cran: fasta | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2018.01999

Insights Into Culturomics of the Rumen Microbiome
Cited by: 32
Author(s): Tamar Zehavi, Maraike Probst, Itzhak Mizrahi
Software Mentions: 3
Published: about 6 years ago

The RpoS Gatekeeper in Borrelia burgdorferi: An Invariant Regulatory Scheme That Promotes Spirochete Persistence in Reservoir Hosts and Niche Diversity
Cited by: 50
Author(s): Melissa J. Caimano, Ashley M. Groshong, Alexia A. Belperron, Jialing Mao, Kelly L. Hawley, Amit Luthra, Danielle E. Graham, Christopher G. Earnhart, Richard T. Marconi, Linda K. Bockenstedt, Jon S. Blevins, Justin D. Radolf
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2015.00197

The transcriptional response of microbial communities in thawing Alaskan permafrost soils
Cited by: 111
Author(s): Marco J. L. Coolen, William D. Orsi
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2018.00028

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome
Cited by: 68
Author(s): Sophie S. Abby, Michael Melcher, Melina Kerou, Mart Krupovìč, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmolb.2020.00160

Gene Duplications in the Genomes of Staphylococci and Enterococci
Cited by: 5
Author(s): José Francisco Sánchez-Herrero, Manuel Bernabeu, Alejandro Prieto, Mário Hüttener, Antonio Juárez
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2016.00186

Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association
Cited by: 134
Author(s): Ki Tae Kim, Jongbum Jeon, Jaeyoung Choi, Kwang Ho Cheong, Hyeunjeong Song, Gobong Choi, Seogchan Kang, Yong Hwan Lee
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2015.00710

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
Cited by: 97
Author(s): James A. Nicholls, R. Toby Pennington, Erik J. M. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone, Catherine Kidner
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2021.682879

High-Throughput Sequencing of Small RNAs for the Sanitary Certification of Viruses in Grapevine
Cited by: 3
Author(s): L. Velasco, Carlos Padilla
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2018.01966

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data
Cited by: 12
Author(s): Ritwika Das, Vasu Arora, Sarika Jaiswal, Mir Asif Iquebal, U. B. Angadi, Samar Fatma, Rakesh Singh, Sandip Shil, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpls.2013.00170

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses
Cited by: 31
Author(s): Gina Turco, James C. Schnable, Brent S. Pedersen, Michael Freeling
Software Mentions: 3
Published: almost 12 years ago

10.1534/g3.113.005967

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data
Cited by: 242
Author(s): J. Graham Ruby, Priya Bellare, Joseph L. DeRisi
Software Mentions: 3
Published: over 11 years ago

10.1534/g3.118.200745

Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies
Cited by: 25
Author(s): Alexander P. Douglass, Caoimhe E. O’Brien, Benjamin Offei, Aisling Y. Coughlan, Raúl A. Ortiz‐Merino, Geraldine Butler, Kevin Byrne, Kenneth H. Wolfe
Software Mentions: 3
Published: over 5 years ago

10.1534/g3.119.400444

Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family inTriticum aestivum
Cited by: 16
Author(s): Harriet R. Benbow, Lars S. Jermiin, Fiona M. Doohan
Software Mentions: 3
Published: over 5 years ago

10.1093/g3journal/jkaa015

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Cited by: 20
Author(s): Peri A Tobias, Benjamin Schwessinger, Cecilia Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, K. S. Sandhu, Grant R. Smith, Josquin Tibbits, David Chagné, Robert Park
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes9060269

Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata
Cited by: 29
Author(s): Rafael Luiz Buogo Coan, Cesar Martins
Software Mentions: 3
Published: over 6 years ago

10.3390/genes10020079

Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies
Cited by: 15
Author(s): Keyur Talsania, Monika Mehta, Castle Raley, Yuliya Kriga, Sujatha Gowda, Carissa Grose, Matthew Drew, Veronica J. Roberts, Kwong Tai Cheng, Sandra Burkett, Steffen Oeser, Robert S. Stephens, Daniel Soppet, Xiongfeng Chen, Parimal Kumar, Oksana German, Tatyana I. Smirnova, Christopher Hautman, Jyoti Shetty, Bao Tran, Yongmei Zhao, Dominic Esposito
Software Mentions: 3
Published: almost 6 years ago

10.3390/genes11010027

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)
Cited by: 28
Author(s): Sunil Kumar Sahu, Min Ling, Anna Yssel, Robert Kariba, Samuel Muthemba, Sanjie Jiang, Bo Song, Prasad S. Hendre, Alice Muchugi, Ramni Jamnadass, Shu Min Kao, Jonathan Featherston, Nyree J. C. Zerega, Xun Xu, Huanming Yang, Allen Van Deynze, Yves Van de Peer, Xin Liu, Sunil Kumar Sahu
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes12010092

Contribution of Mitochondrial DNA Heteroplasmy to the Congenital Cardiac and Palatal Phenotypic Variability in Maternally Transmitted 22q11.2 Deletion Syndrome
Cited by: 0
Author(s): Boris Rebolledo‐Jaramillo, María Gabriela Obregón, Victoria Huckstadt, Abel Gomez, Gabriela M. Repetto
Software Mentions: 3
Published: almost 4 years ago

10.1186/gb-2007-8-4-r61

Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Cited by: 403
Author(s): Victor Kunin, Rotem Sorek, Philip Hugenholtz
Software Mentions: 3
Published: almost 18 years ago

10.1186/gb-2010-11-5-r47

Computational challenges in the analysis of ancient DNA
Cited by: 112
Author(s): Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Edward Green
Software Mentions: 3
Published: almost 15 years ago

10.1186/s13059-014-0572-2

De novo assembly of bacterial transcriptomes from RNA-seq data
Cited by: 764
Author(s): Brian Tjaden
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-020-02134-9

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Cited by: 637
Author(s): Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy
Software Mentions: 3
Published: about 4 years ago

10.1093/gbe/evv186

Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes
Cited by: 38
Author(s): Christopher M. Austin, Mun Hua Tan, Larry Croft, Michael P. Hammer, Han Ming Gan
Software Mentions: 3
Published: about 9 years ago

10.1093/gbe/evw047

In-silicoidentification of candidate genes for fertility restoration in cytoplasmic male sterile perennial ryegrass (Lolium perenneL.)
Cited by: 13
Author(s): Timothy Sykes, Steven Yates, Istvàn Nagy, Torben Asp, Ian Small, Bruno Studer
Software Mentions: 3
Published: over 8 years ago

10.1093/gbe/evx242

Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia
Cited by: 18
Author(s): Taruna Schuelke, Guangxi Wu, Anthony Westbrook, Keith Woeste, David C. Plachetzki, Kirk Broders, Matthew D. MacManes
Software Mentions: 3
Published: almost 7 years ago

10.1093/gbe/evz256

Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants
Cited by: 38
Author(s): Weiwen Wang, Robert Lanfear
Software Mentions: 3
Published: about 5 years ago

10.1186/s13073-014-0090-6

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Cited by: 816
Author(s): Michael Inouye, Harriet Dashnow, Lesley Raven, Mark B. Schultz, Bernard J. Pope, Takehiro Tomita, Justin Zobel, Kathryn E. Holt
Software Mentions: 3
Published: about 10 years ago

10.1093/gigascience/giy018

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission
Cited by: 32
Author(s): Scott M. Geib, Brian E. Hall, Theodore DeRego, Forest T. Bremer, Kyle Cannoles, Sheina B. Sim
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giy036

Field of genes: using Apache Kafka as a bioinformatic data repository
Cited by: 10
Author(s): Brendan Lawlor, Richard Lynch, Micheál Mac Aogáin, Paul Walsh
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giaa138

iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Cited by: 17
Author(s): Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
Software Mentions: 3
Published: almost 4 years ago

10.1093/gigascience/giab008

Twelve years of SAMtools and BCFtools
Cited by: 3,237
Author(s): Petr Danecek, James K. Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M. Keane, Shane McCarthy, Robert M. Davies, Heng Li
Software Mentions: 3
Published: almost 4 years ago

10.1093/gigascience/giab066

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.
Cited by: 6
Author(s): Aundrea K. Westfall, Rory S. Telemeco, Mariana B. Grizante, Damien S. Waits, Amanda D. Clark, Dasia Y. Simpson, Randy L. Klabacka, Alexis Sullivan, George H. Perry, Michael W. Sears, Christian L. Cox, Robert M. Cox, Matthew E. Gifford, Henry B. John‐Alder, Tracy Langkilde, Michael J. Angilletta, Adam D. Leaché, Marc Tollis, Kenro Kusumi, Tonia S. Schwartz
Software Mentions: 3
Published: about 3 years ago

10.1038/s41437-021-00438-5

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish
Cited by: 7
Author(s): Axel Jensen, Mette Lillie, Kristofer Bergström, Per Larsson, Jacob Höglund
Software Mentions: 3
Published: over 3 years ago

10.1186/s43008-020-00041-z

The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM): introducing a new repository of barcoded Chytridiomyceta and Blastocladiomycota cultures
Cited by: 17
Author(s): D. Rabern Simmons, Anne E. Bonds, Buck T. Castillo, Rebecca A. Clemons, Alexander D. Glasco, Jillian M. Myers, Natasha Thapa, Peter M. Letcher, Martha J. Powell, Joyce E. Longcore, Timothy Y. James
Software Mentions: 3
Published: about 4 years ago

10.1186/s43008-020-00051-x

Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)
Cited by: 5
Author(s): Felix Grewe, Claudio Gennaro Ametrano, Todd J. Widhelm, Steven D. Leavitt, Isabel Distefano, Wetchasart Polyiam, David Pizarro, Mats Wedin, Ana Crespo, Pradeep K. Divakar, H. Thorsten Lumbsch
Software Mentions: 3
Published: almost 4 years ago

10.1016/S1674-8301(11)60059-6

Active motif finder – a bio-tool based on mutational structures in DNA sequences
Cited by: 0
Author(s): M. Udayakumar, Palaniyandi Shanmuga-priya, K. Hemavathi, R. Seenivasagam
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.ppat.1000181

Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins
Cited by: 35
Author(s): David Pérez-Caballero, Steven J. Soll, Paul D. Bieniasz
Software Mentions: 3
Published: about 16 years ago

10.1038/srep36629

High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays
Cited by: 32
Author(s): Mikael Engmark, Mikael Rørdam Andersen, Andreas Hougaard Laustsen, Jigar Patel, Eric Sullivan, Federico De Masi, Christian Skjødt Hansen, Jens Vindahl Kringelum, Bruno Lomonte, José Marı́a Gutiérrez, Ole Lund
Software Mentions: 3
Published: about 8 years ago

10.1038/srep46395

Complex multifractal nature in Mycobacterium tuberculosis genome
Cited by: 8
Author(s): Suvra Mandal, Tanmoy Roychowdhury, Keilash Chirom, Alok Bhattacharya, R. K. Brojen Singh
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-11040-3

SOCS2 Binds to and Regulates EphA2 through Multiple Mechanisms
Cited by: 3
Author(s): Carissa Pilling, Jonathan A. Cooper
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-27177-8

Assigning biological function using hidden signatures in cystine-stabilized peptide sequences
Cited by: 5
Author(s): S. M. Ashiqul Islam, Christopher Michel Kearney, Erich J. Baker
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-29620-2

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches
Cited by: 31
Author(s): Isaac Darko Otchere, Mireia Coscollá, Leonor Sánchez-Busó, Adwoa Asante-Poku, Daniela Brites, Chloé Loiseau, Conor J. Meehan, Stephen Osei-Wusu, Audrey Forson, Clement Laryea, Abdallah Iddrisu Yahayah, Akosua Baddoo, Gloria Akosua Ansa, Samuel Yaw Aboagye, Prince Asare, Sònia Borrell, Florian Gehre, Patrick Beckert, Thomas A. Kohl, Sanoussi N'dira, Christian Beisel, Martín Antonio, Stefan Niemann, Bouke C. de Jong, Julian Parkhill, Simon R. Harris, Sébastien Gagneux, Dorothy Yeboah-Manu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-31289-6

Role of solvent accessibility for aggregation-prone patches in protein folding
Cited by: 6
Author(s): Avinash Mishra, Shoba Ranganathan, B. Jayaram, Abdul Sattar
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-37651-y

Three ancient documents solve the jigsaw of the parchment purple spot deterioration and validate the microbial succession model
Cited by: 25
Author(s): Luciana Migliore, Nicoletta Perini, F. Mercuri, S. Orlanducci, Alessandro Rubechini, María Cristina Thaller
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-40873-3

PTMselect: optimization of protein modifications discovery by mass spectrometry
Cited by: 13
Author(s): Renaud T Perchey, Laure Tonini, Marie Tosolini, Jean‐Jacques Fournié, Frédéric Lopez, Arnaud Besson, Frédéric Pont
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-57071-w

Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management
Cited by: 7
Author(s): Simo N. Maduna, Adam Vivian‐Smith, Ólöf Dóra Bartels Jónsdóttir, Albert K. Imsland, Cornelya F. C. Klütsch, Tommi Nyman, Hans Geir Eiken, Snorre B. Hagen
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-58825-7

Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges
Cited by: 51
Author(s): Anindya Sundar Panja, Smarajit Maiti, Bidyut Bandyopadhyay
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-66051-4

Tiered approach for the identification of Mal d 1 reduced, well tolerated apple genotypes
Cited by: 19
Author(s): Emilia Romer, Soraya Chebib, Karl‐Christian Bergmann, Katrin Plate, Sylvia Becker, Christina Ludwig, Chen Meng, Thilo C. Fischer, Werner Dierend, Wilfried Schwab
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-77723-6

Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
Cited by: 13
Author(s): Sonam Gaba, Abha Kumari, Marnix H. Medema, Rajeev Kaushik
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-92641-x

Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies
Cited by: 12
Author(s): Suman Pokhrel, Benjamin R. Kraemer, Scott Burkholz, Daria Mochly‐Rosen
Software Mentions: 3
Published: over 3 years ago

10.4056/sigs.651139

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
Cited by: 60
Author(s): David M. Tanenbaum, Johannes Goll, Sean D. Murphy, P. Naresh Kumar, Nikhat Zafar, Mathangi Thiagarajan, Ramana Madupu, Tanja M. Davidsen, Leonid Kagan, Saul Kravitz, Douglas B. Rusch, Shibu Yooseph
Software Mentions: 3
Published: over 14 years ago

10.4056/sigs.1694706

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
Cited by: 45
Author(s): Hernán Lorenzi, Jeff Hoover, Jason M. Inman, Todd Safford, Sean D. Murphy, Leonid Kagan, Shannon J. Williamson
Software Mentions: 3
Published: over 13 years ago

10.1186/s40793-016-0138-x

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
Cited by: 107
Author(s): Marcel Huntemann, Natalia Ivanova, Konstantinos Mavromatis, H. James Tripp, David Páez-Espino, Kristin Tennessen, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati, Torben Nielsen, Victor Markowitz, Nikos C. Kyrpides
Software Mentions: 3
Published: over 8 years ago

10.3390/toxins13010029

New Insectotoxin from Tibellus Oblongus Spider Venom Presents Novel Adaptation of ICK Fold
Cited by: 3
Author(s): Yuliya V. Korolkova, Ekaterina E. Maleeva, Alexander Mikov, Anna A. Lobas, Elizaveta M. Solovyeva, Mikhail V. Gorshkov, Yaroslav A. Andreev, Steve Peigneur, Jan Tytgat, Fedor D. Kornilov, Владислав А. Лушпа, K.S. Mineev, Sergey A. Kozlov
Software Mentions: 3
Published: almost 4 years ago

10.1128/mSphereDirect.00257-17

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales
Cited by: 52
Author(s): Anne E. Booker, Mikayla A. Borton, Rebecca A. Daly, Susan A. Welch, Carrie Nicora, David Hoyt, Tom Wilson, Samuel O. Purvine, Richard A. Wolfe, Shikha Sharma, Paula J. Mouser, David R. Cole, Mary Lipton, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00295-18

A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by Actinobacteria
Cited by: 35
Author(s): Mallory J. Choudoir, Sam Rossabi, Matthew J. Gebert, Detlev Helmig, Noah Fierer
Software Mentions: 3
Published: over 5 years ago

10.1038/s41396-019-0450-8

Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches
Cited by: 20
Author(s): Szymon P. Szafrański, Mogens Kilian, Ines Yang, Gesa Bei der Wieden, Andreas Winkel, Jan Hegermann, Meike Stiesch
Software Mentions: 3
Published: over 5 years ago

10.1099/ijsem.0.001467

Apiotrichum terrigenum sp. nov., a soil-associated yeast found in both the UK and mainland Europe
Cited by: 11
Author(s): Stephen A. James, Christopher J. Bond, Rachael Stanley, R. Srinivasa Rao, Gábor Péter, Dénes Dlauchy, Ian N. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.1099/ijsem.0.002013

Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur
Cited by: 59
Author(s): Samina Naseeb, Stephen A. James, Haya Alsammar, Christopher J. Michaels, Beatrice Gini, Carmen Nueno‐Palop, Christopher J. Bond, Henry A. McGhie, Ian N. Roberts, Daniela Delneri
Software Mentions: 3
Published: over 7 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.39842

Environmentally-induced epigenetic conversion of a piRNA cluster
Cited by: 23
Author(s): Karine Casier, Valérie Delmarre, Nathalie Gueguen, Catherine Hermant, Elise Viodé, Chantal Vaury, Stéphane Ronsseray, Emilie Brasset, Laure Teysset, Antoine Boivin
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.31250

eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast
Cited by: 34
Author(s): Pilar Martín-Marcos, Fujun Zhou, Charm Karunasiri, Fan Zhang, Jinsheng Dong, Jagpreet S. Nanda, Shardul D. Kulkarni, Neelam Dabas Sen, Mercedes Tamame, Michael Zeschnigk, Jon R. Lorsch, Alan G. Hinnebusch
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms19030738

The Coordinated Activities of nAChR and Wnt Signaling Regulate Intestinal Stem Cell Function in Mice
Cited by: 25
Author(s): Toshio Takahashi, Akira Shiraishi, Jun Murata
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22020514

Transcriptome Analysis and Identification of Lipid Genes in Physaria lindheimeri, a Genetic Resource for Hydroxy Fatty Acids in Seed Oil
Cited by: 3
Author(s): Grace Q. Chen, Won Nyeong Kim, Kumiko Johnson, Mid-Eum Park, Kyeong‐Ryeol Lee, Hyun Uk Kim
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1000151

Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
Cited by: 9
Author(s): Raja Mazumder, Sona Vasudevan
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pcbi.1000218

Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins
Cited by: 22
Author(s): Mark Yandell, Barry Moore, Fidel Salas, Christopher J. Mungall, Andrew R. MacBride, Charles I. White, Martin G. Reese
Software Mentions: 2
Published: about 16 years ago

10.12688/f1000research.2-143.v2

A fragmented alignment method detects a putative phosphorylation site and a putative BRC repeat in the Drosophila melanogaster BRCA2 protein
Cited by: 2
Author(s): Sandeep Chakraborty
Software Mentions: 2
Published: about 11 years ago

10.1002/2211-5463.12047

Pre‐<scp>mRNA</scp>splicing is modulated by antifungal drugs in the filamentous fungusNeurospora crassa
Cited by: 13
Author(s): Niege Silva Mendes, Patrícia M. Silva, Rafael Silva‐Rocha, Nilce Maria Martinez-Rossi, Antônio Rossi
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.6080

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses
Cited by: 0
Author(s): Clícia Grativol, Flávia Thiebaut, Sara Sangi, Patrícia da Fonseca Montessoro, Walaci da Silva Santos, Adriana S. Hemerly, Paulo Cavalcanti Gomes Ferreira
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2148-9-74

Evolutionary history of the iroquois/Irx genes in metazoans
Cited by: 37
Author(s): Pierre Kerner, Aissam Ikmi, Dario Coen, Michel Vervoort
Software Mentions: 2
Published: over 15 years ago

10.7717/peerj.6182

A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis
Cited by: 20
Author(s): Linda Grillová, Keith A. Jolley, David Šmajs, Mathieu Picardeau
Software Mentions: 2
Published: almost 6 years ago

10.3389/fbioe.2020.00635

Prediction of G Protein-Coupled Receptors With CTDC Extraction and MRMD2.0 Dimension-Reduction Methods
Cited by: 8
Author(s): Xingyue Gu, Zhihua Chen, Donghua Wang
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.1332

miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data
Cited by: 19
Author(s): Abhinav Kaushik, Shradha Saraf, Sunil Kumar Mukherjee, Dinesh Gupta
Software Mentions: 2
Published: about 9 years ago

10.1186/s12862-016-0717-x

Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish
Cited by: 23
Author(s): Robert B. Laprairie, Eileen M. Denovan‐Wright, Jonathan Wright
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-54268-x

Isolation and comparative genomics of Mycobacterium tuberculosis isolates from cattle and their attendants in South India
Cited by: 12
Author(s): Kannan Palaniyandi, Narender Kumar, Veerasamy Maroudam, Ahmed Kabir Refaya, Chandrakumar Dolla, S. Balaji, Dhanaraj Baskaran, Kannan Thiruvengadam, Ananthi Rajendran, Sujatha Narayanan, Dhinakar Raj, Soumya Swaminathan, Sharon J. Peacock
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcimb.2018.00236

High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems
Cited by: 48
Author(s): Agustı́n Estrada-Peña, Alejandro Cabezas-Cruz, Thomas V. Pollet, Muriel Vayssier‐Taussat, Jean-François Cosson
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.8699

ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines
Cited by: 7
Author(s): Angelo Damian Armijos Carrion, Damien Daniel Hinsinger, Joeri S. Strijk
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.00434

MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data
Cited by: 10
Author(s): Huijing Zhao, Tihao Huang, Junqing Li, Guojun Liu, Xiguo Yuan
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.2781

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based onrbcLandmatKsequence data
Cited by: 10
Author(s): Thomas Horn, Annette Häser
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13568-014-0022-2

Microbial community in microbial fuel cell (MFC) medium and effluent enriched with purple photosynthetic bacterium (Rhodopseudomonas sp.)
Cited by: 43
Author(s): Tae‐Jin Park, Weijun Ding, Shaoan Cheng, Manreetpal Singh Brar, Angel Po Yee, Hein Min Tun, Fung Ping Leung
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.4386

Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis
Cited by: 23
Author(s): Cheryl L. Morrison, Luke R. Iwanowicz, Thierry M. Work, Elizabeth Fahsbender, Mya Breitbart, Cynthia R. Adams, Deborah D. Iwanowicz, Lakyn R. Sanders, Mathias Ackermann, Robert S. Cornman
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.8385

Obama chez moi! The invasion of metropolitan France by the land planarian Obama nungara (Platyhelminthes, Geoplanidae)
Cited by: 18
Author(s): Jean‐Lou Justine, Leigh Winsor, Delphine Gey, Pierre Gros, Jessica Thévenot
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-9-S1-S8

The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays
Cited by: 7
Author(s): Shu Hwa Chen, Chen Zen Lo, Ming Chi Tsai, Chao A. Hsiung, Chung Yen Lin
Software Mentions: 2
Published: almost 17 years ago

10.3390/pathogens9060513

Functional and Mass Spectrometric Evaluation of an Anti-Tick Antigen Based on the P0 Peptide Conjugated to Bm86 Protein
Cited by: 18
Author(s): Alina Rodríguez-Mallón, Luis Javier González, Pedro E. Encinosa Guzmán, Gervásio Henrique Bechara, Gustavo Seron Sanches, Satomy Pousa, Gleysin Cabrera, Ania Cabrales, Hilda Garay, Raúl Mejías, José Raúl López Álvarez, Yamil Bello Soto, Fabiola Almeida, Osmany Guirola, Rafmary Rodríguez Fernández, Alier Fuentes Castillo, Luis Méndez, Samanta Jiménez, Alexei F. Licea-Navarro, Madelón Portela, Rosario Durán, Mario Pablo Estrada
Software Mentions: 2
Published: over 4 years ago

10.1186/s13071-017-2245-y

The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes
Cited by: 28
Author(s): Wen X. Li, Dong Zhang, K. Boyce, Bingwen Xi, Hong Zou, Shan Wu, Ming Li, Gui T. Wang
Software Mentions: 2
Published: over 7 years ago

10.1017/S0031182019000544

Genetic characterization ofEchinococcusisolates from various intermediate hosts in the Qinghai-Tibetan Plateau Area, China
Cited by: 11
Author(s): Xiumin Han, Yingna Jian, Xueyong Zhang, Liang Ma, Wenjun Zhu, Qiliang Cai, Shile Wu, Xiangqian Wang, Bingqiang Shi
Software Mentions: 2
Published: over 5 years ago

10.3897/zookeys.930.47620

The millipedes collected by the Museum "La Specola" on Madagascar 1989/1991, with the description of three new species of giant pill-millipedes (Diplopoda, Sphaerotheriida, Arthrosphaeridae)
Cited by: 2
Author(s): Thomas Wesener‍, Pooja Avinipully Anilkumar
Software Mentions: 2
Published: over 4 years ago

10.3897/zookeys.869.33997

Taxonomic revision of the genus Copelatus of Madagascar (Coleoptera, Dytiscidae, Copelatinae): the non- erichsonii group species
Cited by: 6
Author(s): Tolotra Ranarilalatiana, Lala Harivelo Raveloson Ravaomanarivo, Johannes Bergsten
Software Mentions: 2
Published: over 5 years ago

10.3390/v11121084

Bovine Foamy Virus: Shared and Unique Molecular Features In Vitro and In Vivo
Cited by: 16
Author(s): Magdalena Materniak-Kornas, Juan Tan, Anke Heit-Mondrzyk, Agnes Hotz‐Wagenblatt, Martin Löchelt
Software Mentions: 2
Published: about 5 years ago

10.3390/vaccines9030236

Single-Shot Vaccines against Bovine Respiratory Syncytial Virus (BRSV): Comparative Evaluation of Long-Term Protection after Immunization in the Presence of BRSV-Specific Maternal Antibodies
Cited by: 8
Author(s): J. F. Valarcher, Sara Hägglund, Katarina Näslund, Luc Jouneau, Ester Malmström, Olivier Boulesteix, Anne Pinard, Dany Leguéré, Alain Deslis, David T. Gauthier, Catherine Dubuquoy, Vincent Pietralunga, Aude Rémot, Alexander Falk, Ganna Shevchenko, Sara Bergström Lind, Claudia von Brömssen, Karin Vargmar, Baoshan Zhang, Peter D. Kwong, María José Rodríguez, Marga García Durán, Isabelle Schwartz-Cornil, Geraldine Taylor, Sabine Riffault
Software Mentions: 2
Published: over 3 years ago

10.3897/mycokeys.53.34761

PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens
Cited by: 16
Author(s): Cécile Gueidan, John A. Elix, Patrick M. McCarthy, Claude Roux, Max Mallen‐Cooper, Gintaras Kantvilas
Software Mentions: 2
Published: over 5 years ago

10.1016/j.omto.2020.05.011

Hypomethylation Causes MIR21 Overexpression in Tumors
Cited by: 27
Author(s): Jun Lü, Ting Tan, Ling Zhu, Huiyue Dong, Ronghua Xian
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2019.00717

Envelope-Specific Recognition Patterns of HIV Vaccine-Induced IgG Antibodies Are Linked to Immunogen Structure and Sequence
Cited by: 6
Author(s): Yuka Nadai, Kathrin Held, Sarah Joseph, Mohamed Ahmed, Verena Hoffmann, David Peterhoff, Marco Missanga, Asli Bauer, Agricola Joachim, Ulf Reimer, Johannes Zerweck, Sheena McCormack, Alethea Cope, Roger Tatoud, Robin J. Shattock, Merlin L. Robb, Eric G. Sandstroem, Michael Höelscher, Leonard Maboko, Muhammad Bakari, Arne Kroidl, Ralf Wagner, Jonathan Weber, Georgios Pollakis, Christof Geldmacher
Software Mentions: 2
Published: over 5 years ago

10.1111/j.1365-2958.2008.06481.x

A novel streptococcal integrative conjugative element involved in iron acquisition
Cited by: 58
Author(s): Zoe Heather, Matthew T. G. Holden, Karen F. Steward, Julian Parkhill, Lijiang Song, Gregory L. Challis, Carl Robinson, Nicholas Davis-Poynter, Andrew S. Waller
Software Mentions: 2
Published: about 16 years ago

10.1093/molbev/msy212

Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate
Cited by: 16
Author(s): Kai Zeng, Benjamin C. Jackson, Henry J Barton
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2018.01686

ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline
Cited by: 15
Author(s): Oren Avram, Anna Vaisman-Mentesh, Dror Yehezkel, Haim Ashkenazy, Tal Pupko, Yariv Wine
Software Mentions: 2
Published: over 6 years ago

10.1186/1759-8753-4-13

Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
Cited by: 8
Author(s): Bárbara Negre, Patricia Simpson
Software Mentions: 2
Published: almost 12 years ago

10.3389/fimmu.2017.01796

Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library
Cited by: 21
Author(s): Audrey Hémadou, Véronique Giudicelli, Melissa Smith, Marie Paule Lefranc, Patrice Duroux, Sofia Kossida, Cheryl Heiner, N. Lance Hepler, John Kuijpers, Alexis Groppi, Jonas Korlach, Philippe Mondon, Florence Ottonès, Marie‐Josée Jacobin‐Valat, Jeanny Laroche‐Traineau, Gisèle Clofent‐Sanchez
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2020.628374

Protective Effects of Lactobacillus plantarum 16 and Paenibacillus polymyxa 10 Against Clostridium perfringens Infection in Broilers
Cited by: 17
Author(s): Li Gong, Baikui Wang, Yuguang Zhou, Li Tang, Zihan Zeng, Huihua Zhang, Weifen Li
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2148-9-94

Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids
Cited by: 20
Author(s): Pierre Kerner, Johanne Hung, Julien Béhague, Martine Le Gouar, Guillaume Balavoine, Michel Vervoort
Software Mentions: 2
Published: over 15 years ago

Projects: cran: fasta

Papers Mentioning fasta 848