pypi: blast | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009065

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago

10.3390/ijms21218148

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: about 4 years ago

10.1016/j.devcel.2018.11.009

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo
Cited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 6 years ago

10.1099/mgen.0.000165

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection
Cited by: 45
Author(s): Jane Hawkey, David B. Ascher, Louise M. Judd, Ryan R. Wick, Xenia Kostoulias, Heather Cleland, Denis Spelman, Alex Padiglione, Anton Y. Peleg, Kathryn E. Holt
Software Mentions: 11
Published: over 6 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: almost 5 years ago

10.1186/1471-2164-13-462

NG6: Integrated next generation sequencing storage and processing environment
Cited by: 54
Author(s): Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas, Christophe Klopp
Software Mentions: 10
Published: almost 13 years ago

10.1186/s12864-021-07493-6

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Cited by: 19
Author(s): Richard Edwards, Matthew A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina D. Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanović, Robert A. Zammit, E Aiden, Wesley C. Warren, J. William O. Ballard
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-021-07742-8

Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
Cited by: 5
Author(s): Heidi Kaech, Alice B. Dennis, Christoph Vorburger
Software Mentions: 10
Published: over 3 years ago

10.1093/gigascience/giz146

Systematic processing of ribosomal RNA gene amplicon sequencing data
Cited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: almost 5 years ago

10.1111/mec.15179

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem
Cited by: 25
Author(s): Elias Broman, Caroline Raymond, Christian Sommer, Jonas S. Gunnarsson, Simon Creer, Francisco J. A. Nascimento
Software Mentions: 10
Published: over 5 years ago

10.1099/mgen.0.000511

Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Cited by: 12
Author(s): Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Iréna Kukavica-Ibrulj, Nicholas P. Tucker, D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter M. Hawkey, Kevin W Southern, Martin Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley
Software Mentions: 9
Published: over 3 years ago

10.1038/s42003-021-01948-y

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Cited by: 9
Author(s): Chrats Melkonian, Lucas Fillinger, Siavash Atashgahi, Ulisses Nunes da Rocha, Eric Kuiper, Brett G. Olivier, Martin Braster, Willi Gottstein, Rick Helmus, John R. Parsons, Hauke Smidt, Marcelle van der Waals, Jan Gerritse, Bernd W. Brandt, Wilfred F. M. Röling, Douwe Molenaar, Rob J.M. van Spanning
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.69249

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
Cited by: 38
Author(s): Ursula Oggenfuss, Thomas Badet, Thomas Wicker, Fanny E. Hartmann, Navreet Singh, Leen Nanchira Abraham, Petteri Karisto, Tiziana Vonlanthen, Christopher C. Mundt, Bruce A. McDonald, Daniel Croll
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: over 3 years ago

10.1111/1755-0998.13266

Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs
Cited by: 11
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Zhengfei Wang, Yandong Ren, Huayun Guo, Tingting Qi, Yue‐Tian Li, Huabin Zhang, Senhao Jiang, Baoming Ge, Fujun Xuan, Yue Sun, Shusheng She, Tin Yam Chan, Zhongli Sha, Hui Jiang, Haorong Li, Wei Jiang, Yanli Qin, Kun Wang, Qiang Qiu, Wen Wang, Xinzheng Li, Ngan Kee Ng, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 9
Published: about 4 years ago

10.1186/s12859-020-03667-3

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
Cited by: 49
Author(s): Yi Yue, Hao Huang, Qi Zhao, Huimin Dou, Xinyi Liu, Tian-Fei Han, Yue Chen, Xiangjun Song, Youhua Zhang, Jing Tu
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0152747

The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr
Cited by: 32
Author(s): Jürgen Behr, Andreas Geißler, Jonas Schmid, Anja Zehe, Rudi F. Vogel
Software Mentions: 9
Published: over 8 years ago

10.1128/mBio.01527-20

A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates
Cited by: 11
Author(s): Nathan B. Pincus, Egon A. Ozer, Jonathan P. Allen, M. Nguyen, James J. Davis, Deborah R. Winter, Chih Hsien Chuang, Cheng-Hsun Chiu, Laura Zamorano, Antonio Oliver, Alan R. Hauser
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-017-17704-4

High STAP1 expression in DUX4-rearranged cases is not suitable as therapeutic target in pediatric B-cell precursor acute lymphoblastic leukemia
Cited by: 10
Author(s): Elisabeth M. P. Steeghs, Marjolein Bakker, Alex Q. Hoogkamer, Judith M. Boer, Quirine J. Hartman, Femke Stalpers, Gabriele Escherich, Valérie de Haas, Hester A. de Groot-Kruseman, Rob Pieters, Monique L. den Boer
Software Mentions: 9
Published: almost 7 years ago

10.3389/fpls.2018.01625

Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
Cited by: 9
Author(s): Shirin Akhter, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, Jens F. Sundström
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-019-40949-0

Extensive conservation of the proneuropeptide and peptide prohormone complement in mollusks
Cited by: 17
Author(s): André Luiz de Oliveira, Andrew Calcino, Andreas Wanninger
Software Mentions: 8
Published: over 5 years ago

10.3390/biom10010026

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors
Cited by: 12
Author(s): Guillermı́n Agüero-Chapin, Deborah Galpert Cañizares, Reinaldo Molina Ruiz, Evys Ancede-Gallardo, Gisselle Pérez-Machado, G Riva, Agostinho Antunes
Software Mentions: 8
Published: almost 5 years ago

10.1093/molbev/msaa135

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Cited by: 25
Author(s): Jaelle C. Brealey, Henrique G. Leitão, Tom van der Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski
Software Mentions: 8
Published: over 4 years ago

10.1099/mgen.0.000627

Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia
Cited by: 8
Author(s): Ido Bar, Prabhakaran Thanjavur Sambasivam, Jenny Davidson, Lina M Farfan-Caceres, Robert C. Lee, Kristy Hobson, Kevin Moore, R Ford
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.36495

Firefly genomes illuminate parallel origins of bioluminescence in beetles
Cited by: 95
Author(s): Timothy R. Fallon, Sarah E. Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J. Martin, Adam J. Bewick, Megan G Behringer, Humberto Julio Debat, Isaac Wong, John C. Day, Anton Suvorov, Christian J. Silva, Kathrin F. Stanger‐Hall, David W. Hall, Robert J. Schmitz, David R. Nelson, Sara M. Lewis, Shuji Shigenobu, Seth Bybee, Amanda M. Larracuente, Yuichi Oba, Jing‐Ke Weng
Software Mentions: 8
Published: about 6 years ago

10.3389/fgene.2019.00853

SeqDeχ: A Sequence Deconvolution Tool for Genome Separation of Endosymbionts From Mixed Sequencing Samples
Cited by: 0
Author(s): Alice Chiodi, Francesco Comandatore, Davide Sassera, Giulio Petroni, Claudio Bandi, Matteo Brilli
Software Mentions: 8
Published: about 5 years ago

10.1186/s13059-021-02427-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Cited by: 56
Author(s): Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Vallès-Colomer, Willem M. de Vos, Nicola Segata
Software Mentions: 7
Published: over 3 years ago

10.1111/mec.15160

Impacts of long‐term elevated atmospheric CO2 concentrations on communities of arbuscular mycorrhizal fungi
Cited by: 19
Author(s): Irena Maček, Dave R. Clark, Nataša Šibanc, Gerald M. Moser, Dominik Vodnik, Christoph Müller, Alex J. Dumbrell
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-019-6415-5

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex
Cited by: 19
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Michael E. Pfrender, James Brown, John K. Colbourne, Leda Mirbahai
Software Mentions: 7
Published: almost 5 years ago

10.1099/mgen.0.000303

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'
Cited by: 5
Author(s): Tegan M. Harris, Erin P. Price, Derek S. Sarovich, Niels Nørskov‐Lauritsen, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12870-018-1429-8

Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum
Cited by: 10
Author(s): Yihan Wang, Weimei Jiang, Wenqing Ye, Chengxin Fu, Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis, Ying‐Xiong Qiu
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-019-1768-2

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes
Cited by: 60
Author(s): Geoffrey M. Attardo, Adly M. M. Abd-Alla, Álvaro Acosta-Serrano, James Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jo Caers, Guy Caljon, Mikkel Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson, Michael J. Lehane, Vasileios Panagiotis Lenis, Ernesto Lowy-Gallego, Rosaline W. Macharia, Anna R. Malacrida, Heather G. Marco, Daniel Masiga, G. Maslen, Irina Matetovici, Richard P Meisel, Irene K. Meki, Veronika Michalková, Wolfgang J. Miller, Patrick Minx, Paul O. Mireji, Lino Ometto, Andrew G. Parker, Rita V. M. Rio, Clair Rose, Andrew J. Rosendale, Omar Rota‐Stabelli, Grazia Savini, Liliane Schoofs, Francesca Scolari, Martin Swain, Peter Takáč, Chad Tomlinson, George Tsiamis, Jan Van Den Abbeele, Aurélien Vigneron, Jingwen Wang, Wesley C. Warren, Robert M. Waterhouse, Matthew T. Weirauch, Brian L. Weiss, Richard K. Wilson, Xin Zhao, Serap Aksoy
Software Mentions: 7
Published: about 5 years ago

10.3389/fcimb.2020.00131

Dysbiosis in Peripheral Blood Mononuclear Cell Virome Associated With Systemic Lupus Erythematosus
Cited by: 4
Author(s): Gangqiang Guo, Lele Ye, Xinyu Shi, Kejing Yan, Jingjing Huang, Kangming Lin, Dong Xing, Sisi Ye, Yuqing Wu, Baoqing Li, Chaosheng Chen, Xiangyang Xue, Huidi Zhang
Software Mentions: 7
Published: over 4 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: over 8 years ago

10.1099/mgen.0.000244

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges
Cited by: 10
Author(s): Lauren Brooks, Mo Kaze, Mark Sistrom
Software Mentions: 7
Published: almost 6 years ago

10.1111/tpj.14349

The genome of cowpea (Vigna unguiculata [L.] Walp.)
Cited by: 215
Author(s): Stefano Lonardi, María Muñoz‐Amatriaín, Qihua Liang, Shengqiang Shu, Steve Wanamaker, Sassoum Lo, Jaakko Tanskanen, Alan H. Schulman, Tingting Zhu, Ming‐Cheng Luo, Hind Alhakami, Rachid Ounit, Abid Hasan, Jérôme Verdier, Philip A. Roberts, Jansen Rodrigo Pereira Santos, Arsenio Ndeve, Jaroslav Doležel, Jan Vrána, S. Hokin, Andrew Farmer, Steven B. Cannon, Timothy J. Close
Software Mentions: 7
Published: over 5 years ago

10.1099/mgen.0.000162

Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages
Cited by: 17
Author(s): Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H. Aliyu, Nazreen F. Hadjirin, Mark A. Holmes, Estée Török, Nicholas Brown, Julian Parkhill, Sharon J. Peacock
Software Mentions: 7
Published: over 6 years ago

10.1128/mSystems.00264-19

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex
Cited by: 46
Author(s): Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0239381

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses
Cited by: 8
Author(s): Nafis Ul Alam, Umar Faruq Chowdhury
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0083984

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes
Cited by: 34
Author(s): Timothy B. Sackton, John H. Werren, Andrew G. Clark
Software Mentions: 7
Published: almost 11 years ago

10.1038/s41598-018-19607-4

Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations
Cited by: 26
Author(s): Luke Braidwood, Diego F. Quito-Avila, Darlene Cabanas, Alberto Bressan, Anne Wangai, David C. Baulcombe
Software Mentions: 7
Published: almost 7 years ago

10.3389/fpls.2014.00708

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Cited by: 19
Author(s): Deblina Patra, Mario Fasold, David Langenberger, Gerhard Steger, Ivo Große, Peter F. Stadler
Software Mentions: 7
Published: almost 10 years ago

10.3390/genes11040428

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks
Cited by: 9
Author(s): Qiao Wen Tan, Wooi-Boon Goh, Marek Mutwil
Software Mentions: 6
Published: over 4 years ago

10.3390/genes11121500

Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis
Cited by: 7
Author(s): Panqiao Wang, Xiaqing Yu, Zhanguo Zhu, Yufei Zhai, Qinzheng Zhao, Meng Yang, Ji Li, Qunfeng Lou, Jinfeng Chen
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-019-44034-4

Transcript expression profiling in two contrasting cultivars and molecular cloning of a SKP-1 like gene, a component of SCF-ubiquitin proteasome system from mungbean Vigna radiate L.
Cited by: 8
Author(s): Nandita Bharadwaj, Sharmistha Barthakur, Akash Deep Biswas, Monoj Kumar Das, Manpreet Kour, Anand Ramteke, Nirmali Gogoi
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.484

The mitochondrial genome ofParagonimus westermani(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: over 10 years ago

10.1128/AEM.01285-16

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: about 8 years ago

10.3390/v11080677

Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation
Cited by: 4
Author(s): Stéphane Aris‐Brosou, Louis Parent, Neke Ibeh
Software Mentions: 6
Published: over 5 years ago

10.1099/mgen.0.000064

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
Cited by: 95
Author(s): Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Timothy P. Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
Software Mentions: 6
Published: over 8 years ago

10.7554/eLife.57347

Universal and taxon-specific trends in protein sequences as a function of age
Cited by: 17
Author(s): Jennifer E. James, Sara M. Willis, Paul Nelson, Catherine Weibel, Luke Kosinski, Joanna Masel
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giaa137

Long-read assembly of the Brassica napus reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: almost 4 years ago

10.1186/gb-2013-14-2-r16

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Cited by: 104
Author(s): Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A. Tsonis, Thilo Borchardt, Thomas Braun
Software Mentions: 6
Published: almost 12 years ago

10.1111/1755-0998.13252

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
Cited by: 84
Author(s): Valentina Peona, Mozes P. K. Blom, Luohao Xu, Reto Burri, Shawn Sullivan, Ignas Bunikis, Ivan Liachko, Tri Haryoko, Knud A. Jønsson, Qi Zhou, Martin Irestedt, Alexander Suh
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-016-3020-8

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Cited by: 27
Author(s): Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle R. Campbell, Frances M. Van Dolah
Software Mentions: 6
Published: about 8 years ago

10.3389/fmicb.2019.02278

Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, Austria
Cited by: 4
Author(s): Philipp Baloh, Nora Els, Robert O. David, Catherine Larose, Karin Whitmore, Birgit Sattler, Hinrich Grothe
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-017-3860-x

Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
Cited by: 29
Author(s): Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H. Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
Software Mentions: 6
Published: over 7 years ago

10.1111/eva.12047

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
Cited by: 14
Author(s): John D. Kirwan, Michaël Bekaert, Jennifer M. Commins, Kalina T. J. Davies, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 6
Published: over 11 years ago

10.3389/fcell.2021.690167

Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs
Cited by: 0
Author(s): Miao Wang, Dong Chen, Huoqing Zheng, Luping Zhao, Xiao‐Feng Xue, Fengyun Yu, Yu Zhang, Chao Cheng, Qingsheng Niu, Shuai Wang, Yi Zhang, Liming Wu
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-014-0399-6

Integrating protein structural dynamics and evolutionary analysis with Bio3D
Cited by: 279
Author(s): Lars Skjærven, Xin‐Qiu Yao, Guido Scarabelli, Barry J. Grant
Software Mentions: 6
Published: almost 10 years ago

10.1099/mgen.0.000211

PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Cited by: 35
Author(s): Guilhem Royer, Jean‐Winoc Decousser, Catherine Branger, Mathieu Dubois, Claudine Médigue, Erick Denamur, David Vallenet
Software Mentions: 6
Published: about 6 years ago

10.1099/mgen.0.000042

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan
Cited by: 11
Author(s): Maia A. Rabaa, Duy Pham Thanh, Sirigade Ruekit, Sonam Wangchuk, Tandin Dorji, Kinzang Pem Tshering, To Nguyen Thi Nguyen, Phat Voong Vinh, Tuyen Ha Thanh, Chau Nguyen Ngoc Minh, Paul Turner, Pinaki Sar, Guy Thwaites, Kathryn E. Holt, Nicholas R. Thomson, Ladaporn Bodhidatta, Carl J. Mason, Stephen Baker
Software Mentions: 6
Published: almost 9 years ago

10.3389/fgene.2020.565626

A Near-Chromosome Level Genome Assembly of Anopheles stephensi
Cited by: 14
Author(s): Afiya Razia Chida, Samathmika Ravi, Suvratha Jayaprasad, Kiran Paul, Jaysmita Saha, Chinjusha Suresh, Saurabh Whadgar, Naveen Kumar, Raksha Rao K, Chaitali Ghosh, Bibha Choudhary, Suresh Subramani, Subhashini Srinivasan
Software Mentions: 6
Published: about 4 years ago

10.1099/mgen.0.000156

Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
Cited by: 23
Author(s): Rodrigo P. Baptista, João Luís Reis-Cunha, Jeremy D. DeBarry, Égler Chiari, Jessica C. Kissinger, Daniella Castanheira Bartholomeu, Andréa Mara Macedo
Software Mentions: 6
Published: over 6 years ago

10.1186/s13068-018-1116-x

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Cited by: 54
Author(s): Shihui Yang, Jessica M. Vera, Jeff Grass, Giannis Savvakis, Oleg V. Moskvin, Yongqiang Yang, Sean J. McIlwain, Yucai Lyu, Irene Zinonos, Alexander S. Hebert, Joshua J. Coon, Donna M. Bates, Trey K. Sato, Steven D. Brown, Michael E. Himmel, Min Zhang, Robert Landick, Katherine M. Pappas, Yaoping Zhang
Software Mentions: 6
Published: over 6 years ago

10.1186/s12915-019-0731-8

The round goby genome provides insights into mechanisms that may facilitate biological invasions
Cited by: 28
Author(s): Irene Adrian‐Kalchhauser, Anders Blomberg, Tomas Larsson, Zuzana Musilová, Claire R. Peart, Martin Pippel, Monica Hongrø Solbakken, Jaanus Suurväli, Jean‐Claude Walser, Joanna Y. Wilson, Magnus Alm Rosenblad, Demián Burguera, Silvia Gutnik, Nico K. Michiels, Mats Töpel, Kirill Pankov, Siegfried Schloissnig, Sylke Winkler
Software Mentions: 6
Published: almost 5 years ago

10.1111/mec.13914

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait
Cited by: 44
Author(s): Jill K. Olofsson, Matheus E Bianconi, Guillaume Besnard, Luke T. Dunning, Marjorie R. Lundgren, Hélène Holota, Maria S. Vorontsova, Oriane Hidalgo, Ilia J. Leitch, Patrik Nosil, Colin P. Osborne, Pascal‐Antoine Christin
Software Mentions: 6
Published: almost 8 years ago

10.1016/j.cell.2018.09.040

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Cited by: 116
Author(s): Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayón, S. Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M. Luscombe, James Briscoe
Software Mentions: 6
Published: about 6 years ago

10.1186/s12859-016-1420-z

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
Cited by: 9
Author(s): Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
Software Mentions: 6
Published: almost 8 years ago

10.3390/ijms19020357

Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.)
Cited by: 28
Author(s): Sylvia Salgon, Morgane Raynal, Sylvain Lebon, Jean Michel Baptiste, M. C. Daunay, Jacques Dintinger, Cyril Jourda
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-020-06831-4

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Cited by: 13
Author(s): Shubha Suresh, Teresa J. Crease, Melania E. Cristescu, Frédéric J. J. Chain
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms21010269

Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L.
Cited by: 20
Author(s): Bi‐Yu Tang, Lingling Xie, Tao Yi, Junheng Lv, Huiping Yang, Xiang Cheng, Feng Liu, Xuexiao Zou
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.574361

Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back
Cited by: 16
Author(s): Aline Sondra Adler, Christof Holliger
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.wroa.2019.100033

Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge
Cited by: 74
Author(s): Manuel Layer, Aline Sondra Adler, Eva Reynaert, Antonio Hernández, Marco Pagni, Eberhard Morgenroth, Christof Holliger, Nicolas Derlon
Software Mentions: 5
Published: over 5 years ago

10.1038/srep33813

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)
Cited by: 20
Author(s): Charles J. Mason, Erin D. Scully, Scott M. Geib, Kelli Hoover
Software Mentions: 5
Published: about 8 years ago

10.3390/ijerph18168591

Toxicological Comparison of Mancozeb and Zoxamide Fungicides at Environmentally Relevant Concentrations by an In Vitro Approach
Cited by: 11
Author(s): Gabriele Lori, Roberta Tassinari, Laura Narciso, Ion Udroiu, Antonella Sgura, Francesca Maranghi, Sabrina Tait
Software Mentions: 5
Published: over 3 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: almost 10 years ago

10.1038/srep17084

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures
Cited by: 22
Author(s): Laetitia G. E. Wilkins, Aude Rogivue, Frédéric Schütz, Luca Fumagalli, Claus Wedekind
Software Mentions: 5
Published: almost 9 years ago

10.7717/peerj.4619

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs
Cited by: 6
Author(s): Tianle Chao, Zhibin Ji, Lei Hou, Jin Wang, Chunlan Zhang, Guizhi Wang
Software Mentions: 5
Published: over 6 years ago

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 5
Published: over 3 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: almost 10 years ago

10.1038/srep27722

Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Cited by: 6
Author(s): Natalie C. Fonville, Karthik Raja Velmurugan, Hongseok Tae, Zalman Vaksman, Lauren J. McIver, Harold R. Garner
Software Mentions: 5
Published: over 8 years ago

10.1093/gigascience/giy132

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
Cited by: 21
Author(s): Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret Staton
Software Mentions: 5
Published: about 6 years ago

10.1111/mpp.13003

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae , increase host susceptibility by manipulating secondary metabolite content of rice
Cited by: 8
Author(s): Lander Bauters, Tina Kyndt, Tim De Meyer, Kris Morreel, Wout Boerjan, Hannes Lefevere, Godelieve Gheysen
Software Mentions: 5
Published: about 4 years ago

10.3390/antibiotics10040419

Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital
Cited by: 3
Author(s): Tiago Cabral Borelli, Gabriel Lencioni Lovate, Ana Flavia Tonelli Scaranello, Lucas F. Ribeiro, Livia S. Zaramela, Felipe Marcelo Pereira-dos-Santos, Rafael Silva‐Rocha, María‐Eugenia Guazzaroni
Software Mentions: 5
Published: over 3 years ago

10.1111/mec.13481

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental <scp>DNA</scp>
Cited by: 318
Author(s): Jesse A. Port, James L. O’Donnell, Ofelia C. Romero‐Maraccini, Paul Leary, Steven Y. Litvin, Kerry J. Nickols, Kevan M. Yamahara, Ryan P. Kelly
Software Mentions: 5
Published: almost 9 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: about 7 years ago

10.7554/eLife.58305

Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila
Cited by: 38
Author(s): Robin E. Harris, Michael J. Stinchfield, Spencer L. Nystrom, Daniel J. McKay, Iswar K. Hariharan
Software Mentions: 5
Published: over 4 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: over 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: about 7 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: over 3 years ago

10.1099/mgen.0.000341

An assessment of genome annotation coverage across the bacterial tree of life
Cited by: 44
Author(s): Briallen Lobb, Benjamin Tremblay, Gabriel Moreno–Hagelsieb, Andrew C. Doxey
Software Mentions: 5
Published: over 4 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: over 6 years ago

10.3390/microorganisms9081711

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts
Cited by: 6
Author(s): Marie-Charlotte Cheutin, Sébastien Villéger, Christina C. Hicks, James P. W. Robinson, Nicholas A. J. Graham, Clémence Marconnet, Claudia Ximena Ortiz Restrepo, Yvan Bettarel, Thierry Bouvier, Jean‐Christophe Auguet
Software Mentions: 5
Published: over 3 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: about 10 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: over 5 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: about 10 years ago

Projects: pypi: blast

Papers Mentioning blast 1,819