering
Cited by: 25
Author(s): Leonor García-Bayona, Michael J. Coyne, Laurie E. Comstock
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1003323

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci
Cited by: 343
Author(s): Christopher L. Schardl, Carolyn A. Young, Uljana Hesse, Stefan G. Amyotte, Kalina Andreeva, Patrick J. Calie, Damien J. Fleetwood, David Haws, Neil Moore, Birgitt Oeser, Daniel G. Panaccione, Kathryn Schweri, Christine R. Voisey, Mark L. Farman, Jerzy W. Jaromczyk, Bruce A. Roe, Donal M. O’Sullivan, Barry Scott, Paul Tudzynski, Zhiqiang An, Elissaveta G. Arnaoudova, Charles T. Bullock, Nikki D. Charlton, Li Chen, Murray P. Cox, Randy D. Dinkins, Simona Florea, Anthony E. Glenn, Anna Gordon, Ulrich Güldener, Daniel R. Harris, Walter Hollin, Jolanta Jaromczyk, Richard D. Johnson, Anar Khan, Eckhard Leistner, Adrian Leuchtmann, Chunjie Li, Jin Ge Liu, Jinze Liu, Miao Liu, Wade J. Mace, Caroline Machado, Padmaja Nagabhyru, Juan Pan, Jan Schmid, Kazuo Sugawara, Ulrike Steiner, Johanna E. Takach, Eiji Tanaka, James D. Webb, Ella V. Wilson, Jennifer L. Wiseman, Ruriko Yoshida, Zheng Zeng
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1004531

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency
Cited by: 21
Author(s): Richard N. McLaughlin, Janet M. Young, Lei Yang, Rafik Neme, Holly A. Wichman, Harmit S. Malik
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pgen.1002602

The Atypical Calpains: Evolutionary Analyses and Roles in Caenorhabditis elegans Cellular Degeneration
Cited by: 24
Author(s): Peter Joyce, Rahul Satija, Maozi C Chen, Patricia E. Kuwabara
Software Mentions: 3
Published: over 14 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/s12859-017-1902-7

Scaling bioinformatics applications on HPC
Cited by: 8
Author(s): Mike Mikailov, Fu-Jyh Luo, Stuart J. Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong, Nicholas Petrick
Software Mentions: 3
Published: almost 9 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

10.1111/tpj.14596

Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network
Cited by: 16
Author(s): Rafe Lyall, Stephen A Schlebusch, Jessica Proctor, Mayur Prag, Steven G. Hussey, Robert A. Ingle, Nicola Illing
Software Mentions: 3
Published: almost 7 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 7 years ago

10.7717/peerj.7421

Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weedAmbrosia artemisiifoliaL. (Asteraceae)
Cited by: 13
Author(s): Kinga Mátyás, Géza Hegedűs, János Taller, Eszter Farkas, Kincső Decsi, Barbara Kutasy, Nikoletta Kálmán, Erzsébet Nagy, Balázs Kolics, Eszter Virág
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-6-S4-S22

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae
Cited by: 3
Author(s): Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata
Software Mentions: 3
Published: almost 21 years ago

10.7717/peerj.9387

The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods
Cited by: 4
Author(s): Polina Drozdova, Alexandra Saranchina, M. M. Morgunova, Alena Kizenko, Yulia Lubyaga, Boris Baduev, Maxim A. Timofeyev
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

10.1099/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

10.1186/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

10.7717/peerj.3134

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Cited by: 44
Author(s): Sean P. Jungbluth, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé
Software Mentions: 3
Published: over 9 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 7 years ago

10.1111/tpj.12600

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression
Cited by: 31
Author(s): Katie Baker, Micha Bayer, Nicola Cook, Steven Dreißig, Taniya Dhillon, Joanne Russell, Pete E. Hedley, Jenny Morris, Luke Ramsay, Isabelle Colas, Robbie Waugh, Brian J. Steffenson, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell
Software Mentions: 3
Published: about 12 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/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

10.1002/1878-0261.12119

Novel landscape of HLA-G isoforms expressed in clear cell renal cell carcinoma patients
Cited by: 62
Author(s): Diana Tronik‐Le Roux, Julie Renard, Jérôme Verine, Victor Renault, Emmanuel Tubacher, Joël LeMaoult, Nathalie Rouas‐Freiss, Jean‐François Deleuze, François Desgrandschamps, Edgardo D. Carosella
Software Mentions: 3
Published: about 9 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

10.1111/mec.14459

The effects of pastoral intensification on the feeding interactions of generalist predators in streams
Cited by: 6
Author(s): Caitlin E. Pearson, William Oliver Christian Symondson, Elizabeth L. Clare, Stephen James Ormerod, Esther Iparraguirre Bolaños, Ian P. Vaughan
Software Mentions: 3
Published: almost 9 years ago

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

10.1186/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

10.1186/1471-2105-10-416

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

10.1186/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: over 7 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/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

10.1186/1471-2164-14-837

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: almost 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: almost 6 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/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

10.1186/1471-2164-15-262

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

10.1186/1471-2148-9-215

The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes
Cited by: 104
Author(s): Zi-Wen Li, Xue-zhi Li, Qiuhan Yu, Xiang Zhang, Hirohisa Kishino, Ze Zhang
Software Mentions: 3
Published: about 17 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

10.1099/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

10.3390/pathogens8020061

The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects
Cited by: 16
Author(s): Won Hyung Choi, In Ah Lee
Software Mentions: 3
Published: over 7 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/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

10.7717/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: almost 9 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: over 5 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: almost 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/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: almost 9 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: about 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: about 6 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: almost 17 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: about 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

10.1371/journal.pgen.1008850

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
Cited by: 37
Author(s): Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E. Wheeler, Liljana Petrovska, Timothy J. Dallman, Evelien M. Adriaenssens, Neil Hall, Robert A. Kingsley
Software Mentions: 3
Published: over 6 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: about 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: over 14 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

Projects: pypi: blast

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Papers Mentioning blast 1,819