pypi: msa | Projects | Ecosyste.ms: Papers

10.1186/s13073-021-00910-1

Landscape and selection of vaccine epitopes in SARS-CoV-2
Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago

10.1371/journal.pone.0243927

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 years ago

10.7554/eLife.67784

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Cited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: over 3 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: almost 5 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

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 4 years ago

10.1534/g3.120.401174

Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in Drosophila mtDNA Haplotypes
Cited by: 3
Author(s): Richard Sejour, Roger A. Sanguino, Monika Mikolajczak, Walishah Ahmadi, Eugenia Villa-Cuesta
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0255169

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts
Cited by: 25
Author(s): Rafail Nikolaos Tasakis, Georgios Samaras, Anna Jamison, Michelle Lee, Alexandra Paulus, Gabrielle Whitehouse, Laurent Verkoczy, F. Nina Papavasiliou, Marilyn Diaz
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0236226

Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response
Cited by: 10
Author(s): Fatemeh Gholizadeh, Ghader Mirzaghaderi
Software Mentions: 7
Published: about 4 years ago

10.1002/ece3.3170

Phylogeography of a migratory songbird across its Canadian breeding range: Implications for conservation units
Cited by: 17
Author(s): Samuel Haché, Erin M. Bayne, Marc‐André Villard, H. C. Proctor, Corey S. Davis, Diana Stralberg, Jasmine K. Janes, Michael T. Hallworth, Kenneth R. Foster, Easwaramurthyvasi Chidambara-vasi, Alexandra A. Grossi, Jamieson C. Gorrell, Richard Krikun
Software Mentions: 7
Published: over 7 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

10.3390/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

10.3390/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

10.1038/s41438-020-0316-2

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Cited by: 16
Author(s): Sagar Patel, Michael Robben, Anne Fennell, Jason P. Londo, Dilmini Alahakoon, Roberto Villegas-Diaz, Padmapriya Swaminathan
Software Mentions: 6
Published: over 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

10.1371/journal.pone.0123609

Mapsnp: An R Package to Plot a Genomic Map for Single Nucleotide Polymorphisms
Cited by: 5
Author(s): Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Cheng Zhang, Guoqiang Wang, Yin Yao Shugart
Software Mentions: 5
Published: over 9 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-019-1856-3

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION
Cited by: 47
Author(s): Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D’Hert, Peter De Rijk, Mojca Stražišar, Christine Van Broeckhoven, Kristel Sleegers
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2020.00706

Mitochondrial Genome Polymorphisms in the Human Pathogenic Fungus Cryptococcus neoformans
Cited by: 21
Author(s): Yue Wang, Jianping Xu
Software Mentions: 5
Published: over 4 years ago

10.3389/fcell.2021.628699

A New Zebrafish Model for Pseudoxanthoma Elasticum
Cited by: 2
Author(s): Dávid Czimer, Klaudia Porok, Dániel Csete, Zsolt Gyüre, Viktória Lavró, Krisztina Fülöp, Zelin Chen, Hella Gyergyák, Gábor Tusnády, Shawn M. Burgess, Attila Mócsai, András Váradi, Máté Varga
Software Mentions: 5
Published: over 3 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: about 5 years ago

10.1038/s41438-020-00411-z

Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior
Cited by: 27
Author(s): Lara Pereira, Miguel Santo Domingo, Valentino Ruggieri, Jason Argyris, Michael A. Phillips, Guangwei Zhao, Qiang Lian, Yong Xu, Yue He, Sanwen Huang, Marta Pujol, Jordi García-Más
Software Mentions: 4
Published: about 4 years ago

10.1111/mec.14377

Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation
Cited by: 59
Author(s): Karel Janko, Jan Pačes, Hilde Wilkinson‐Herbots, Rui J. Costa, Jan Röslein, Pavel Drozd, Nataliia Iakovenko, Jakub Rídl, Miluše Hroudová, Ján Kočí, Radka Reifová, Vendula Šlechtová, Lukáš Choleva
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2021.716750

Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes
Cited by: 3
Author(s): Rahman Ebrahimzadegan, Fatemeh Orooji, Pengtao Ma, Ghader Mirzaghaderi
Software Mentions: 4
Published: about 3 years ago

10.1111/j.1365-294X.2010.04838.x

Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression
Cited by: 37
Author(s): Maria D. S. Nunes, Pablo Orozco-ter Wengel, Michaela Kreissl, Christian Schlötterer
Software Mentions: 4
Published: about 14 years ago

10.3390/genes10030181

ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements
Cited by: 4
Author(s): Fei Yuan, Hoa Nguyen, Dan Graur
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.7627

Challenges and opportunities for comparative studies of survival rates: An example with male pinnipeds
Cited by: 1
Author(s): Jamie L. Brusa, Jay J. Rotella, Katharine M. Banner, Patrick R. Hutchins
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2020.00373

Tissue-Specific Requirement for the GINS Complex During Zebrafish Development
Cited by: 2
Author(s): Máté Varga, Kitti Csályi, István Bertyák, Dóra K. Menyhárd, Richard J. Poole, Kara L. Cerveny, Dorottya Kövesdi, Balázs L. Barátki, Hannah Rouse, Zsuzsa Vad, Thomas A. Hawkins, Heather L. Stickney, Florencia Cavodeassi, Quenten Schwarz, Rodrigo Young, Stephen W. Wilson
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-017-4293-2

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera
Cited by: 16
Author(s): Emma Whittington, Desiree Forsythe, Kirill Borziak, Timothy L. Karr, James R. Walters, Steve Dorus
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-021-03197-x

Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean
Cited by: 5
Author(s): Nicholas Dietz, Rachel Combs-Giroir, Grace Cooper, Minviluz G. Stacey, Carrie Miranda, Kristin Bilyeu
Software Mentions: 3
Published: about 3 years ago

10.1099/mgen.0.000221

Identification of novel adenovirus genotype 90 in children from Bangladesh
Cited by: 9
Author(s): Charlotte J. Houldcroft, Mathew A. Beale, Abu Sayeed, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.22242.2

AlignmentViewer: Sequence Analysis of Large Protein Families
Cited by: 7
Author(s): Roc Reguant, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier
Software Mentions: 3
Published: about 4 years ago

10.1111/j.1365-2052.2010.02025.x

Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof-of-concept study for the identification of escapees
Cited by: 31
Author(s): Kevin A. Glover, Geir Dahle, Jon‐Ivar Westgaard, Torild Johansen, Halvor Knutsen, Knut Eirik Jørstad
Software Mentions: 3
Published: about 14 years ago

10.3389/fmed.2021.635547

Tracking the Origin of Austrian Human Brucellosis Cases Using Whole Genome Sequencing
Cited by: 14
Author(s): Justine Schaeffer, Sandra Revilla‐Fernández, Erwin Hofer, R. Posch, Anna Stoeger, Christoph Leth, F. Schmoll, Vesna Djordjević, Brankica Lakićević, Kazimir Matović, Peter Hufnagl, Alexander Indra, Franz Allerberger, Werner Ruppitsch
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.625782

Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota
Cited by: 25
Author(s): Silvia Molino, Alberto Lerma-Aguilera, Nuria Jiménez‐Hernández, María José Gosalbes, José Ángel Rufián-Henares, M. Pilar Francino
Software Mentions: 3
Published: over 3 years ago

10.1093/jxb/erab278

Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling
Cited by: 16
Author(s): Wasim A Iqbal, Isabel G Miller, Rebecca L Moore, Iain J Hope, Daniel Cowan‐Turner, Maxim V. Kapralov
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-25346-3

Critical amino acids for the insecticidal activity of Vip3Af from Bacillus thuringiensis: Inference on structural aspects
Cited by: 26
Author(s): Núria Banyuls, Carmen Sara Hernández‐Rodríguez, Jeroen Van Rie, Juan Ferré
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-64913-5

Oxidosqualene cyclases involved in the biosynthesis of triterpenoids in Quercus suber cork
Cited by: 16
Author(s): Lucas Busta, Olga Serra, Ok-Tae Kim, Marisa Molinas, Irene Peré-Fossoul, Mercè Figueras, Reinhard Jetter
Software Mentions: 3
Published: over 4 years ago

10.1093/aobpla/plz002

The influence of a relict distribution on genetic structure and variation in the Mediterranean tree,Platanus orientalis
Cited by: 9
Author(s): Rosita Rinaldi, Donata Cafasso, Sandro Strumia, Antonietta Cristaudo, Federico Sebastiani, Silvia Fineschi
Software Mentions: 2
Published: almost 6 years ago

10.1038/srep27133

A novel suicide shuttle plasmid for Streptococcus suis serotype 2 and Streptococcus equi ssp. zooepidemicus gene mutation
Cited by: 11
Author(s): Rui Li, Ping Zhang, Yiqi Su, Huixing Lin, Hui Zhang, Lei Yu, Zhe Ma, Hongjie Fan
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms21218175

Identifying Cancer-Relevant Mutations in the DLC START Domain Using Evolutionary and Structure-Function Analyses
Cited by: 3
Author(s): Ashton S Holub, Renee Bouley, Ruben C. Petreaca, Aman Y. Husbands
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-46740-5

Predicting Antigenicity of Influenza A Viruses Using biophysical ideas
Cited by: 6
Author(s): Abdoelnaser M. Degoot, Emmanuel S. Adabor, Faraimunashe Chirove, Wilfred Ndifon
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-56894-x

In silico analysis of alternative splicing on drug-target gene interactions
Cited by: 10
Author(s): Yanrong Ji, Rama K. Mishra, Ramana V. Davuluri
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.isci.2021.102822

Bidirectional electroactive microbial biofilms and the role of biogenic sulfur in charge storage and release
Cited by: 12
Author(s): Paniz Izadi, Marten Niklas Gey, Nicolas Schlüter, Uwe Schröder
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-82730-2

A mutant α1antitrypsin in complex with heat shock proteins as the primary antigen in type 1 diabetes in silico investigation
Cited by: 0
Author(s): Paola Finotti, Andrea Pagetta
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12936-018-2193-9

Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo
Cited by: 11
Author(s): Robert Verity, Nicholas J. Hathaway, Andreea Waltmann, Stephanie M. Doctor, Oliver J Watson, Jaymin C. Patel, Kashamuka Mwandagalirwa, Antoinette Tshefu, Jeffrey A. Bailey, Azra C. Ghani, Jonathan J. Juliano, Steven R. Meshnick
Software Mentions: 2
Published: almost 7 years ago

Projects: pypi: msa

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