Ecosyste.ms: Papers

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

Projects: cran: seqinr

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/seqinr

Biological Sequences Retrieval and Analysis
24 versions
Latest release: over 1 year ago
67 dependent packages
15,640 downloads last month

Papers Mentioning seqinr 110

10.1186/s12859-020-03860-4
Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: almost 4 years ago
10.3389/fimmu.2020.00082
Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: almost 5 years ago
10.1371/journal.pgen.1009538
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Cited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 3 years ago
10.1186/1471-2105-13-133
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Cited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago
10.3389/fmicb.2021.689262
Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018)
Cited by: 9
Author(s): Vicente Lopez-Chavarrias, María Ugarte‐Ruiz, Carmen Bárcena, Adolfo Olarra, María Teresa Antonio García, José Luís Saez, Cristina de Frutos, Tania Serrano, I. Abad Perez, M. Moreno, Lucas Domı́nguez, Julio Álvarez
Software Mentions: 13
Published: over 3 years ago
10.1186/s40168-018-0569-2
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: about 6 years ago
10.1371/journal.pone.0212956
Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Cited by: 24
Author(s): Colin Lischik, Leonie Adelmann, Joachim Wittbrodt
Software Mentions: 13
Published: over 5 years ago
10.3389/fmicb.2019.02597
New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: about 5 years ago
10.1371/journal.pcbi.1005404
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 8 years ago
10.1177/1176934320956575
Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: almost 5 years ago
10.1371/journal.pgen.1003209
Centromere-Like Regions in the Budding Yeast Genome
Cited by: 36
Author(s): Philippe Lefrançois, Raymond K. Auerbach, Christopher M. Yellman, G. Shirleen Roeder, M Snyder
Software Mentions: 10
Published: almost 12 years ago
10.3389/fpls.2014.00078
Plasma membrane lipid–protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana
Cited by: 24
Author(s): Henrik Zauber, Asdrúbal Burgos, Prashanth Garapati, Waltraud X. Schulze
Software Mentions: 9
Published: over 10 years ago
10.1371/journal.pone.0067048
Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes
Cited by: 40
Author(s): Christoph Fischer, Stephan Koblmüller, Christian Gülly, Christian Schlötterer, Christian Sturmbauer, Gerhard G. Thallinger
Software Mentions: 9
Published: over 11 years ago
10.1371/journal.ppat.1009374
SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event
Cited by: 31
Author(s): Madlen Stange, Alfredo Mari, Tim Roloff, Helena M. B. Seth-Smith, Michael Schweitzer, Myrta Brunner, Karoline Leuzinger, Kirstine Kobberøe Søgaard, Alexander Gensch, Sarah Tschudin‐Sutter, Simon Fuchs, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Rita Schneider-Sliwa, Manuel Battegay, Hans H. Hirsch, Adrian Egli
Software Mentions: 9
Published: over 3 years ago
10.1186/s12864-015-2319-1
Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago
10.1038/s41598-019-44597-2
NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule
Cited by: 3
Author(s): Francisco Requena, Helena G Asenjo, Guillermo Barturen, Jordi Martorell-Marugán, Pedro Carmona-Sáez, David Landeira
Software Mentions: 8
Published: over 5 years ago
10.1111/mec.14054
The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
Cited by: 60
Author(s): Rodrigo Pracana, Anurag Priyam, Levantis Ilya, Richard A. Nichols, Yannick Wurm
Software Mentions: 8
Published: over 7 years ago
10.7717/peerj.5179
<i>AnnotationBustR</i>: an R package to extract subsequences from GenBank annotations
Cited by: 9
Author(s): Samuel R. Borstein, Brian C. O’Meara
Software Mentions: 8
Published: over 6 years ago
10.3390/v12111240
TBEV Subtyping in Terms of Genetic Distance
Cited by: 19
Author(s): Andrei A. Deviatkin, Galina G. Karganova, Yulia A. Vakulenko
Software Mentions: 8
Published: about 4 years ago
10.1155/2014/851425
Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence
Cited by: 22
Author(s): Edgar E. Lara-Ramírez, Ma Isabel Salazar, María de Jesús López-López, Juan Santiago Salas-Benito, Alejandro Sánchez-Varela, Xianwu Guo
Software Mentions: 7
Published: almost 11 years ago
10.7554/eLife.30952
Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals
Cited by: 158
Author(s): Inge Kühl, María Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 7
Published: about 7 years ago
10.1186/1471-2334-14-539
The distribution of incubation and relapse times in experimental human infections with the malaria parasite Plasmodium vivax
Cited by: 12
Author(s): Andrew A. Lover, Xiahong Zhao, Gengfeng Zheng, Richard Coker, Alex R. Cook
Software Mentions: 7
Published: about 10 years ago
10.3390/genes12010081
Non-Redundant tRNA Reference Sequences for Deep Sequencing Analysis of tRNA Abundance and Epitranscriptomic RNA Modifications
Cited by: 8
Author(s): Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Software Mentions: 6
Published: almost 4 years ago
10.3389/fmicb.2021.614957
Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains
Cited by: 34
Author(s): Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Adriana Ambrosini, Jackson Freitas Brilhante de São José, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Software Mentions: 6
Published: over 3 years ago
10.12688/f1000research.21763.1
vhcub: Virus-host codon usage co-adaptation analysis
Cited by: 12
Author(s): Ali Mostafa Anwar, Mohamed Soudy, Radwa Mohamed
Software Mentions: 6
Published: almost 5 years ago
10.1155/2016/9185496
Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information
Cited by: 12
Author(s): Siyu Han, Yanchun Liang, Ying Liu, Wei Du
Software Mentions: 6
Published: almost 9 years ago
10.3390/biom10060938
CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information
Cited by: 5
Author(s): Kriti Chopra, Bhawna Burdak, Kaushal Sharma, Ajit Kembhavi, Shekhar C. Mande, Radha Chauhan
Software Mentions: 6
Published: over 4 years ago
10.1016/j.ccell.2017.07.004
Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: over 7 years ago
10.7554/eLife.46454
Combinations of Spok genes create multiple meiotic drivers in Podospora
Cited by: 53
Author(s): Aaron A. Vogan, Sandra Lorena Ament‐Velásquez, Alexandra Granger-Farbos, Jesper Svedberg, Eric Bastiaans, A.J.M. Debets, Virginie Coustou, Hélène Yvanne, Corinne Clavé, Sven J. Saupe, Hanna Johannesson
Software Mentions: 6
Published: over 5 years ago
10.1093/ve/veaa004
Pervasive and non-random recombination in near full-length HIV genomes from Uganda
Cited by: 7
Author(s): Heather E Grant, Emma B. Hodcroft, Deogratius Ssemwanga, John M. Kitayimbwa, Gonzalo Yebra, Luis Roger Esquivel Gomez, Dan Frampton, Astrid Gall, Paul Kellam, Túlio de Oliveira, Nicholas Bbosa, Rebecca N. Nsubuga, Freddie Kibengo, Tsz Ho Kwan, Samantha Lycett, Rowland R. Kao, David L. Robertson, Oliver Ratmann, Christophe Fraser, Deenan Pillay, Pontiano Kaleebu, Andrew Brown
Software Mentions: 6
Published: almost 5 years ago
10.3390/v12101148
Review of Hepatitis E Virus in Rats: Evident Risk of Species Orthohepevirus C to Human Zoonotic Infection and Disease
Cited by: 36
Author(s): Gábor Reuter, Ákos Boros, Péter Pankovics
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pntd.0007609
A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing
Cited by: 37
Author(s): Joel Barratt, Meredith Lane, Emir Talundzic, Travis Richins, Gemma Robertson, Fabio Formenti, Bobbi S. Pritt, Guilherme G. Verocai, Robson da Paixão de Souza, Neci Mato Soares, Rebecca J. Traub, Dora Buonfrate, Richard S. Bradbury
Software Mentions: 6
Published: about 5 years ago
10.1093/gbe/evab069
Synteny-Based Genome Assembly for 16 Species of <i>Heliconius</i> Butterflies, and an Assessment of Structural Variation across the Genus
Cited by: 13
Author(s): Fernando Seixas, Nathaniel B. Edelman, James Mallet
Software Mentions: 6
Published: over 3 years ago
10.3390/genes11121465
Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining
Cited by: 2
Author(s): Giacomo Mutti, Alessandro Raveane, Andrea Pagano, Francesco Bertolini, Ornella Semino, Alma Balestrazzi, Anca Macovei
Software Mentions: 6
Published: almost 4 years ago
10.1038/s41598-019-44254-8
Honey bee predisposition of resistance to ubiquitous mite infestations
Cited by: 17
Author(s): Bart J. G. Broeckx, Lina De Smet, T. Blacquière, Kevin Maebe, Mikalai Khalenkow, Mario Van Poucke, Bjørn Dahle, Peter Neumann, Kim B. Nguyen, Guy Smagghe, Dieter Deforce, Filip Van Nieuwerburgh, Luc Peelman, Dirk C. de Graaf
Software Mentions: 5
Published: over 5 years ago
10.7554/eLife.46883
Proteome-wide signatures of function in highly diverged intrinsically disordered regions
Cited by: 115
Author(s): Taraneh Zarin, Bob Strome, Alex N Nguyen Ba, Simon Alberti, Julie D. Forman‐Kay, Alan M. Moses
Software Mentions: 5
Published: over 5 years ago
10.1590/0037-8682-0470-2019
Evaluation of genome similarities using a wavelet-domain approach
Cited by: 2
Author(s): Leila Maria Ferreira, Thelma Sáfadi, Juliano Lino Ferreira
Software Mentions: 5
Published: almost 5 years ago
10.1111/j.1420-9101.2010.02223.x
Similar evolutionary potentials in an obligate ant parasite and its two host species
Cited by: 30
Author(s): Pleuni S. Pennings, Alexandra Achenbach, Susanne Foitzik
Software Mentions: 5
Published: almost 14 years ago
10.1186/s13068-021-01975-1
Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Cited by: 14
Author(s): Monika Tõlgo, Silvia Hüttner, Peter Rugbjerg, Nguyễn Thanh Thủy, Vu Nguyen Thanh, Johan Larsbrink, Lisbeth Olsson
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-017-14650-z
Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females
Cited by: 18
Author(s): Louise Pease, Peter Clegg, Carole J. Proctor, Daryl P. Shanley, Simon Cockell, Mandy J. Peffers
Software Mentions: 5
Published: about 7 years ago
10.1534/g3.116.032276
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in<i>Saccharomyces cerevisiae</i>
Cited by: 39
Author(s): Benjamin Neymotin, Victoria M. Ettorre, David Gresham
Software Mentions: 5
Published: about 8 years ago
10.1093/g3journal/jkab146
The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-<i>Caenorhabditis</i> nematodes
Cited by: 3
Author(s): Astra S. Bryant, Elissa A. Hallem
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-015-2146-4
Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
Cited by: 134
Author(s): Marek L. Borowiec, Ernest K. Lee, Joanna C. Chiu, David C. Plachetzki
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pone.0258207
A new phenothiazine derivate is active against Clostridioides difficile and shows low cytotoxicity
Cited by: 3
Author(s): Troels Ronco, Francisca Maria Aragao, Lasse Saaby, Jørn B. Christensen, A. Permin, Andrew R. Williams, Stig Milan Thamsborg, Rikke Heidemann Olsen
Software Mentions: 4
Published: about 3 years ago
10.1186/s12864-021-07555-9
Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67
Cited by: 6
Author(s): Cui Zhang, Cihan Oguz, Sue Huse, Xia Lu, Jian Wu, Yu‐Chih Peng, Margaret Caroline MacHin Smith, Jack Chen, Carole A. Long, Justin Lack, Xin‐zhuan Su
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2019.03134
Designing Probiotic Therapies With Broad-Spectrum Activity Against a Wildlife Pathogen
Cited by: 16
Author(s): Xavier A. Harrison, Thomas R. Sewell, Matthew C. Fisher, Rachael E. Antwis
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0199950
The analysis of genome composition and codon bias reveals distinctive patterns between avian and mammalian circoviruses which suggest a potential recombinant origin for Porcine circovirus 3
Cited by: 20
Author(s): Giovanni Franzo, Joaquím Segalés, Claudia Maria Tucciarone, Mattia Cecchinato, Michele Drigo
Software Mentions: 4
Published: over 6 years ago
10.1093/molbev/msw161
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
Cited by: 82
Author(s): Sara Pinosio, Stefania Giacomello, Patricia Faivre-Rampant, Gail Taylor, Véronique Jorge, Marie Christine Le Paslier, Giusi Zaina, Catherine Bastien, Federica Cattonaro, Fabio Marroni, Michèle Morgante
Software Mentions: 4
Published: over 8 years ago
10.1186/s12864-021-07559-5
Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
Cited by: 8
Author(s): Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato
Software Mentions: 4
Published: over 3 years ago
10.1080/21505594.2020.1790282
Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
Cited by: 10
Author(s): Shuonan Pan, Chunxiao Mou, Huiguang Wu, Zhenhai Chen
Software Mentions: 4
Published: over 4 years ago
10.3389/fgene.2018.00476
The Paralogous Genes PDR18 and SNQ2, Encoding Multidrug Resistance ABC Transporters, Derive From a Recent Duplication Event, PDR18 Being Specific to the Saccharomyces Genus
Cited by: 12
Author(s): Cláudia P. Godinho, Paulo Jorge Dias, Elise Ponçot, Isabel Sá‐Correia
Software Mentions: 4
Published: about 6 years ago
10.1186/s12859-021-04180-x
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets
Cited by: 15
Author(s): Teresita M. Porter, Mehrdad Hajibabaei
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2164-13-549
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
Cited by: 17
Author(s): Heidrun Sigrid Windisch, Magnus Lucassen, Stephan Frickenhaus
Software Mentions: 4
Published: almost 13 years ago
10.1186/s12864-020-6662-5
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Cited by: 12
Author(s): Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yoshihisa Yamashita, Shuichi Naito, Atsushi Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima, Hitoshi Onouchi
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pntd.0007241
Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities
Cited by: 26
Author(s): Meruyert Beknazarova, Joel Barratt, Richard S. Bradbury, Meredith Lane, Harriet Whiley, Kirstin Ross
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-020-73307-6
Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Cited by: 6
Author(s): Hiro Takahashi, Shido Miyaki, Hitoshi Onouchi, Taichiro Motomura, Nobuo Idesako, Atsushi Takahashi, Masataka Murase, Shuichi Fukuyoshi, Toshinori Endo, Kenji Satou, Shuichi Naito, Motoyuki Itoh
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pntd.0009719
Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Cited by: 6
Author(s): Luisa Berná, Gonzalo Greif, Sebastián Pita, Paula Faral-Tello, Florencia Díaz-Viraqué, Rita de Cássia Moreira de Souza, Gustavo Adolfo Vallejo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 4
Published: about 3 years ago
10.1186/1472-6785-14-22
Causes and consequences of fine-scale population structure in a critically endangered freshwater seal
Cited by: 28
Author(s): Mia Valtonen, Jukka U. Palo, Jouni Aspi, Minna Ruokonen, Mervi Kunnasranta, Tommi Nyman
Software Mentions: 4
Published: almost 11 years ago
10.1264/jsme2.ME19077
Distribution of SNSs in Mimivirus Genomes and the Classification of Mimiviruses Isolated from Japan
Cited by: 1
Author(s): Motohiro Akashi, Masaharu Takemura
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12862-014-0259-z
Mitochondrial genomes of the Baltic clam Macoma balthica(Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities
Cited by: 16
Author(s): Alice Saunier, Pascale Garcia, Vanessa Becquet, Nathalie Marsaud, Frédéric Escudié, Eric Pante
Software Mentions: 3
Published: almost 10 years ago
10.1186/1471-2164-11-80
Tracking chromosomal positions of oligomers - a case study with Illumina's BovineSNP50 beadchip
Cited by: 8
Author(s): Armin O. Schmitt, Ralf Bortfeldt, Gudrun A. Brockmann
Software Mentions: 3
Published: almost 15 years ago
10.1186/1743-422X-8-406
Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features
Cited by: 18
Author(s): Léonor Palmeira, Bénédicte Machiels, Céline Lété, Alain Vanderplasschen, Laurent Gillet
Software Mentions: 3
Published: over 13 years ago
10.3390/v12090991
Comprehensive Analysis of Codon Usage on Porcine Astrovirus
Cited by: 11
Author(s): Huiguang Wu, Zhengyu Bao, Chunxiao Mou, Zhenhai Chen, Jingwen Zhao
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pgen.0010026
A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana
Cited by: 384
Author(s): Matthew A. Hannah, Arnd G. Heyer, Dirk K. Hincha
Software Mentions: 3
Published: over 19 years ago
10.1371/journal.pntd.0001209
Evidence of Gene Conversion in Genes Encoding the Gal/GalNac Lectin Complex of Entamoeba
Cited by: 14
Author(s): Gareth D. Weedall, James Sherrington, Steve Paterson, Neil Hall
Software Mentions: 3
Published: over 13 years ago
10.1371/journal.pone.0146706
Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations
Cited by: 6
Author(s): Irina N. Shilova, Julie Robidart, Edward F. DeLong, Jonathan P. Zehr
Software Mentions: 3
Published: almost 9 years ago
10.1371/journal.pone.0213241
PhyloPi: An affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility
Cited by: 1
Author(s): Phillip Armand Bester, Andrie de Vries, Stephanus Riekert, Kim Steegen, Gert van Zyl, Dominique Goedhals
Software Mentions: 3
Published: over 5 years ago
10.15252/embr.201947952
Expression and phase separation potential of heterochromatin proteins during early mouse development
Cited by: 11
Author(s): Manuel Guthmann, Adam Burton, Maria-Elena Torres-Padilla
Software Mentions: 3
Published: about 5 years ago
10.1534/g3.113.008185
Genome of <i>Drosophila suzukii</i>, the Spotted Wing <i>Drosophila</i>
Cited by: 116
Author(s): Joanna C. Chiu, Xuanting Jiang, Li Zhao, Christopher A. Hamm, Julie M. Cridland, Perot Saelao, Kelly A. Hamby, Ernest K. Lee, Rosanna S. Kwok, Guojie Zhang, Frank G. Zalom, Vaughn M. Walton, David J. Begun
Software Mentions: 3
Published: almost 11 years ago
10.1534/g3.119.400758
Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies
Cited by: 20
Author(s): Clémentine François, Faustine Durand, Emeric Figuet, Nicolas Galtier
Software Mentions: 3
Published: almost 5 years ago
10.1093/g3journal/jkaa026
<i>De novo</i> assembly of a chromosome-scale reference genome for the northern flicker <i>Colaptes auratus</i>
Cited by: 3
Author(s): Jack P. Hruska, Joseph D. Manthey
Software Mentions: 3
Published: almost 4 years ago
10.1093/gbe/evw291
Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in <i>Drosophila</i>
Cited by: 26
Author(s): Benjamin C. Jackson, José Luis Campos, Penelope R. Haddrill, Brian Charlesworth, Kai Zeng
Software Mentions: 3
Published: almost 8 years ago
10.1371/journal.ppat.1005576
Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae
Cited by: 15
Author(s): Joshua Chang Mell, Cristina Viadas, Javier Moleres, Sunita Sinha, Ariadna Fernández-Calvet, Eric A. Porsch, Joseph W. St. Geme, Corey Nislow, Rosemary J. Redfield, Junkal Garmendia
Software Mentions: 3
Published: over 8 years ago
10.1038/s41597-020-00598-9
ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records
Cited by: 6
Author(s): Matthijs P. van den Burg, Salvador Herrando‐Pérez, David R. Vieites
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-72873-z
Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany
Cited by: 12
Author(s): Felix Sauer, Linda Jaworski, L. Erdbeer, Anna Heitmann, Jonas Schmidt‐Chanasit, Ellen Kiel, Renke Lühken
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-021-90278-4
SARS-CoV-2 and other human coronavirus show genome patterns previously associated to reduced viral recognition and altered immune response
Cited by: 5
Author(s): Giovanni Franzo
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-021-91208-0
Focused peptide library screening as a route to a superior affinity ligand for antibody purification
Cited by: 3
Author(s): Krištof Bozovičar, Barbara Jenko Bizjan, Anže Meden, Jernej Kovač, Tomaž Bratkovič
Software Mentions: 3
Published: over 3 years ago
10.3390/ijms22179657
K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses
Cited by: 6
Author(s): Zigui Chen, Filippo Utro, Daniel E. Platt, Rob DeSalle, Laxmi Parida, Paul K.S. Chan, Robert D. Burk
Software Mentions: 3
Published: about 3 years ago
10.1186/s12862-015-0411-4
Positive selection in octopus haemocyanin indicates functional links to temperature adaptation
Cited by: 6
Author(s): Michael Oellermann, Jan M. Strugnell, Bernhard Lieb, Felix Christopher Mark
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0048295
Mutational Bias and Translational Selection Shaping the Codon Usage Pattern of Tissue-Specific Genes in Rice
Cited by: 25
Author(s): Qingpo Liu
Software Mentions: 2
Published: about 12 years ago
10.1038/hdy.2014.80
The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations
Cited by: 31
Author(s): Benjamin C. Jackson, José Luis Campos, Kai Zeng
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0123624
Evolutionary Distance of Amino Acid Sequence Orthologs across Macaque Subspecies: Identifying Candidate Genes for SIV Resistance in Chinese Rhesus Macaques
Cited by: 3
Author(s): Cody T. Ross, Morteza Roodgar, David Glenn Smith
Software Mentions: 2
Published: over 9 years ago
10.3390/jof7070515
Cultivable Yeast Microbiota from the Marine Fish Species Genypterus chilensis and Seriolella violacea
Cited by: 10
Author(s): Benjamín Valderrama, José J. Ruiz, María Soledad Gutiérrez, Krisler Alveal, Mario Caruffo, Marcia Oliva, Héctor Flores, Alfonso Silva, Mauricio Toro, Angélica Reyes-Jara, Paola Navarrete
Software Mentions: 2
Published: over 3 years ago
10.3390/genes11060617
Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids
Cited by: 9
Author(s): Anatolie Marta, Dmitrij Dedukh, Oldřich Bartoš, Zuzana Majtánová, Karel Janko
Software Mentions: 2
Published: over 4 years ago
10.3389/fgene.2014.00316
Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs
Cited by: 6
Author(s): Damien Ulveling, Marcel E. Dinger, Claire Francastel, Florent Hubé
Software Mentions: 2
Published: about 10 years ago
10.3389/fgene.2021.620253
Capture Sequencing to Explore and Map Rare Casein Variants in Goats
Cited by: 4
Author(s): Siham A. Rahmatalla, Danny Arends, Ammar Said Ahmed, Lubna M. A. Hassan, Stefan Krebs, Monika Reißmann, Gudrun A. Brockmann
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.cub.2020.10.030
Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria
Cited by: 18
Author(s): Stephan Köstlbacher, Astrid Collingro, Tamara Halter, Daryl Domman, Matthias Horn
Software Mentions: 2
Published: almost 4 years ago
10.3390/life11040344
Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus
Cited by: 1
Author(s): Kevin Calderon Gallegos, Johan F. Galindo, Clara Isabel Bermúdez-Santana
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0188037
Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment
Cited by: 31
Author(s): Dmitri Kamashev, Yu. K. Agapova, С. М. Расторгуев, Anna A. Talyzina, K.М. Boyko, D.A. Korzhenevskiy, Anna V. Vlaskina, Р. Г. Василов, В. И. Тимофеев, Tatiana V. Rakitina
Software Mentions: 2
Published: about 7 years ago
10.1186/s12862-015-0511-1
Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11
Cited by: 55
Author(s): Caitlyn Vlasschaert, Xuhua Xia, Josée Coulombe, Douglas A. Gray
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0115650
Comparing Multiple Criteria for Species Identification in Two Recently Diverged Seabirds
Cited by: 10
Author(s): Teresa Militão, Elena Gómez-Díaz, Antigoni Kaliontzopoulou, Jacob González‐Solís
Software Mentions: 2
Published: almost 10 years ago
10.3389/fmicb.2015.00696
Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins
Cited by: 64
Author(s): Karyna Rosario, Ryan O. Schenck, Rachel C. Harbeitner, Stephanie Lawler, Mya Breitbart
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0257519
The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region
Cited by: 3
Author(s): Matheus Pontes‐Nogueira, Marcio Roberto Martins, Laura R. V. Alencar, Ricardo J. Sawaya
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0036443
A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes
Cited by: 39
Author(s): Christine N. Meynard, David Mouillot, Nicolas Mouquet, Emmanuel J. P. Douzery
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0083842
Proteomic Characterization of Murid Herpesvirus 4 Extracellular Virions
Cited by: 22
Author(s): Sarah Vidick, Baptiste Leroy, Léonor Palmeira, Bénédicte Machiels, Jan Mast, Sylvie François, Ruddy Wattiez, Alain Vanderplasschen, Laurent Gillet
Software Mentions: 1
Published: almost 11 years ago
10.1038/s41598-017-02860-4
Gene-body CG methylation and divergent expression of duplicate genes in rice
Cited by: 26
Author(s): Xutong Wang, Zhibin Zhang, Tiansi Fu, Lanjuan Hu, Chunming Xu, Lei Gong, Jonathan F. Wendel, Liu B
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0043111
Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes
Cited by: 130
Author(s): Susanta K. Behura, David W. Severson
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0019075
A Comprehensive Deep Sequencing Strategy for Full-Length Genomes of Influenza A
Cited by: 45
Author(s): Dirk W. Höper, Bernd Hoffmann, Martin Beer
Software Mentions: 1
Published: over 13 years ago
10.1186/s12859-016-1222-3
Phylogenetic tree construction using trinucleotide usage profile (TUP)
Cited by: 3
Author(s): Si Chen, Lih Yuan Deng, Dale Bowman, Jyh Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian, Henry Horng Shing Lu
Software Mentions: 1
Published: about 8 years ago
10.3390/v13071281
Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16
Cited by: 2
Author(s): Wei Liu, Junhua Li, Hongli Du, Zhihua Ou
Software Mentions: 1
Published: over 3 years ago