Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: blast

https://packages.ecosyste.ms/registries/pypi.org/packages/blast

a simple web-based, multi-platform music/mp3 player written in python, HTML/CSS and javascript
3 versions
Latest release: almost 12 years ago
120 downloads last month

Papers Mentioning blast 1,819

10.1155/2020/3275315
Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma
Cited by: 1
Author(s): Qi Li, Qifan Zhang, Xiangdong Cheng, Xie Weng, Mian Chen, Xiaoyun Hu, Jing Huang, Jinzhang Chen
Software Mentions: 4
Published: over 3 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: about 8 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: over 8 years ago
10.1186/s12915-015-0119-3
Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish
Cited by: 87
Author(s): Masato Yoshizawa, Beatriz G. Robinson, Erik R. Duboué, Pavel Mašek, James B. Jaggard, Kelly E. O’Quin, Richard Borowsky, William R. Jeffery, Alex C. Keene
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pone.0168397
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data
Cited by: 8
Author(s): Guillaume Carissimo, Marius van den Beek, Kenneth D. Vernick, Christophe Antoniewski
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0088998
Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity
Cited by: 58
Author(s): Ron Ophir, Amir Sherman, Mor Rubinstein, Ravit Eshed, Michal Sharabi Schwager, Rotem Harel-Beja, Irit Bar-Ya’akov, Doron Holland
Software Mentions: 4
Published: about 10 years ago
10.7554/eLife.26580
Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Cited by: 56
Author(s): Feiqiao Brian Yu, Paul C. Blainey, Frederik Schulz, Tanja Woyke, Mark Horowitz, Stephen R. Quake
Software Mentions: 4
Published: almost 7 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: over 3 years ago
10.1371/journal.pbio.1002307
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
Cited by: 51
Author(s): Gregory J. Hogan, Patrick O. Brown, Daniel Herschlag
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pcbi.1008222
Genome Complexity Browser: Visualization and quantification of genome variability
Cited by: 1
Author(s): Alexander I. Manolov, Dmitry N. Konanov, Dmitry E. Fedorov, Ivan Osmolovsky, Rinat Vereshchagin, Elena N. Ilina
Software Mentions: 4
Published: over 3 years ago
10.1099/vir.0.017327-0
Characterization of a novel wood mouse virus related to murid herpesvirus 4
Cited by: 29
Author(s): David J. Hughes, Anja Kipar, Steven G. Milligan, Charles Cunningham, Mandy Sanders, Michael A. Quail, Marie Adèle Rajandream, Stacey Efstathiou, Rory Bowden, C Chastel, Malcolm J. Bennett, Jeffery T. Sample, Bart Barrell, Andrew J. Davison, James P. Stewart
Software Mentions: 4
Published: over 14 years ago
10.1099/ijsem.0.004795
Listeria cossartiae sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments
Cited by: 51
Author(s): Catharine R Carlin, Jingqiu Liao, Daniel Weller, Xiaodong Guo, Renato H. Orsi, Martin Wiedmann
Software Mentions: 4
Published: about 3 years ago
10.1128/mSphere.01255-20
The Majority of Typhoid Toxin-Positive <i>Salmonella</i> Serovars Encode ArtB, an Alternate Binding Subunit
Cited by: 9
Author(s): Ahmed Gaballa, Rachel A. Cheng, Anna Sophia Harrand, Alexa R. Cohn, Martin Wiedmann
Software Mentions: 4
Published: about 3 years ago
10.1128/mBio.00530-17
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
Cited by: 53
Author(s): Connor T. Skennerton, Karuna Chourey, Ramsunder Iyer, Robert L. Hettich, Gene W. Tyson, Victoria J. Orphan
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-020-72291-1
SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng
Cited by: 9
Author(s): Dan Zhang, Wei Li, Zhongjian Chen, Fang Wei, Yunlong Liu, Li‐Zhi Gao
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-020-75553-0
Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species
Cited by: 13
Author(s): Manosh Kumar Biswas, Mita Bagchi, Ujjal Kumar Nath, Dhiman Biswas, Sathishkumar Natarajan, Denison Michael Immanuel Jesse, Jong-In Park, Ill–Sup Nou
Software Mentions: 4
Published: over 3 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: about 10 years ago
10.7717/peerj.4535
Reference gene selection for qRT-PCR assays in<i>Stellera chamaejasme</i>subjected to abiotic stresses and hormone treatments based on transcriptome datasets
Cited by: 18
Author(s): Xin Liu, Hongwei Guan, Min Jae Song, Yànpíng Fù, Xiao Han, Lei Meng, Jingyu Ren, Bin Guo, Wei He, Yahui Wei
Software Mentions: 4
Published: about 6 years ago
10.1038/s41598-019-42865-9
Differences in resource use lead to coexistence of seed-transmitted microbial populations
Cited by: 15
Author(s): Gloria Torres-Cortés, Benjamin J. Garcia, Stéphane Compant, Samir Rezki, Piet Jones, Anne Préveaux, Martial Briand, Alain Roulet, Olivier Bouchez, Daniel Jacobson, Matthieu Barret
Software Mentions: 4
Published: about 5 years ago
10.3390/v11060484
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Cited by: 24
Author(s): René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John C. Anders, Antonis Chatzinotas
Software Mentions: 4
Published: almost 5 years ago
10.1038/s41598-018-26259-x
Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO
Cited by: 22
Author(s): Marie‐Alice Fraiture, Assia Saltykova, Stefan Hoffman, Raf Winand, Dieter Deforce, Kevin Vanneste, Sigrid C. J. De Keersmaecker
Software Mentions: 4
Published: almost 6 years ago
10.1038/s41598-017-14959-9
Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes
Cited by: 2
Author(s): Zhipu Luo, Alan Kelleher, Rabih Darwiche, Elissa M. Hudspeth, Oluwatosin Kudirat Shittu, Aparna Krishnavajhala, Roger Schneiter, Job E. López, Oluwatoyin A. Asojo
Software Mentions: 4
Published: over 6 years ago
10.1093/ve/vey007
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
Cited by: 51
Author(s): Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Nicholas J. Croucher, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle Gourlay, M Kate Grabowski, Barbara Gunsenheimer‐Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D. Kouyos, Oliver Laeyendecker, Kirsi Liitsola, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Marion Cornelissen, Paul Kellam, Peter Reiss, Christophe Fraser
Software Mentions: 4
Published: over 6 years ago
10.1186/s12957-021-02248-9
Potential role of chimeric genes in pathway-related gene co-expression modules
Cited by: 7
Author(s): Piaopiao Li, Yingxia Li, Lei Ma
Software Mentions: 4
Published: about 3 years ago
10.1038/s41598-019-39787-x
A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains
Cited by: 7
Author(s): Ivan Polsinelli, Luigimaria Borruso, Rosanna Caliandro, Luca Triboli, Alfonso Esposito, Stefano Benini
Software Mentions: 4
Published: about 5 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: about 14 years ago
10.1002/1878-0261.12692
DAPK3 participates in the mRNA processing of immediate early genes in chronic lymphocytic leukaemia
Cited by: 2
Author(s): Fraser Thomas, Katie Holmes, Sarah Kreuz, Peter Hillmen, Pascal Lefèvre
Software Mentions: 4
Published: about 4 years ago
10.1099/mgen.0.000108
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: about 7 years ago
10.3390/genes7040013
Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: about 8 years ago
10.1093/g3journal/jkab190
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes
Cited by: 3
Author(s): Jaclyn M. Noshay, Zhikai Liang, Peng Zhou, Peter A. Crisp, Alexandre P. Marand, Candice N. Hirsch, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 4
Published: almost 3 years ago
10.1002/1878-0261.12052
A genome-wide siRNA screen for regulators of tumor suppressor p53 activity in human non-small cell lung cancer cells identifies components of the RNA splicing machinery as targets for anticancer treatment
Cited by: 50
Author(s): Ellen Siebring-van Olst, Maxime Blijlevens, Renée X. de Menezes, Ida H. van der Meulen-Muileman, Egbert F. Smit, Victor W. van Beusechem
Software Mentions: 4
Published: about 7 years ago
10.3389/fpls.2016.00266
Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat
Cited by: 14
Author(s): Mariateresa Volpicella, Immacolata Fanizza, Claudia Leoni, Ágata Gadaleta, Domenica Nigro, B. Gattulli, Giacomo Mangini, Antonio Blanco, Luigi R. Ceci
Software Mentions: 3
Published: about 8 years ago
10.3389/fpls.2020.607651
Isolation of Four Microalgal Strains From the Lake Massaciuccoli: Screening of Common Pollutants Tolerance Pattern and Perspectives for Their Use in Biotechnological Applications
Cited by: 8
Author(s): Carolina Chiellini, Lorenzo Guglielminetti, Sabrina Sarrocco, Adriana Ciurli
Software Mentions: 3
Published: over 3 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: almost 5 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: over 16 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: over 3 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: over 6 years ago
10.1111/mec.15168
Dynamic virulence‐related regions of the plant pathogenic fungus <i>Verticillium dahliae</i> 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: almost 5 years ago
10.3389/fpls.2018.00217
Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut
Cited by: 70
Author(s): Feng Cui, Na Sui, Guangyou Duan, Yiyang Liu, Han Yan, Shanshan Liu, Shubo Wan, Guowei Li
Software Mentions: 3
Published: about 6 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: about 10 years ago
10.3389/fmicb.2020.01692
Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production
Cited by: 18
Author(s): Jonas De Roos, Marko Verce, Stefan Weckx, Luc De Vuyst
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpls.2019.01015
Detection of First Marker Trait Associations for Resistance Against Sclerotinia sclerotiorum in Brassica juncea–Erucastrum cardaminoides Introgression Lines
Cited by: 39
Author(s): Kusum Rana, Chhaya Atri, Javed Akhatar, Ramanjeet Kaur, Anna Goyal, Mohini Singh, Nitin Kumar, Anju Sharma, P. Sandhu, Gurpreet Kaur, Martin J. Barbetti, S. S. Banga
Software Mentions: 3
Published: almost 5 years ago
10.1534/g3.111.001834
Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (<i>Glycine max</i> (L.) Merr.) and Wild Soybean (<i>Glycine soja</i> 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: about 12 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: over 3 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: over 9 years ago
10.3389/fmicb.2017.00825
Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets
Cited by: 63
Author(s): Ting Yu, Cui Zhu, Shicheng Chen, Lei Gao, Hang Lv, Ruowei Feng, Qingfeng Zhu, Jianing Xu, Zhuang Chen, Zongyong Jiang
Software Mentions: 3
Published: about 7 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: about 3 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: over 4 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: over 4 years ago
10.3389/fmicb.2018.01272
Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis
Cited by: 8
Author(s): Jednipit Borthong, Ryosuke Omori, Chihiro Sugimoto, Orasa Suthienkul, Ryo Nakao, Kimihito Ito
Software Mentions: 3
Published: almost 6 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: over 6 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: 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: over 4 years ago
10.1111/1755-0998.12240
Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome <i>c</i> 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: about 10 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: almost 3 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: over 6 years ago
10.3389/fmicb.2021.642587
Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria
Cited by: 18
Author(s): Tessa E. Reid, Vanessa Nessner Kavamura, Maïder Abadie, Adriana Torres-Ballesteros, Mark Pawlett, Ian M. Clark, J. Arthur Harris, Tim H. Mauchline
Software Mentions: 3
Published: about 3 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: about 4 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: about 3 years ago
10.3389/fmicb.2021.635772
Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles
Cited by: 5
Author(s): Eugeni Belda, Boubacar Coulibaly, Tullu Bukhari, Karin Eiglmeier, Raymond Kone, Mamadou B. Coulibaly, Soumanaba Zongo, Megan Barry, Awa Gnémé, Wamdaogo Moussa Guelbéogo, Abdoul Habib Béavogui, Sékou F. Traorè, N’Falé Sagnon, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 3
Published: about 3 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: about 4 years ago
10.3389/fmicb.2021.707281
Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups
Cited by: 3
Author(s): Runmao Lin, Y. L. Xia, Yao Liu, Danhua Zhang, Xiang Xiao, Xianyu Niu, Linjia Jiang, Xiaolin Wang, Aiping Zheng
Software Mentions: 3
Published: over 2 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: about 8 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: almost 6 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: over 8 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: about 6 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: 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: almost 3 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 5 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: over 6 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: about 5 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 5 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: over 3 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: about 3 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: over 9 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: over 18 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: about 10 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: almost 4 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 6 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: about 4 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: over 5 years ago
10.1111/febs.14976
<i>Burkholderia pseudomallei</i> <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: almost 5 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 4 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: almost 8 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: about 15 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: over 2 years ago
10.1534/g3.116.031120
Genome-Wide Analysis of Polyadenylation Events in <i>Schmidtea mediterranea</i>
Cited by: 12
Author(s): Vairavan Lakshmanan, Dhiru Bansal, Jahnavi Kulkarni, Deepak Poduval, Srikar Krishna, Vidyanand Sasidharan, Praveen Anand, Aswin Sai Narain Seshasayee
Software Mentions: 3
Published: over 7 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: almost 17 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: over 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: almost 7 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: over 5 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: about 5 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: over 11 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 8 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: over 14 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 14 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: almost 6 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: about 9 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: almost 3 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: over 4 years ago