pypi: blast | Projects | Ecosyste.ms: Papers

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: over 10 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: about 5 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: almost 9 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: over 11 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: over 6 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: about 5 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: almost 10 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: about 5 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: almost 8 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: over 7 years ago

10.1038/sdata.2018.305

The sequence and de novo assembly of hog deer genome
Cited by: 7
Author(s): Wei Wang, Yan Huang, Shiyi Chen, Zhenzhen Li, Jun Yi, Lili Niu, Jia-Po Deng, Weigang Chen, Yunfeng Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xiaoxi Yu, Shuai Pang, Wanlong Huang, Yue Han, Guangjian Liu, Jianqiu Yu
Software Mentions: 4
Published: almost 7 years ago

10.1111/imb.12585

Developmental expression and evolution of hexamerin and haemocyanin from Folsomia candida (Collembola)
Cited by: 3
Author(s): Yangyang Liang, Wei Xie, Yigang Luan
Software Mentions: 4
Published: over 6 years ago

10.1038/srep23518

The chemosensory receptors of codling moth Cydia pomonella–expression in larvae and adults
Cited by: 46
Author(s): William B. Walker, Francisco Gonzalez, Stephen F. Garczynski, Peter Witzgall
Software Mentions: 4
Published: over 9 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 11 years ago

10.7717/peerj.4535

Reference gene selection for qRT-PCR assays inStellera chamaejasmesubjected 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: over 7 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: over 6 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: over 6 years ago

10.1093/gbe/evw262

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps
Cited by: 38
Author(s): Ben J. G. Sutherland, Thierry Gosselin, Éric Normandeau, Manuel Lamothe, Nathalie Isabel, Céline Audet, Louis Bernatchez
Software Mentions: 4
Published: almost 9 years ago

10.1080/21505594.2020.1768018

Transcriptional host–pathogen responses of Pseudogymnoascus destructans and three species of bats with white-nose syndrome
Cited by: 19
Author(s): Christina M. Davy, Michael E. Donaldson, Hana Banďouchová, Ana M. Breit, Nicole Dorville, Yvonne A. Dzal, Veronika Kováčová, Emma L. Kunkel, Natália Martínková, Kaleigh J. O. Norquay, James E. Paterson, Jan Zukal, Jiří Pikula, Craig K. R. Willis, Christopher J. Kyle
Software Mentions: 4
Published: over 5 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: over 4 years ago

10.1186/s13059-019-1785-1

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center
Cited by: 21
Author(s): Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus C. de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock, Nicholas R. Thomson
Software Mentions: 4
Published: about 6 years ago

10.5808/GI.2020.18.1.e6

Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
Cited by: 2
Author(s): Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, Erin L. Crowgey
Software Mentions: 4
Published: over 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: over 15 years ago

10.1186/gb-2013-14-12-r141

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
Cited by: 79
Author(s): Jin‐Hua Xiao, Zhen Yue, Ling-Yi Jia, Xinhua Yang, Lihua Niu, Zhuo Wang, Peng Zhang, Bao‐Fa Sun, Shunmin He, Zi Li, Tuanlin Xiong, Xintian Wen, Haifeng Gu, Bo Wang, John H. Werren, Robert W. Murphy, David A. Wheeler, Li‐Ming Niu, Guang-Chang Ma, Ting Tang, Sheng‐Nan Bian, Ningxin Wang, Caiqiong Yang, Nan Wang, Yanlong Fu, Wenzhu Li, Soojin V. Yi, Xingyu Yang, Qing Zhou, Changxin Lu, Chunyan Xu, Li He, Lili Yu, Ming Chen, Yawen Zheng, Shaowei Wang, Shuang Zhao, Yanhong Li, Yangyang Yu, Xiaoju Qian, Yuchen Cai, Lianle Bian, Shu Zhang, Junyi Wang, Ye Yin, Hui Xiao, Guan-Hong Wang, Hui Yu, Wei-Jian Wu, James M. Cook, Jun Wang, Dawei Huang
Software Mentions: 4
Published: almost 13 years ago

10.1186/gb-2013-14-2-r15

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Cited by: 217
Author(s): Stephen R. Fairclough, Zehua Chen, Eric M. Kramer, Qiandong Zeng, Sarah Young, Hugh M. Robertson, Emina Begović, Daniel J. Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B. Franz Lang, Brian J. Haas, Chad Nusbaum, Nicole King
Software Mentions: 4
Published: almost 13 years ago

10.3389/fmicb.2018.00593

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
Cited by: 51
Author(s): Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, M. L. Gullino, Marc W. Allard, E.J. Levin, D. Spadaro, Samir Droby
Software Mentions: 4
Published: over 7 years ago

10.3390/genes12070952

Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis
Cited by: 4
Author(s): Elizaveta Grigoreva, А.А. Ткаченко, Serafima Arkhimandritova, Aleksandar Beatovic, Pavel Ulianich, В. А. Волков, Dmitry Karzhaev, Cécile Ben, Laurent Gentzbittel, Elena Potokina
Software Mentions: 4
Published: over 4 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: over 8 years ago

10.3389/fmicb.2018.01657

Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains
Cited by: 29
Author(s): Hinda Doucouré, Pérez-Quintero Al, Ganna Reshetnyak, C. Tekete, Florence Auguy, Emilie Thomas, Ralf Koebnik, Boris Szurek, Ousmane Koïta, Verdier, Sébastien Cunnac
Software Mentions: 4
Published: about 7 years ago

10.1186/gb-2008-9-1-r7

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Cited by: 2,092
Author(s): Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan Allen, Joshua Orvis, Owen White, C. Robin Buell, Jennifer Wortman
Software Mentions: 4
Published: almost 18 years ago

10.1186/s13059-016-1062-5

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types
Cited by: 17
Author(s): Brad Nelms, Levi Waldron, Luis Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Software Mentions: 4
Published: about 9 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 4 years ago

10.3389/fmicb.2018.01635

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Cited by: 49
Author(s): Marie E. Kroeger, Tom O. Delmont, A. Murat Eren, Kyle Meyer, Jiarong Guo, Kiran Yasmin Khan, Jorge L. Mazza Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clóvis Daniel Borges, James M. Tiedje, Siu Mui Tsai, Klaus Nüsslein
Software Mentions: 3
Published: over 7 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: over 6 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 18 years ago

10.3389/fmicb.2014.00531

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships
Cited by: 58
Author(s): Maggie C. Y. Lau, Connor Cameron, Cara Magnabosco, C. Titus Brown, Faye Schilkey, Sharon L. Grim, Sarah Hendrickson, Michael J. Pullin, Barbara Sherwood Lollar, Esta van Heerden, Thomas L. Kieft, Tullis C. Onstott
Software Mentions: 3
Published: about 11 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 8 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: over 6 years ago

10.3389/fimmu.2019.00120

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr
Cited by: 14
Author(s): Laura M. Braden, S. K. Whyte, Alyson Brown, Carter Van Iderstine, Corinne Letendre, David B. Groman, J. Lewis, Sara L. Purcell, Tiago S. Hori, Mark D. Fast
Software Mentions: 3
Published: over 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: over 11 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 4 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 4 years ago

10.3390/microorganisms8101621

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis
Cited by: 16
Author(s): Guillaume Dubrulle, Adeline Picot, Stéphanie Madec, Matthieu Le Corre, Audrey Pawtowski, Riccardo Baroncelli, Michel Zivy, Thierry Balliau, Gaétan Le Floch, Flora Pensec
Software Mentions: 3
Published: about 5 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 11 years ago

10.3389/fcimb.2020.00041

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

10.3390/microorganisms7100444

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes
Cited by: 40
Author(s): Dipti Deo, Dimple Davray, Ram Kulkarni
Software Mentions: 3
Published: about 6 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 6 years ago

10.3389/fgene.2018.00371

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

10.1002/2211-5463.12084

Age‐dependent transcriptional and epigenomic responses to light exposure in the honey bee brain
Cited by: 15
Author(s): Nils B. Becker, Robert Kucharski, Wolfgang Rößler, Ryszard Maleszka
Software Mentions: 3
Published: over 9 years ago

10.1111/j.1742-4658.2009.06893.x

Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms
Cited by: 58
Author(s): Emmanuel Debrand, Yasmine El Jai, Lorraine Spence, Neil Bate, Uta Praekelt, Catrin Pritchard, Susan J. Monkley, David R. Critchley
Software Mentions: 3
Published: over 16 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 6 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 11 years ago

10.1111/febs.14976

Burkholderia pseudomallei <scp>d</scp> ‐alanine‐ <scp>d</scp> ‐alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target
Cited by: 3
Author(s): L. Diaz-Saez, Leah S. Torrie, Stuart P. McElroy, David W. Gray, William N. Hunter
Software Mentions: 3
Published: over 6 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 4 years ago

10.3389/fmicb.2021.707281

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups
Cited by: 3
Author(s): Runmao Lin, Y. L. Xia, Yao Liu, Danhua Zhang, Xiang Xiao, Xianyu Niu, Linjia Jiang, Xiaolin Wang, Aiping Zheng
Software Mentions: 3
Published: about 4 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 5 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 4 years ago

10.1111/j.1462-2920.2008.01706.x

probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity
Cited by: 175
Author(s): Alexander Loy, Roland Arnold, Patrick Tischler, Thomas Rattei, Michael Wagner, Matthias Horn
Software Mentions: 3
Published: about 17 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 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: over 4 years ago

10.1099/mgen.0.000352

Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones
Cited by: 30
Author(s): Catherine Ludden, Arun Gonzales Decano, Dorota Jamrozy, Derek Pickard, Dearbháile Morris, Julian Parkhill, Sharon J. Peacock, Martin Cormican, Tim Downing
Software Mentions: 3
Published: over 5 years ago

10.1111/1462-2920.14800

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family
Cited by: 4
Author(s): Catherine Badel, Gaël Erauso, Annika L. Gomez, Ryan Catchpole, Mathieu Gonnet, Jacques Oberto, Patrick Forterre, Violette Da Cunha
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.3798

Transcriptome response of Atlantic salmon (Salmo salar) to competition with ecologically similar non-native species
Cited by: 8
Author(s): Xiaoping He, Aimee Lee S. Houde, Bryan D. Neff, Daniel D. Heath
Software Mentions: 3
Published: almost 8 years ago

10.15252/emmm.201911210

Glufosinate constrains synchronous and metachronous metastasis by promoting anti‐tumor macrophages
Cited by: 27
Author(s): Alessio Menga, Marina Serra, Simona Todisco, Carla Riera-Domingo, Ummi Ammarah, Manuel Ehling, Erika M. Palmieri, Maria Antonietta Di Noia, Rosanna Gissi, Maria Favia, Ciro Leonardo Pierri, Paolo E. Porporato, Alessandra Castegna, Massimiliano Mazzone
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.5991

New genome assembly of the barn owl (Tyto alba alba)
Cited by: 8
Author(s): Anne‐Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid‐Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M. San‐Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xénarios, Alexandre Roulin, Jérôme Goudet
Software Mentions: 3
Published: over 5 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 4 years ago

10.3389/fcimb.2020.00374

TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon
Cited by: 36
Author(s): José M. C. Ribeiro, Ben J. Mans
Software Mentions: 3
Published: over 5 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 7 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 8 years ago

10.1002/ece3.6749

The insertion of a mitochondrial selfish element into the nuclear genome and its consequences
Cited by: 2
Author(s): Julien Dutheil, Karin Münch, Klaas Schotanus, Eva H. Stukenbrock, Regine Kahmann
Software Mentions: 3
Published: about 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: almost 7 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 8 years ago

10.1016/j.csbj.2016.09.004

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations
Cited by: 21
Author(s): Hervé Seligmann
Software Mentions: 3
Published: almost 10 years ago

10.1111/1462-2920.13203

Molecular genetic and physical analysis of gas vesicles in buoyant enterobacteria
Cited by: 35
Author(s): Yosuke Tashiro, Rita E. Monson, Joshua P. Ramsay, George P. C. Salmond
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: almost 20 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 4 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 11 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: almost 8 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 10 years ago

10.1371/journal.pone.0123911

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera)
Cited by: 98
Author(s): Karen M. Kapheim, Vikyath D. Rao, Carl J. Yeoman, Brenda A. Wilson, Bryan A. White, Nigel Goldenfeld, Gene E. Robinson
Software Mentions: 3
Published: over 10 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: 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 12 years ago

10.1371/journal.pone.0226056

Activation of GPR56, a novel adhesion GPCR, is necessary for nuclear androgen receptor signaling in prostate cells
Cited by: 10
Author(s): Julie Pratibha Singh, Manisha Dagar, Gunjan Dagar, Sudhir Kumar, Sudhir Rawal, Ravi Datta Sharma, Rakesh K. Tyagi, Gargi Bagchi
Software Mentions: 3
Published: about 5 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 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: almost 8 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 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 18 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 8 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: about 7 years ago

10.1371/journal.pone.0212514

Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification
Cited by: 11
Author(s): Dengqun Liao, Juan Zhu, Zhang Menghuan, Peng Sun, Jianhe Wei, Jianjun Qi
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: about 13 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 9 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 16 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: almost 16 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 7 years ago

10.1371/journal.pone.0125964

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species
Cited by: 34
Author(s): S. P. Singh, Suresh Chand, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0053779

Mining of Novel Thermo-Stable Cellulolytic Genes from a Thermophilic Cellulose-Degrading Consortium by Metagenomics
Cited by: 44
Author(s): Yu Xia, Feng Ju, Hhp Fang, Tong Zhang
Software Mentions: 3
Published: almost 13 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 6 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 9 years ago

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Papers Mentioning blast 1,819