cran: fasta | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/btab102

Genozip: a universal extensible genomic data compressor
Cited by: 15
Author(s): Divon Mordechai Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas
Software Mentions: 3
Published: almost 4 years ago

10.1093/bioinformatics/btab048

De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance
Cited by: 7
Author(s): Corentin Molitor, Tomasz J. Kurowski, Pedro Machado Almeida, Pramod Eerolla, Daniel Spindlow, Sandeep Kashyap, Bijendra Singh, H. C. Prasanna, Andrew J. Thompson, Fady Mohareb
Software Mentions: 3
Published: almost 4 years ago

10.1093/bioinformatics/bty338

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Cited by: 49
Author(s): Matthew B. Stocks, Irina Mohorianu, Matthew Beckers, Claudia Paicu, Simon Moxon, Joshua Thody, Tamás Dalmay, Vincent Moulton
Software Mentions: 3
Published: over 6 years ago

10.6026/97320630013269

Potential Hemoglobin A/F role in clinical Malaria
Cited by: 1
Author(s): Vikky Awasthi, Debprasad Chattopadhyay, Jyoti Das
Software Mentions: 3
Published: about 7 years ago

10.1155/2014/187105

Genome-Wide Uncovering of STAT3-Mediated miRNA Expression Profiles in Colorectal Cancer Cell Lines
Cited by: 18
Author(s): Jufeng Zhang, Xia Luo, Huiming Li, Ling Deng, Ying Wang
Software Mentions: 3
Published: almost 11 years ago

10.1155/2014/462135

miRSeq: A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling
Cited by: 16
Author(s): Pan Cheng, Kuo‐Wang Tsai, Tzu Min Hung, Wei Chen Lin, Chao Pan, Hong‐Ren Yu, Sung Chou Li
Software Mentions: 3
Published: almost 11 years ago

10.1155/2019/8016120

Study on miRNAs in Pan-Cancer of the Digestive Tract Based on the Illumina HiSeq System Data Sequencing
Cited by: 11
Author(s): Cheng-Chou Lai, Xuzhi Liang, Xiu-Yun Liang, Shaolin Ma, Junguo Li, Mingfang Shi, Xu Zhu, Huihua Lan, Jiang‐Hui Zeng
Software Mentions: 3
Published: about 5 years ago

10.1016/j.ccell.2018.11.018

The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease
Cited by: 40
Author(s): Lindsay Kosack, Bettina Wingelhofer, Alexandra Popa, Anna Orlova, Benedikt Agerer, Bojan Vilagos, Peter Marynen, Katja Parapatics, Alexander Lercher, Anna Ringler, Johanna Klughammer, Mark J. Smyth, Kseniya Khamina, Hatoon Baazim, Elvin D. de Araujo, David A. Rosa, Jisung Park, Gary Tin, Siawash Ahmar, Patrick T. Gunning, Christoph Bock, Hannah V. Siddle, Gregory M. Woods, Stefan Kubicek, Elizabeth P. Murchison, Keiryn L. Bennett, Richard Moriggl, Andréas Bergthaler
Software Mentions: 3
Published: almost 6 years ago

10.1007/s00335-019-09799-z

A high-density genetic map and molecular sex-typing assay for gerbils
Cited by: 7
Author(s): Thomas D. Brekke, S.M. Supriya, Megan G Denver, Angharad Thom, Katherine A. Steele, John F. Mulley
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000096

Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing
Cited by: 26
Author(s): Sharif Shaaban, Lauren A. Cowley, Sean P. McAteer, Claire Jenkins, Timothy J. Dallman, James L. Bono, David L. Gally
Software Mentions: 3
Published: almost 8 years ago

10.1099/mgen.0.000049

Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates of Staphylococcus aureus
Cited by: 4
Author(s): Debra Smith, Matthew K. Siggins, Magdalena Gierula, Bruno Pichon, Claire E. Turner, Nicola N. Lynskey, Mia Mosavie, Angela Kearns, Robert J. Edwards, Shiranee Sriskandan
Software Mentions: 3
Published: almost 9 years ago

10.1128/MRA.00257-21

Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing
Cited by: 2
Author(s): Nikola Palevich, Paul Maclean, Luis Carvalho, Ruy Jáuregui
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9081769

B7 Family Molecule VSIG4 Regulates Intestinal Anti-Enterohemorrhagic Escherichia coli Immunity by Altering Gut Flora Diversity
Cited by: 2
Author(s): Zi He, Jiajia Li, Saisai Gong, Li Xing, Ye Sun, Jianxin Wang, Tao Li, Nianzhi Ning, Liangyan Zhang, Wenjing Yu, Di Luo, Hui Wang
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9040855

Use of an Alignment-Free Method for the Geographical Discrimination of GTPVs Based on the GPCR Sequences
Cited by: 0
Author(s): Tesfaye Rufael, Yang Liu, Melaku Sombo, Jacqueline Kasiiti Lichoti, Janchivdorj Erdenebaatar, Bazartseren Boldbaatar, Reingard Grabherr, Tirumala Bharani Kumar Settypalli, Francisco J. Berguido, Angelika Loitsch, Delesa Damena, Giovanni Cattoli, Adama Diallo, Charles Euloge Lamien
Software Mentions: 3
Published: over 3 years ago

10.1093/molbev/msaa257

Divergence and Remarkable Diversity of the Y Chromosome in Guppies
Cited by: 26
Author(s): Pedro Almeida, Benjamin A. Sandkam, Jeffrey J. Morris, Iulia Darolti, Felix Breden, Judith E. Mank
Software Mentions: 3
Published: about 4 years ago

10.1093/molbev/msaa318

A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference
Cited by: 1
Author(s): Jeremy M. Beaulieu, Brian C. O’Meara, Michael A. Gilchrist
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12943-020-01155-z

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme
Cited by: 57
Author(s): Mathilde Cheray, Amandine Etcheverry, Camille Jacques, Romain Pacaud, Gwenola Bougras-Cartron, Marc Aubry, Florent Denoual, Pierre Peterlongo, Arulraj Nadaradjane, Joséphine Briand, Farida Akcha, Dominique Heymann, François M. Vallette, Jean Mosser, Benjamin Ory, Pierre-François Cartron
Software Mentions: 3
Published: over 4 years ago

10.1016/j.molcel.2018.12.023

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex
Cited by: 67
Author(s): C.P. Hill, Vytautė Boreikaitė, Aman Kumar, Ana Casañal, Peter Kubík, Gianluca Degliesposti, Sarah Maslen, Angelica Mariani, Ottilie von Loeffelholz, Mathias Girbig, Mark Skehel, Lori A. Passmore
Software Mentions: 3
Published: over 5 years ago

10.1093/ve/veab001

Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices
Cited by: 9
Author(s): Michela Chiumenti, Beatriz Navarro, Thierry Candresse, Ricardo Flores, Francesco Di Serio
Software Mentions: 3
Published: almost 4 years ago

10.1093/ve/veab064

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
Cited by: 649
Author(s): Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abudahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W. Attwood, David M. Aanensen, Edward C. Holmes, Oliver G. Pybus, Andrew Rambaut
Software Mentions: 3
Published: over 3 years ago

10.12688/wellcomeopenres.11275.1

Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data
Cited by: 8
Author(s): Mandy J. Peffers, Andrew R. Jones, Antony McCabe, James Anderson
Software Mentions: 3
Published: over 7 years ago

10.1186/s13071-018-3242-5

Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes
Cited by: 21
Author(s): Pavel B. Klimov, Maciej Skoracki, André V. Bochkov
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13071-020-04125-y

Slight temperature changes cause rapid transcriptomic responses in Trypanosoma cruzi metacyclic trypomastigotes
Cited by: 10
Author(s): Lissa Cruz-Saavedra, Marina Muñoz, Luz Helena Patiño, Gustavo Adolfo Calderón Vallejo, Felipe Guhl, Juan David Ramírez
Software Mentions: 3
Published: over 4 years ago

10.3390/pathogens10020167

Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection
Cited by: 5
Author(s): Patrícia Gonzaga Paulino, Gabriela Lopes Vivas Vitari, Antônio Mauro Rezende, Joana Couto, Sandra Antunes, Ana Domingos, Maristela Peckle, Carlos Luiz Massard, Flávio Marcos Gomes Araújo, Huarrisson Azevedo Santos
Software Mentions: 3
Published: almost 4 years ago

10.3390/pathogens9110899

Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species
Cited by: 23
Author(s): Martin Hölzer, Lisa-Marie Barf, Kevin Lamkiewicz, Fabien Vorimore, Marie Lataretu, Alison Favaroni, Christiane Schnee, Karine Laroucau, Konrad Sachse
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.1527

Genome-wide identification of hypoxia-induced enhancer regions
Cited by: 8
Author(s): Nick Kamps-Hughes, Jessica L. Preston, Melissa A Randel, Eric A. Johnson
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.7853

Complete mitochondrial genome sequence ofLabriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China
Cited by: 9
Author(s): Yan YuChen, Gengyun Niu, Yaoyao Zhang, Qianying Ren, Shiyu Du, Bocheng Lan, Meicai Wei
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.1420

Swarm v2: highly-scalable and high-resolution amplicon clustering
Cited by: 397
Author(s): Frédéric Mahé, Torbjørn Rognes, Christopher Quince, Colomban de Vargas, Micah Dunthorn
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.391

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
Cited by: 26
Author(s): Aureliano Bombarely, Jeremy E. Coate, Jeff J. Doyle
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.6898

Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons
Cited by: 24
Author(s): Xavier Pochon, Patricia Wecker, Michael Stat, Véronique Berteaux‐Lecellier, Gaël Lecellier
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.5515

Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data
Cited by: 5
Author(s): Robert A. Petit, James M. Hogan, Matthew Ezewudo, Sandeep J. Joseph, Timothy D. Read
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.11354

A Python script to merge Sanger sequences
Cited by: 0
Author(s): Cen Chen, Bingguo Lu, Xiaofang Huang, Chuyun Bi, Lili Zhao, Yunzhuo Hu, Xuanyang Chen, Shu‐Fang Lin, Kai Huang
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.9852

ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
Cited by: 6
Author(s): Alastair Skeffington, Andreas Donath
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.4742

DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes
Cited by: 3
Author(s): Alexander Seitz, Friederike Hanssen, Kay Nieselt
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.7421

Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weedAmbrosia artemisiifoliaL. (Asteraceae)
Cited by: 13
Author(s): Kinga Mátyás, Géza Hegedűs, János Taller, Eszter Farkas, Kincső Decsi, Barbara Kutasy, Nikoletta Kálmán, Erzsébet Nagy, Balázs Kolics, Eszter Virág
Software Mentions: 3
Published: about 5 years ago

10.1111/pbi.12513

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
Cited by: 96
Author(s): Helena Staňková, Alex Hastie, Saki Chan, Jan Vrána, Zuzana Tulpová, Marie Kubaláková, Paul Visendi, Satomi Hayashi, Ming‐Cheng Luo, Jacqueline Batley, David Edwards, Jaroslav Doležel, Hana Šimková
Software Mentions: 3
Published: almost 9 years ago

10.1007/s11816-013-0282-3

Genomics and bioinformatics resources for translational science in Rosaceae
Cited by: 20
Author(s): Sook Jung, Dorrie Main
Software Mentions: 3
Published: over 11 years ago

10.3390/plants9020268

CRISPR/Cas9-Mediated Mutagenesis of RCO in Cardamine hirsuta
Cited by: 1
Author(s): Claire Lessa Alvim Kamei, Bjorn Pieper, Stefan Laurent, Miltos Tsiantis, Peter Huijser
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1008815

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Cited by: 0
Author(s): Phillip A. Richmond, Alice M. Kaye, Godfrain Jacques Kounkou, Tamar V. Av-Shalom, Wyeth W. Wasserman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1007845

PhANNs, a fast and accurate tool and web server to classify phage structural proteins
Cited by: 44
Author(s): Adrian Cantu, Peter Salamon, Victor Seguritan, Jackson Redfield, David Salamon, Robert A. Edwards, Anca M. Segall
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1004805

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cited by: 73
Author(s): Vaclav Cvicek, William A. Goddard, Ravinder Abrol
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1007365

Nucleosome positioning sequence patterns as packing or regulatory
Cited by: 3
Author(s): Erinija Pranckevičienė, Sergey Hosid, Nathan Liang, Ilya Ioshikhes
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1003345

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
Cited by: 120
Author(s): Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1009418

Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers
Cited by: 21
Author(s): Findley R. Finseth, Thomas C. Nelson, Lila Fishman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1002502

Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Arabidopsis Resistance Gene
Cited by: 58
Author(s): Sandra Goritschnig, Ksenia V. Krasileva, Douglas Dahlbeck, Brian J. Staskawicz
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pgen.1006550

Mutation Accumulation in an Asexual Relative of Arabidopsis
Cited by: 52
Author(s): John T Lovell, R. Williamson, Stephen I. Wright, John McKay, Timothy F. Sharbel
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1005406

Tempo and Mode of Transposable Element Activity in Drosophila
Cited by: 97
Author(s): Robert Kofler, Viola Nolte, Christian Schlötterer
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pntd.0009828

Mining nematode protein secretomes to explain lifestyle and host specificity
Cited by: 9
Author(s): Lucienne Tritten, Cristina Ballesteros, Robin N. Beech, Timothy G. Geary, Yovany Moreno
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pntd.0002616

Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development
Cited by: 62
Author(s): Jatin Shrinet, Shanu Jain, Jaspreet Jain, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pntd.0002591

Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains
Cited by: 19
Author(s): Julie Clément, Ève Toulza, Mathieu Gautier, Hugues Parrinello, David Roquis, Jérôme Boissier, Anne Rognon, Hélène Moné, Gabriel Mouahid, Jérǒme Buard, Guillaume Mitta, Christoph Grunau
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pntd.0007576

ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.
Cited by: 3
Author(s): David Aciole Barbosa, Fabiano Bezerra Menegídio, Valquíria Campos Alencar, Rafael S. Gonçalves, Juliana de Fátima Santos Silva, Renata Ozelami Vilas Boas, Yara Natércia Lima Faustino de Maria, Daniela Jabés, Regina Costa de Oliveira, Luiz R. Nunes
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0002557

Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi
Cited by: 23
Author(s): Christina Bronowski, María Fookes, Ruth Gilderthorp, Kevin E. Ashelford, Simon R. Harris, Ajib Phiri, Neil Hall, Michael A. Gordon, John Wain, C. A. Hart, Paul Wigley, Nicholas R. Thomson, Craig Winstanley
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0015617

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology
Cited by: 61
Author(s): Martin Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Reginald H. Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A. Aziz Aboobaker
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0146283

Multiple and Diverse vsp and vlp Sequences in Borrelia miyamotoi, a Hard Tick-Borne Zoonotic Pathogen
Cited by: 34
Author(s): Alan G. Barbour
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0192362

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification
Cited by: 21
Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. N. Rao, K. Surekha, V. Ravindra Babu
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0232528

Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction
Cited by: 13
Author(s): Maxim V. Shapovalov, Roland L. Dunbrack, Slobodan Vučetić
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0010795

Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis
Cited by: 90
Author(s): Dion Lepp, Bryan Roxas, Valeria R. Parreira, Pradeep Reddy Marri, Everett L. Rosey, Joshua Gong, J. Glenn Songer, Gayatri Vedantam, John F. Prescott
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0183898

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci
Cited by: 33
Author(s): Sanjay Kumar Shukla, Zhan Ye, Scott Sandberg, Iris Reyes, Thomas R. Fritsche, Matthew Keifer
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0157718

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance
Cited by: 132
Author(s): Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Isabell Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0091938

Characterisation and Comparison of Lactating Mouse and Bovine Mammary Gland miRNomes
Cited by: 50
Author(s): Sandrine Le Guillou, Sylvain Marthey, Dénis Laloë, Johann Laubier, Lenha Mobuchon, Christine Leroux, Fabienne Le Provost
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0176469

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads
Cited by: 59
Author(s): Thomas Nordahl Petersen, Oksana Lukjancenko, Martin Christen Frølund Thomsen, Maria Maddalena Sperotto, Ole Lund, Frank Møller Aarestrup, Thomas Sicheritz-Pontén
Software Mentions: 3
Published: over 7 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

10.1371/journal.pone.0171410

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks
Cited by: 174
Author(s): Ramzan Umarov, Victor Solovyev
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0150599

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment
Cited by: 45
Author(s): Ben Bond‐Lamberty, H. Bolton, Sarah Fansler, Alejandro Heredia-Langner, Chongxuan Liu, Lee Ann McCue, J.L. Smith, Vanessa Bailey
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0103357

Purifying Selection in Deeply Conserved Human Enhancers Is More Consistent than in Coding Sequences
Cited by: 8
Author(s): Dilrini De Silva, Richard A. Nichols, Greg Elgar
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0134719

Differential mRNA Accumulation upon Early Arabidopsis thaliana Infection with ORMV and TMV-Cg Is Associated with Distinct Endogenous Small RNAs Level
Cited by: 14
Author(s): Diego Zavallo, Humberto Julio Debat, Gabriela Conti, Carlos Augusto Manacorda, Marcelo Rodríguez, Sebastián Asurmendi
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0231814

BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries?
Cited by: 73
Author(s): Mikko Pentinsaari, Sujeevan Ratnasingham, Scott E. Miller, Paul D. N. Hebert
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0129384

MLgsc: A Maximum-Likelihood General Sequence Classifier
Cited by: 4
Author(s): Thomas Junier, Vincent Hervé, Tina Wunderlin, Pilar Junier
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0085104

On the Origin and Evolutionary History of NANOG
Cited by: 21
Author(s): Pierluigi Scerbo, Gabriel V. Markov, Céline Vivien, Laurent Kodjabachian, Barbara Demeneix, Laurent Coen, Fabrice Girardot
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0255612

Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes
Cited by: 10
Author(s): Rajesh Kumar Vaid, Zoozeal Thakur, Taruna Anand, Sanjay Kumar, Bhupendra Nath Tripathi
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0182392

metaSNV: A tool for metagenomic strain level analysis
Cited by: 93
Author(s): Paul Igor Costea, Robin Munch, Luís Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0253797

High-throughput sequencing reveals genetic determinants associated with antibiotic resistance in Campylobacter spp. from farm-to-fork
Cited by: 13
Author(s): Shaimaa F. Mouftah, José F. Cobo‐Díaz, Avelino Álvarez‐Ordóñez, Menattallah Elserafy, Nehal A. Saif, Asmaa Sadat, Ayman El-Shibiny, Mohamed Elhadidy
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0036456

Determining the Repertoire of Immunodominant Proteins via Whole-Genome Amplification of Intracellular Pathogens
Cited by: 12
Author(s): Michael J. Dark, Anna Lundgren, Anthony F. Barbet
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0046334

A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients
Cited by: 51
Author(s): Ron M. Kagan, Erik P. Johnson, Martin Siaw, Pinaki Biswas, Douglass Chapman, Zhaohui Su, Jamie L. Platt, Rick L. Pesano
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0022060

Modeling Disordered Regions in Proteins Using Rosetta
Cited by: 26
Author(s): Ray Yu Ruei Wang, Yanping Han, Kristina Krassovsky, William Sheffler, Michael D. Tyka, David Baker
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0251878

Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
Cited by: 2
Author(s): Eric Garcia, Daniel B Wright, Remy Gatins, May B. Roberts, Hudson T. Pinheiro, Eva Salas, Jei-Ying Chen, Jacob R. Winnikoff, Giacomo Bernardi
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0124633

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
Cited by: 762
Author(s): Manuel Stemmer, Thomas Thumberger, Maria del Sol Keyer, Joachim Wittbrodt, Juan L. Mateo
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0098402

Blood Feeding and Plasmodium Infection Alters the miRNome of Anopheles stephensi
Cited by: 39
Author(s): Shanu Jain, Vandita Rana, Jatin Shrinet, Anil Sharma, T. Adak, Sujatha Sunil, Raj K. Bhatnagar
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0050978

Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae
Cited by: 91
Author(s): Martin Carr, Douda Bensasson, Casey M. Bergman
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12014-017-9159-8

Distinct proteome pathology of circulating microparticles in systemic lupus erythematosus
Cited by: 18
Author(s): Ole Østergaard, Christoffer Tandrup Nielsen, Julia T. Tanassi, Line V. Iversen, Søren Jacobsen, Niels H. H. Heegaard
Software Mentions: 3
Published: over 7 years ago

10.1016/j.csbj.2016.09.004

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations
Cited by: 21
Author(s): Hervé Seligmann
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.dib.2020.105820

Multi-tissue Siberian sturgeon RNA sequencing data
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, Denise Vizziano-Cantonnet
Software Mentions: 3
Published: over 4 years ago

10.1093/database/bau102

PolyprOnline: polyproline helix II and secondary structure assignment database
Cited by: 35
Author(s): Romain Chebrek, Sylvain Léonard, Alexandre G. de Brevern, Jean‐Christophe Gelly
Software Mentions: 3
Published: about 10 years ago

10.1093/database/baz131

RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou’s five-step rule
Cited by: 49
Author(s): Lei Zheng, Shenghui Huang, Nengjiang Mu, Haoyue Zhang, Jiayu Zhang, Yu Chang, Lei Yang, Yongchun Zuo
Software Mentions: 3
Published: almost 6 years ago

10.1093/database/baz155

PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
Cited by: 58
Author(s): Elisa Banchi, Claudio Gennaro Ametrano, Samuele Greco, D Stanković, Alberto Pallavicini
Software Mentions: 3
Published: almost 5 years ago

10.1093/database/bau022

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
Cited by: 64
Author(s): Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder
Software Mentions: 3
Published: almost 11 years ago

10.1093/database/baaa046

ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)
Cited by: 1
Author(s): Jeevan Karloss Antony Samy, Odd Arne Rognli, Mallikarjuna Rao Kovi
Software Mentions: 3
Published: almost 5 years ago

10.1002/ece3.1928

Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect
Cited by: 31
Author(s): Jeffrey D. Lozier, Jason M. Jackson, Michael E. Dillon, James P. Strange
Software Mentions: 3
Published: almost 9 years ago

10.1155/2013/160168

Expression Profiling and Proteomic Analysis of JIN Chinese Herbal Formula in Lung Carcinoma H460 Xenografts
Cited by: 1
Author(s): Liqin Zheng, Weiyi Zhang, Miao Jiang, Huarong Zhang, Fei Xiong, Yang Yu, Meijuan Chen, Jing Zhou, Xiaoming Dai, Yuping Tang, Ming Jiang, Mingyan Wang, Ge Cheng, Jin‐Ao Duan, Wei Yu, Biaoyang Lin, Haian Fu, Xu Zhang
Software Mentions: 3
Published: almost 12 years ago

10.12688/f1000research.5486.1

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
Cited by: 16
Author(s): Andrew C.R. Martin
Software Mentions: 3
Published: about 10 years ago

10.12688/f1000research.13724.1

Identification of microsatellite loci in sea anemones Aulactinia stella and Cribrinopsis albopunctata (family Actiniidae)
Cited by: 0
Author(s): Е. С. Бочарова, Alexey A. Sergeev, A. A. Volkov
Software Mentions: 3
Published: over 6 years ago

10.12688/f1000research.2-103.v1

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors
Cited by: 139
Author(s): Thomas B. Kepler
Software Mentions: 3
Published: over 11 years ago

10.1093/femsec/fiaa057

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost
Cited by: 25
Author(s): Yaxin Xue, Inge Jonassen, Lise Øvreås, Neslihan Taş
Software Mentions: 3
Published: over 4 years ago

10.3389/fcimb.2020.00374

TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon
Cited by: 36
Author(s): José M. C. Ribeiro, Ben J. Mans
Software Mentions: 3
Published: over 4 years ago

10.3389/fcimb.2020.00041

Tick-Borne Encephalitis Virus Infection Alters the Sialome of Ixodes ricinus Ticks During the Earliest Stages of Feeding
Cited by: 9
Author(s): Charles E. Hart, José M. C. Ribeiro, Mária Kazimírová, Saravanan Thangamani
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2021.618170

A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data
Cited by: 0
Author(s): Nikolaos Pechlivanis, Anastasis Togkousidis, Maria Tsagiopoulou, Stefanos P. Sgardelis, Ilias Kappas, Fotis Psomopoulos
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00292

FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments
Cited by: 3
Author(s): Josiah Seaman, Richard J. A. Buggs
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2016.00681

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires
Cited by: 16
Author(s): Donald W. Lee, Ilja V. Khavrutskii, Anders Wallqvist, Sina Bavari, Christopher L. Cooper, Sidhartha Chaudhury
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2020.01081

Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods
Cited by: 30
Author(s): Carolyne Caetano Gonçalves, Thiago Bruce, Caio de Oliveira Gorgulho Silva, Edivaldo Ximenes Ferreira Fillho, Eliane Ferreira Noronha, Magnus Carlquist, Nádia Skorupa Parachin
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2014.00034

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN
Cited by: 88
Author(s): Marc G. Dumont, Claudia Lüke, Yangfan Deng, Peter Frenzel
Software Mentions: 3
Published: almost 11 years ago

Projects: cran: fasta

Papers Mentioning fasta 848