pypi: blast | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000207

Taxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia
Cited by: 20
Author(s): Prabhu B. Patil, Sanjeet Kumar, Samriti Midha, Vikas Gautam
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes1010070

Next Generation Sequencing of miRNAs – Strategies, Resources and Methods
Cited by: 111
Author(s): Susanne Motameny, Stefanie Wolters, Peter Nürnberg, Björn Schumacher
Software Mentions: 5
Published: almost 14 years ago

10.3389/fmicb.2018.03243

Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil
Cited by: 22
Author(s): Magdalena Wutkowska, Anna Vader, Sunil Mundra, Elisabeth J. Cooper, Pernille Bronken Eidesen
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-966

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Cited by: 29
Author(s): Johannes A. Hofberger, Beifei Zhou, Haibao Tang, Jonathan D. G. Jones, M. Eric Schranz
Software Mentions: 5
Published: over 9 years ago

10.3390/genes11040415

Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep
Cited by: 14
Author(s): Kisun Pokharel, Jaana Peippo, Melak Weldenegodguad, Mervi Honkatukia, Menghua Li, Juha Kantanen
Software Mentions: 5
Published: about 4 years ago

10.3389/fpls.2018.01728

Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions
Cited by: 37
Author(s): Heike Lehnert, Albrecht Serfling, Wolfgang Friedt, Frank Ordon
Software Mentions: 5
Published: over 5 years ago

10.3390/cells9122566

Comparative Transcriptomics Analyses in Livers of Mice, Humans, and Humanized Mice Define Human-Specific Gene Networks
Cited by: 13
Author(s): Cuiping Jiang, Ping Li, Xiangbo Ruan, Yonghe Ma, Kenji Kawai, Hiroshi Suemizu, Haiming Cao
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-021-07517-1

Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
Cited by: 1
Author(s): Valérie Ducret, Adam Richards, Mathieu Videlier, Thibault Scalvenzi, Karen Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet, Anthony Herrel
Software Mentions: 5
Published: about 3 years ago

10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: over 9 years ago

10.1111/jbi.12471

Speciation in the dark: diversification and biogeography of the deep‐sea gastropod genusScaphanderin the Atlantic Ocean
Cited by: 26
Author(s): Mari Heggernes Eilertsen, Manuel António E. Malaquias
Software Mentions: 5
Published: over 9 years ago

10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes
Cited by: 11
Author(s): Carol L. Ecale Zhou, Jeffrey A. Kimbrel, Robert A. Edwards, Katelyn McNair, Brian Souza, Stephanie Malfatti
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0159093

Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: almost 3 years ago

10.1186/s40168-017-0322-2

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments
Cited by: 147
Author(s): Nina Dombrowski, Kiley W. Seitz, Andreas Teske, Brett J. Baker
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-019-5960-2

Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT
Cited by: 19
Author(s): Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 5
Published: almost 5 years ago

10.1099/mgen.0.000269

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198
Cited by: 57
Author(s): Jane Hawkey, Simon Le Hello, Benoît Doublet, Sophie A. Granier, René S. Hendriksen, W. Florian Fricke, Pieter‐Jan Ceyssens, Camille Gomart, Helen Billman‐Jacobe, Kathryn E. Holt, François‐Xavier Weill
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0248967

The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease
Cited by: 13
Author(s): Einar Marius Hjellestad Martinsen, Tomas Mikal Eagan, Elise Orvedal Leiten, Ingvild Haaland, Gunnar Reksten Husebø, Kristel Svalland Knudsen, Christine Drengenes, Walter Sanseverino, Andreu Paytuví-Gallart, Rune Nielsen
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-017-1299-7

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Cited by: 235
Author(s): Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R. Colwell, Gail Rosen, Christopher E. Mason
Software Mentions: 5
Published: over 6 years ago

10.1111/1751-7915.13519

Raman–deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota
Cited by: 44
Author(s): Yi Wang, Jiabao Xu, Lingchao Kong, Tang Liu, Lingbo Yi, Hongjuan Wang, Wei E. Huang, Kewei Chen
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0005693

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas
Cited by: 53
Author(s): Naomi L. Forrester, Joel O. Wertheim, Vivian G. Dugan, Albert J. Auguste, David L. Lin, Alexandra Adams, Rubing Chen, Rodion Gorchakov, Grace Leal, José G. Estrada-Franco, Jyotsna Pandya, Rebecca Halpin, Kumar Hari, Ravi Jain, Timothy B. Stockwell, Suman Das, David E. Wentworth, Martin D. Smith, Sergei L. Kosakovsky Pond, Scott C. Weaver
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2164-15-946

Conservation analysis of the CydX protein yields insights into small protein identification and evolution
Cited by: 35
Author(s): Rondine J. Allen, Evan P. Brenner, Caitlin E. VanOrsdel, Jessica J. Hobson, David J. Hearn, Matthew R. Hemm
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0176596

Evolution of microRNA in primates
Cited by: 31
Author(s): Jennifer C. McCreight, Sean E. Schneider, Damien B. Wilburn, Willie J. Swanson
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0028634

Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome
Cited by: 52
Author(s): Nicholas R. Polato, J. Cristobal Vera, Iliana B. Baums
Software Mentions: 5
Published: over 12 years ago

10.3389/fpls.2019.00223

Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage
Cited by: 56
Author(s): Stefan Petrasch, Christian J. Silva, Saskia D Mesquida-Pesci, Karina Gallegos, Casper van den Abeele, Victor Papin, Francisco Javier Fernández-Acero, Steven J. Knapp, Bárbara Blanco-Ulate
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0169087

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Cited by: 74
Author(s): Axel Künstner, Maria Hoffmann, Bonnie A. Fraser, Verena A. Kottler, Eshita Sharma, Detlef Weigel, Christine Dreyer
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2021.656334

A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon
Cited by: 15
Author(s): Sigmund Ramberg, Bjørn Høyheim, Tone-Kari K Østbye, Rune Andreassen
Software Mentions: 5
Published: about 3 years ago

10.1128/mBio.02500-19

A Conserved Streptococcal Virulence Regulator Controls the Expression of a Distinct Class of M-Like Proteins
Cited by: 7
Author(s): Jonathan D. D’Gama, Zhe Ma, Hailong Zhang, Li Xu, Hongjie Fan, Ellen Ruth A. Morris, Noah D. Cohen, Colette Cywes‐Bentley, Gerald B. Pier, Matthew K. Waldor
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0195461

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome
Cited by: 80
Author(s): Kris A. Christensen, Jong S. Leong, Dionne Sakhrani, Carlo A. Biagi, David R. Minkley, Ruth E. Withler, Eric B. Rondeau, Ben F. Koop, Robert H. Devlin
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2021.625019

Novel Non-coding RNA Analysis in Multiple Myeloma Identified Through High-Throughput Sequencing
Cited by: 5
Author(s): Minqiu Lu, Yin Wu, Wen Gao, Ying Tian, Guorong Wang, Aijun Liu, Wen-Ming Chen
Software Mentions: 5
Published: almost 3 years ago

10.1111/eva.12638

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale
Cited by: 31
Author(s): Alicia Dalongeville, Marco Andrello, David Mouillot, Stéphane Lobreaux, Marie‐Josée Fortin, Frida Ben Rais Lasram, Jonathan Belmaker, Delphine Rocklin, Stéphanie Manel
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-24126-3

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species
Cited by: 31
Author(s): Barbora Pafčo, Dagmar Čížková, Jakub Kreisinger, Hideo Hasegawa, Peter Vallo, Kathryn Shutt, Angelique Todd, Klára J. Petrželková, David Modrý
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-61216-7

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm
Cited by: 72
Author(s): Simone Scalabrin, Lucile Toniutti, Gabriele Di Gaspero, Davide Scaglione, Gabriele Magris, Michele Vidotto, Sara Pinosio, Frederica Cattonaro, Federica Magni, Irena Jurman, Mario Cerutti, F. S. Liverani, Luciano Navarini, Lorenzo Del Terra, Gloria Pellegrino, Manuela Rosanna Ruosi, Nicola Vitulo, Giorgio Valle, Alberto Pallavicini, G. Graziosi, Patricia E. Klein, Nolan Bentley, Seth C. Murray, William Solano, Amin Al Hakimi, Timothy Schilling, Christophe Montagnon, Michèle Morgante, Benoît Bertrand
Software Mentions: 5
Published: about 4 years ago

10.1111/eva.12189

Fine‐scale genetic correlates to condition and migration in a wild cervid
Cited by: 21
Author(s): Joseph M. Northrup, Aaron B. A. Shafer, Charles R. Anderson, David W. Coltman, George Wittemyer
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-021-98907-8

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination
Cited by: 12
Author(s): Heqin Li, Haiwang Yue, Jiping Xie, Junzhou Bu, Li Li, Xueying Xin, Yanming Zhao, Haiyan Zhang, Li Yang, Jianhua Wang, Xuwen Jiang
Software Mentions: 4
Published: over 2 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/s41598-020-75553-0

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

10.1128/mSphere.01255-20

The Majority of Typhoid Toxin-Positive Salmonella 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

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: about 8 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

10.3389/fmicb.2021.675048

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments
Cited by: 6
Author(s): Zhongdong Huang, Shiqing Mo, Lifei Yan, Xiaomei Wei, Yangze Huang, Lizhen Zhang, Shuhui Zhang, Jianzong Liu, Qing Xiao, Hong Lin, Yu Guo
Software Mentions: 4
Published: almost 3 years ago

10.3389/fmicb.2017.00050

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird
Cited by: 52
Author(s): Jakub Kreisinger, Lucie Kropáčková, Adéla Petrželková, Marie Kotasová Adámková, Oldřich Tomášek, Jean‐François Martin, Romana Michálková, Tomáš Albrecht
Software Mentions: 4
Published: over 7 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

10.1038/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

10.3389/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: almost 6 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: about 6 years ago

10.1111/eva.12987

Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?
Cited by: 24
Author(s): Ella Bowles, Kia Marin, Stephanie Mogensen, Pamela MacLeod, Dylan J. Fraser
Software Mentions: 4
Published: almost 4 years ago

10.1002/2211-5463.12705

Analysis of Bn <scp>MTL</scp> , a novel metallothionein‐like protein in the bast fiber crop Ramie ( Boehmeria nivea )
Cited by: 3
Author(s): Gang Gao, Jikang Chen, Ping Chen, Kunmei Chen, Aminu Shehu Abubakar, Chang Yeon Yu, Aiguo Zhu
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2016.01768

Life without dUTPase
Cited by: 20
Author(s): Csaba Kerepesi, J. Szabó, Veronika Papp‐Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G. Vértessy
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0255076

A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction
Cited by: 9
Author(s): Teng Ruei Chen, Sheng Hung Juan, Yu Huang, Lianfang Tian, Wei-Cheng Lo
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0242382

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand
Cited by: 0
Author(s): Arin Ngamniyom
Software Mentions: 4
Published: over 3 years ago

10.3389/fcimb.2018.00361

Comparative Analysis of the Microbial Profiles in Supragingival Plaque Samples Obtained From Twins With Discordant Caries Phenotypes and Their Mothers
Cited by: 11
Author(s): Yuqiao Zheng, Meng Zhang, Jin Li, Yuhong Li, Fei Teng, Han Jiang, Minquan Du
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0028819

Gentle Masking of Low-Complexity Sequences Improves Homology Search
Cited by: 27
Author(s): Martin C. Frith
Software Mentions: 4
Published: over 12 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

10.1038/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/s41598-020-72291-1

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

10.1111/1751-7915.13871

Strain diversity of plant‐associated Lactiplantibacillus plantarum
Cited by: 15
Author(s): Alice Yu, Elissa A. Goldman, Jason T. Brooks, Benjamin L. Golomb, Irene S. Yim, Velitchka Gotcheva, Angel Angelov, Eun Bae Kim, Maria L. Marco
Software Mentions: 4
Published: almost 3 years ago

10.1111/1751-7915.12337

Dynamic changes in microbiota and mycobiota during spontaneous ‘<scp>V</scp>ino <scp>S</scp>anto <scp>T</scp>rentino’ fermentation
Cited by: 41
Author(s): Irene Stefanini, Davide Albanese, A. Cavazza, Elena Franciosi, Carlotta De Filippo, Claudio Donati, Duccio Cavalieri
Software Mentions: 4
Published: over 8 years ago

10.1111/1751-7915.12190

The <scp>R</scp>sm regulon of plant growth‐promoting <scp>P</scp>seudomonas fluorescens <scp>SS</scp>101: role of small <scp>RNA</scp>s in regulation of lipopeptide biosynthesis
Cited by: 17
Author(s): Song Cui, Menno van der Voort, Judith E. van de Mortel, Karl A. Hassan, Liam D. H. Elbourne, Ian T. Paulsen, Joyce E. Loper, Jos M. Raaijmakers
Software Mentions: 4
Published: over 9 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

10.1371/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

10.1186/s12864-017-3745-z

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model
Cited by: 20
Author(s): Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon‐Mom, Perry D. Moerland, Pernette J. Verschure
Software Mentions: 4
Published: about 7 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

10.7717/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: about 6 years ago

10.1186/s12918-018-0566-x

KF-finder: identification of key factors from host-microbial networks in cervical cancer
Cited by: 15
Author(s): Jialu Hu, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: over 6 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

10.7554/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/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

10.1155/2020/3275315

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

10.3390/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

10.1093/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

10.1099/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

10.1186/1471-2164-15-549

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species
Cited by: 239
Author(s): Cene Gostinčar, Robin A. Ohm, Tina Kogej, Silva Sonjak, Monika Turk, Janja Zajc, Polona Zalar, Martín Grube, Hui Sun, James Han, Aarti Sharma, Jennifer Chiniquy, Chew Yee Ngan, Anna Lipzen, Kerrie Barry, Igor V. Grigoriev, Nina Gunde‐Cimerman
Software Mentions: 4
Published: over 10 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

10.1186/1471-2105-12-447

OmniMapFree: A unified tool to visualise and explore sequenced genomes
Cited by: 12
Author(s): J. F. Antoniw, Andrew M Beacham, Tyler Baldwin, Martin Urban, J. J. Rudd, K. E. Hammond‐Kosack
Software Mentions: 4
Published: over 12 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: almost 4 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

10.1186/1471-2164-11-432

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

10.1111/mec.15522

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units
Cited by: 26
Author(s): Rebecca S. Taylor, Micheline Manseau, Rebekah L. Horn, Sonesinh Keobouasone, G. Brian Golding, Paul J. Wilson
Software Mentions: 4
Published: almost 4 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: about 5 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: over 5 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: over 4 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: over 7 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: over 11 years ago

10.1186/s13100-019-0166-3

Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew
Cited by: 17
Author(s): Sonja M. Dunemann, James D. Wasmuth
Software Mentions: 4
Published: almost 5 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: over 7 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: about 4 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: about 8 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: about 4 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: almost 3 years ago

10.1099/mgen.0.000059

Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK
Cited by: 23
Author(s): Ali Al‐Shahib, Anthony Underwood, Baharak Afshar, Claire E. Turner, Theresa Lamagni, Shiranee Sriskandan, Androulla Efstratiou
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-020-07260-z

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum
Cited by: 18
Author(s): Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen, Wuwei Ye
Software Mentions: 4
Published: over 3 years ago

10.1099/mic.0.034538-0

Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2
Cited by: 143
Author(s): Sharon L. Kendall, Philippa Burgess, Ricardo Balhana, Mike Withers, Annemieke Ten Bokum, J.S. Lott, Chen Gao, Iria Uhia-Castro, Neil G. Stoker
Software Mentions: 4
Published: about 14 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: over 16 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

10.1186/1471-2164-15-218

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

Projects: pypi: blast

Papers Mentioning blast 1,819