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: fasta

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

Fast Adaptive Shrinkage/Thresholding Algorithm
1 version
Latest release: about 6 years ago
483 downloads last month

Papers Mentioning fasta 848

10.1099/mgen.0.000224
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Cited by: 110
Author(s): Sergio Arredondo-Alonso, Malbert R. C. Rogers, Johanna C. Braat, Tess D. Verschuuren, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pone.0069666
GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data
Cited by: 21
Author(s): Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Maria Simi, Rita Shaknovich, Fabien Campagne
Software Mentions: 5
Published: almost 11 years ago
10.1038/s41598-020-66374-2
Mutations in virus-derived small RNAs
Cited by: 6
Author(s): Deepti Nigam, Katherine LaTourrette, Hernán García-Ruíz
Software Mentions: 5
Published: almost 4 years ago
10.1186/s40064-015-1609-z
Structural homology guided alignment of cysteine rich proteins
Cited by: 16
Author(s): Thomas Shafee, Andrew Robinson, Nicole. Van Der Weerden, Marilyn A. Anderson
Software Mentions: 5
Published: over 8 years ago
10.1371/journal.pone.0103441
Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: almost 10 years ago
10.1186/s12864-019-6131-1
Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies
Cited by: 19
Author(s): Linda Beauclair, Christelle Ramé, Peter Arensburger, Benoît Piégu, Florian Guillou, Joëlle Dupont, Yves Bigot
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0246901
The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus
Cited by: 6
Author(s): Yamelie A. Martínez, Xianwu Guo, Diana Patricia Portales-Pérez, Gildardo Rivera, Julio Enrique Castañeda-Delgado, Carlos A. García-Pérez, José Antonio Enciso-Moreno, Edgar E. Lara-Ramírez
Software Mentions: 4
Published: over 3 years ago
10.1038/sdata.2014.45
Long-read, whole-genome shotgun sequence data for five model organisms
Cited by: 130
Author(s): Kristi E Kim, Paul Peluso, Primo Babayan, P. Jane Yeadon, Charles Yu, William W. Fisher, Chen-Shan Chin, Nicole A Rapicavoli, David R. Rank, Joaquim Li, David Catcheside, S Celniker, Adam M. Phillippy, Casey M. Bergman, Jane M. Landolin
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2105-14-334
Fastphylo: Fast tools for phylogenetics
Cited by: 17
Author(s): Muhammad Alam Zaib Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimerà, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
Software Mentions: 4
Published: over 10 years ago
10.26508/lsa.202000962
Muscarinic receptor M3 contributes to intestinal stem cell maintenance via EphB/ephrin-B signaling
Cited by: 7
Author(s): Toshio Takahashi, Akira Shiraishi, Jun Murata, Shin Matsubara, Satsuki Nakaoka, Shinji Kirimoto, Masatake Osawa
Software Mentions: 4
Published: almost 3 years ago
10.1093/gigascience/giz110
Evaluation of computational genotyping of structural variation for clinical diagnoses
Cited by: 34
Author(s): Varuna Chander, Richard A. Gibbs, Fritz J. Sedlazeck
Software Mentions: 4
Published: over 4 years ago
10.1093/bib/bby042
Microbial genomic island discovery, visualization and analysis
Cited by: 59
Author(s): Claire Bertelli, Keith E Tilley, Fiona S. L. Brinkman
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0015147
Analysis of Ultra Low Genome Conservation in Clostridium difficile
Cited by: 58
Author(s): Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
Software Mentions: 4
Published: over 13 years ago
10.1073/pnas.2105968118
Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues
Cited by: 149
Author(s): Liguo Zhang, Alexsia Richards, M. Inmaculada Barrasa, Stephen H. Hughes, Richard A. Young, Rudolf Jaenisch
Software Mentions: 4
Published: about 3 years ago
10.1038/srep23518
The chemosensory receptors of codling moth Cydia pomonella–expression in larvae and adults
Cited by: 46
Author(s): William B. Walker, Francisco Gonzalez, Stephen F. Garczynski, Peter Witzgall
Software Mentions: 4
Published: about 8 years ago
10.1186/1471-2105-5-130
Cited by: 92
Author(s): Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen P. Ficklin, Il-Hyung Cho, Albert G. Abbott, Jeffrey Tomkins, Dorrie Main
Software Mentions: 4
Published: over 20 years ago
10.1186/s13059-018-1590-2
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
Cited by: 249
Author(s): Mihaela Pertea, Alaina Shumate, Geo Pertea, Ales Varabyou, Florian P. Breitwieser, Yu Chi Chang, Anil K. Madugundu, Akhilesh Pandey, Steven L. Salzberg
Software Mentions: 4
Published: over 5 years ago
10.1155/2016/7863706
Reconstruction of the Fatty Acid Biosynthetic Pathway ofExiguobacterium antarcticumB7 Based on Genomic and Bibliomic Data
Cited by: 6
Author(s): Regiane Kawasaki, Rafael Azevedo Baraúna, Artur M. S. Silva, Marta S. P. Carepo, Rui Oliveira, Rui Marques, Rommel Thiago Jucá Ramos, Maria Paula Cruz Schneider
Software Mentions: 4
Published: over 8 years ago
10.1186/s13059-020-02131-y
The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication
Cited by: 42
Author(s): Hélène Badouin, Amandine Velt, François Gindraud, Timothée Flutre, Vincent Dumas, Sonia Vautrin, William Marande, Jonathan Corbi, Erika Sallet, Jérémy Ganofsky, Sylvain Santoni, Dominique Guyot, Eugenia Ricciardelli, Kristen Jepsen, Jos Käfer, Hélène Bergès, Éric Duchêne, Franck Picard, Philippe Hugueney, Raquel Tavares, Roberto Baciliéri, Camille Rustenholz, Gabriel Marais
Software Mentions: 4
Published: over 3 years ago
10.1155/2014/264519
A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Cited by: 6
Author(s): Preston Leung, Rowena A. Bull, Andrew R. Lloyd, Fabio Luciani
Software Mentions: 4
Published: over 10 years ago
10.1534/genetics.118.301482
Diverse Lineages of <i>Candida albicans</i> Live on Old Oaks
Cited by: 54
Author(s): Douda Bensasson, Jo Dicks, John M. Ludwig, Christopher J. Bond, Adam Elliston, Ian N. Roberts, Stephen A. James
Software Mentions: 4
Published: over 5 years ago
10.1093/biomethods/bpab005
Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease
Cited by: 7
Author(s): Nasim Ahmed, Imran Amin, Syed Shan-e-Ali Zaidi, Saleem Ur Rahman, Muhammad Farooq, Claude Fauquet, Shahid Mansoor
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0168397
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data
Cited by: 8
Author(s): Guillaume Carissimo, Marius van den Beek, Kenneth D. Vernick, Christophe Antoniewski
Software Mentions: 4
Published: over 7 years ago
10.1016/j.gpb.2018.11.002
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
Cited by: 8
Author(s): Valentina Galata, Cédric Christian Laczny, Christina Backes, Georg Hemmrich-Stanisak, Susanne Schmolke, André Franke, Eckart Meese, Mathias Herrmann, Lutz von Müller, Achim Plum, Rolf Müller, Cord Stähler, Andreas E. Posch
Software Mentions: 4
Published: about 5 years ago
10.6026/97320630014123
Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks
Cited by: 15
Author(s): Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, S. R. Mishra, Sandhya Kp, Rai
Software Mentions: 4
Published: about 6 years ago
10.6026/97320630013249
Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae
Cited by: 33
Author(s): Priyanka Jain, Vinay Sharma, Himanshu Dubey, Pankaj Kumar Singh, Ritu Kapoor, Mandeeep Kumari, Jaya Singh, Deepak Pawar, Deepak Singh Bisht, Amolkumar U. Solanke, Tapan Kumar Mondal, Tilak Raj Sharma
Software Mentions: 4
Published: over 6 years ago
10.3390/genes9080379
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Cited by: 22
Author(s): George C. diCenzo, Klaudia Dębiec, Jan Krzysztoforski, Witold Uhrynowski, Alessio Mengoni, Camilla Fagorzi, Adrian Górecki, Łukasz Dziewit, Tomasz Bajda, Grzegorz Rzepa, Łukasz Drewniak
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0220843
Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs
Cited by: 89
Author(s): Donghyun Shin, Sung-Ho Chang, Paul Bogere, KyeongHye Won, Jae-Ho Choi, Yun‐Sang Choi, Hak Kyo Lee, Jin Hur, Byung-Yong Park, Young-Hoon Kim, Jae-Young Heo
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0025851
Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga
Cited by: 200
Author(s): Michael T. Guarnieri, Ambarish Nag, Sharon Smolinski, Al Darzins, Michael Seibert, Philip T. Pienkos
Software Mentions: 4
Published: over 12 years ago
10.1155/2015/904541
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies
Cited by: 24
Author(s): Alexandre G. de Brevern, Jean-Philippe Meyniel, Cécile Fairhead, Cécile Neuveglise, Alain Malpertuy
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0145031
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
Cited by: 27
Author(s): Margaret Staton, Teodora Best, Sudhir Khodwekar, Sandra A. Owusu, Tao Xu, Yi Xu, Tara Jennings, Richard Cronn, Aru K. Arumuganathan, Mark V. Coggeshall, Oliver Gailing, Haiying Liang, Jeanne Romero‐Severson, Scott E. Schlarbaum, John E. Carlson
Software Mentions: 4
Published: over 8 years ago
10.1534/g3.117.300495
Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies
Cited by: 31
Author(s): Thomas D. Brekke, Katherine A. Steele, John F. Mulley
Software Mentions: 4
Published: over 6 years ago
10.3389/fpls.2016.00847
De novo Transcriptome Sequencing to Dissect Candidate Genes Associated with Pearl Millet-Downy Mildew (Sclerospora graminicola Sacc.) Interaction
Cited by: 36
Author(s): Kalyani S. Kulkarni, Harshvardhan N. Zala, Tejas C. Bosamia, Yogesh Shukla, Sushil Kumar, R. S. Fougat, Mruduka S. Patel, Narayanan Subhash, Chaitanya G. Joshi
Software Mentions: 4
Published: almost 8 years ago
10.1093/bioinformatics/btab090
orfipy: a fast and flexible tool for extracting ORFs
Cited by: 26
Author(s): Urminder Singh, Eve Syrkin Wurtele
Software Mentions: 4
Published: over 3 years ago
10.3389/fphar.2020.00753
Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus
Cited by: 16
Author(s): Justice Afrifa Crentsil, Lauve Rachel Tchokouaha Yamthé, Barbara Anibea, Emmanuel Broni, Samuel K. Kwofie, John Tetteh, Dorcas Osei‐Safo
Software Mentions: 4
Published: almost 4 years ago
10.3389/fmicb.2020.593232
Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment
Cited by: 4
Author(s): Lijuan Yan, Nan Hui, Suvi Simpanen, Laura Tudeer, Martin Romantschuk
Software Mentions: 4
Published: over 3 years ago
10.1534/g3.116.028324
Histone H1 Limits DNA Methylation in Neurospora crassa
Cited by: 18
Author(s): Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
Software Mentions: 4
Published: almost 8 years ago
10.3389/fmicb.2016.00820
Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank
Cited by: 36
Author(s): Steffen Leth Jørgensen, Rui Zhao
Software Mentions: 4
Published: almost 8 years ago
10.3389/fmicb.2012.00410
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures
Cited by: 173
Author(s): Marc Strous, Beate Kraft, Regina Bisdorf, Halina E. Tegetmeyer
Software Mentions: 4
Published: over 12 years ago
10.3389/fmicb.2019.01410
On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics
Cited by: 6
Author(s): K.C.T. Machado, Suereta Fortuin, Gisele G. Tomazella, André Fonseca, Robin M. Warren, Harald G. Wiker, Sandro J. de Souza, Gustavo Souza
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pgen.1006401
Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
Cited by: 52
Author(s): H. Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M. Schmidt, Léon Langereis, Joanna Lukasiewicz, Timothy R. Hughes, Martijn Rep
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pntd.0005791
Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
Cited by: 65
Author(s): Kristian E. Swearingen, Scott E. Lindner, Erika L. Flannery, Ashley M. Vaughan, Robert Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivan Müller, Aaron R. Jex, Robert L. Moritz, Stefan H. I. Kappe, Jetsumon Sattabongkot, Sebastian A. Mikolajczak
Software Mentions: 4
Published: almost 7 years ago
10.3389/fmicb.2018.00251
Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics
Cited by: 27
Author(s): Rafael R. C. Cuadrat, Danny Ionescu, Alberto M. R. Dávila, Hans‐Peter Grossart
Software Mentions: 4
Published: about 6 years ago
10.3389/fmicb.2016.01768
Life without dUTPase
Cited by: 20
Author(s): Csaba Kerepesi, J. Szabó, Veronika Papp‐Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G. Vértessy
Software Mentions: 4
Published: over 7 years ago
10.1186/s12862-015-0416-z
A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea
Cited by: 21
Author(s): Carolina Granados Mendoza, Julia Naumann, Marie‐Stéphanie Samain, Paul Goetghebeur, Yannick De Smet, Stefan Wanke
Software Mentions: 4
Published: almost 9 years ago
10.1371/journal.pone.0070219
Can Yeast (S. cerevisiae) Metabolic Volatiles Provide Polymorphic Signaling?
Cited by: 28
Author(s): J. Roman Arguello, Carolina Sellanes, Yann‐Ru Lou, Robert A. Raguso
Software Mentions: 4
Published: almost 11 years ago
10.1111/all.14694
Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel
Cited by: 5
Author(s): Barbara Darnhofer, Tamara Tomin, Laura Liesinger, Matthias Schittmayer, Peter Valentin Tomazic, Ruth Birner‐Gruenberger
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2229-11-131
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)
Cited by: 101
Author(s): Grit Haseneyer, Thomas Schmutzer, Michael Seidel, Ruonan Zhou, Martin Mascher, C. C. Schön, Stefan Taudien, Uwe Scholz, Nils Stein, Klaus Mayer, Eva Bauer
Software Mentions: 4
Published: over 12 years ago
10.3389/fmed.2020.00161
Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana
Cited by: 14
Author(s): Prince Asare, Isaac Darko Otchere, Edmund Bedeley, Daniela Brites, Chloé Loiseau, Nyonuku Akosua Baddoo, Adwoa Asante-Poku, Stephen Osei-Wusu, Diana Ahu Prah, Sònia Borrell, Miriam Reinhard, Audrey Forson, Kwadwo A. Koram, Sébastien Gagneux, Dorothy Yeboah-Manu
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pgen.0030087
Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: almost 17 years ago
10.1186/1471-2105-12-75
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Cited by: 16
Author(s): Jihoon Kim, Kiltesh Patel, Hyunchul Jung, Winston Patrick Kuo, Lucila Ohno-Machado
Software Mentions: 4
Published: about 13 years ago
10.1371/journal.pgen.1008935
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes
Cited by: 82
Author(s): Shelbi L. Russell, Evan Pepper-Tunick, Jesper Svedberg, Ashley Byrne, Jennie Ruelas Castillo, Christopher Vollmers, Roxanne A. Beinart, Russell Corbett-Detig
Software Mentions: 4
Published: over 3 years ago
10.1186/s12862-016-0700-6
Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
Cited by: 40
Author(s): Ilya Borisenko, Marcin Adamski, Alexander Ereskovsky, Maja Adamska
Software Mentions: 4
Published: almost 8 years ago
10.1371/journal.pone.0125663
Protein Structure and Evolution: Are They Constrained Globally by a Principle Derived from Information Theory?
Cited by: 5
Author(s): Les Hatton, Gregory W. Warr
Software Mentions: 4
Published: about 9 years ago
10.3389/fmicb.2015.00998
Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones
Cited by: 47
Author(s): Jennifer B. Glass, Cécilia B. Kretz, Sangita Ganesh, Piyush Ranjan, Sherry L. Seston, Kristen N. Buck, William M. Landing, Peter L. Morton, James W. Moffett, Stephen J. Giovannoni, Kevin L. Vergin, Frank J. Stewart
Software Mentions: 4
Published: over 8 years ago
10.3390/genes11060610
The Location of the Pseudoautosomal Boundary in Silene latifolia
Cited by: 8
Author(s): Marc Krasovec, Yu Zhang, Dmitry A. Filatov
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12860-019-0241-0
Prediction of novel mouse TLR9 agonists using a random forest approach
Cited by: 4
Author(s): Varun Khanna, Lei Li, Johnson Fung, Shoba Ranganathan, Nikolai Petrovsky
Software Mentions: 4
Published: over 4 years ago
10.1186/1471-2105-14-S7-S10
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
Cited by: 13
Author(s): Ilenia Boria, Lara Boatti, Graziano Pesole, Flavio Mignone
Software Mentions: 4
Published: about 11 years ago
10.3389/fimmu.2021.662443
An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens
Cited by: 17
Author(s): Niclas Olsson, Marlene L Heberling, Lichao Zhang, Suchit Jhunjhunwala, Qui Phung, Sarah Lin, Veronica G. Anania, Jennie R. Lill, Joshua E. Elias
Software Mentions: 4
Published: about 3 years ago
10.1186/s12920-020-0683-4
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection
Cited by: 14
Author(s): Yuyu Li, Guangzhi Wang, Xiaofang Tan, Jian Ouyang, Menghuan Zhang, Xiaofeng Song, Qi Liu, Qibin Leng, Lanming Chen, Lu Xie
Software Mentions: 4
Published: about 4 years ago
10.1186/s12885-019-5402-1
The neoepitope landscape of breast cancer: implications for immunotherapy
Cited by: 64
Author(s): Pooja Narang, Meixuan Chen, Amit Sharma, Karen S. Anderson, Melissa A. Wilson
Software Mentions: 4
Published: about 5 years ago
10.1093/femsec/fiy194
Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny
Cited by: 24
Author(s): Thomas Swierts, Daniel F. R. Cleary, Nicole J. de Voogd
Software Mentions: 4
Published: over 5 years ago
10.1186/1471-2105-10-186
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
Cited by: 6
Author(s): Daniela Eggle, Svenja Debey–Pascher, Marc Beyer, Joachim L. Schultze
Software Mentions: 4
Published: almost 15 years ago
10.1111/j.1574-6968.2011.02339.x
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors
Cited by: 78
Author(s): Simon Heilbronner, Matthew T. G. Holden, Andries J. van Tonder, Joan A. Geoghegan, Timothy J. Foster, Julian Parkhill, Stephen D. Bentley
Software Mentions: 4
Published: almost 13 years ago
10.31557/APJCP.2020.21.9.2593
Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: over 3 years ago
10.1186/s12915-019-0697-6
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
Cited by: 39
Author(s): Joel‐Elias Kuon, Weihong Qi, Pascal Schläpfer, Matthias Hirsch‐Hoffmann, Philipp Rogalla von Bieberstein, Andrea Patrignani, Lucy Poveda, Stefan Grob, Miyako Keller, Rie Shimizu‐Inatsugi, Ueli Grossniklaus, Hervé Vanderschuren, Wilhelm Gruissem
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-016-2650-1
Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)
Cited by: 101
Author(s): Yuanda Lv, Zhikai Liang, Min Ge, Weicong Qi, Tifu Zhang, Feng Lin, Zhaohua Peng, Han Zhao
Software Mentions: 4
Published: about 8 years ago
10.1186/s12859-017-1861-z
LSTrAP: efficiently combining RNA sequencing data into co-expression networks
Cited by: 33
Author(s): Sebastian Proost, Agnieszka Krawczyk
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-019-6427-1
Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences
Cited by: 44
Author(s): Narayan Nicole, Thomas Weinmaier, Emilio J Laserna-Mendieta, Marcus J. Claesson, Fergus Shanahan, Karim Dabbagh, Shoko Iwai, Todd Z. DeSantis
Software Mentions: 4
Published: over 4 years ago
10.7717/peerj-cs.406
Evaluation of Rust code verbosity, understandability and complexity
Cited by: 0
Author(s): Luca Ardito, Luca Barbato, Riccardo Coppola, Michele Valsesia
Software Mentions: 4
Published: about 3 years ago
10.1371/journal.pcbi.1009372
FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution
Cited by: 8
Author(s): Gabriel A. Vignolle, Denise Schaffer, Leopold Zehetner, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl
Software Mentions: 4
Published: over 2 years ago
10.3389/fimmu.2020.583013
Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures
Cited by: 10
Author(s): David Roe, Rui Kuang
Software Mentions: 4
Published: over 3 years ago
10.7717/peerj.2477
Whole genome sequencing of<i>Streptococcus pneumoniae</i>: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
Cited by: 103
Author(s): Georgia Kapatai, Carmen Sheppard, Ali Al‐Shahib, David Litt, Anthony Underwood, Timothy G. Harrison, Norman K. Fry
Software Mentions: 4
Published: over 7 years ago
10.1002/ece3.1107
An Illumina metabarcoding pipeline for fungi
Cited by: 103
Author(s): Miklós Bálint, Philipp-André Schmidt, Rahul Sharma, Marco Thines, Imke Schmitt
Software Mentions: 4
Published: almost 10 years ago
10.1186/s12859-016-1428-4
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Cited by: 45
Author(s): Roberto A. Barrero, Kathryn R. Napier, J. H. Cunnington, L. W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard
Software Mentions: 4
Published: over 7 years ago
10.1002/ece3.5964
Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA
Cited by: 9
Author(s): Haw Chuan Lim, Subir B. Shakya, Michael Harvey, Robert G. Moyle, Robert C. Fleischer, Michael J. Braun, Frederick H. Sheldon
Software Mentions: 4
Published: about 4 years ago
10.1186/s12859-019-3115-8
GenGraph: a python module for the simple generation and manipulation of genome graphs
Cited by: 4
Author(s): Jon Ambler, Shandukani Mulaudzi, Nicola Mulder
Software Mentions: 4
Published: over 4 years ago
10.1186/1471-2105-13-166
Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation
Cited by: 10
Author(s): George Golovko, Kamil Khanipov, Mark Rojas, Antonio Martínez-Alcántara, Jesse J. Howard, Efren Ballesteros, Sharu Gupta, William R. Widger, Yuriy Fofanov
Software Mentions: 4
Published: almost 12 years ago
10.1093/database/bav047
GraP: platform for functional genomics analysis of Gossypium raimondii
Cited by: 12
Author(s): Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2105-10-251
SNAD: sequence name annotation-based designer
Cited by: 6
Author(s): Igor A. Sidorov, Denis A. Reshetov, Alexander E. Gorbalenya
Software Mentions: 4
Published: almost 15 years ago
10.1038/s42003-020-0896-2
Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis
Cited by: 10
Author(s): Maeve O’Huallachain, Felice-Alessio Bava, Mary Shen, Carolina Dallett, Sri Paladugu, Nikolay Samusik, Shichao Yu, Razika Hussein, Grantland Hillman, Samuel G. Higgins, Melanie Lou, Angelica Trejo, Laura Qin, Yu Chuan Tai, Shigemi Kinoshita, Astraea Jager, Deval Lashkari, Yury Goltsev, Sedide B. Ozturk, Garry P. Nolan
Software Mentions: 4
Published: about 4 years ago
10.1186/s13578-018-0227-1
Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages
Cited by: 9
Author(s): Xinyu Feng, Jia-Tong Wu, Shui-Sen Zhou, Jingwen Wang, Wei Hu
Software Mentions: 4
Published: about 6 years ago
10.1111/1755-0998.13210
Disagreement in <i>F</i> <sub>ST</sub> estimators: A case study from sex chromosomes
Cited by: 11
Author(s): William J Gammerdinger, Melissa A. Toups, Beatriz Vicoso
Software Mentions: 4
Published: almost 4 years ago
10.7717/peerj.1025
GenomePeek—an online tool for prokaryotic genome and metagenome analysis
Cited by: 12
Author(s): Katelyn McNair, Robert A. Edwards
Software Mentions: 4
Published: almost 9 years ago
10.1016/j.dib.2017.02.013
Reference datasets of tuf A and UPA markers to identify algae in metabarcoding surveys
Cited by: 6
Author(s): Vanessa R. Marcelino, Heroen Verbruggen
Software Mentions: 4
Published: about 7 years ago
10.1074/mcp.M115.049205
Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula
Cited by: 37
Author(s): David Lyon, María Ángeles Castillejo, Vlora Mehmeti-Tershani, Christiana Staudinger, Christoph Kleemaier, Stefanie Wienkoop
Software Mentions: 4
Published: almost 8 years ago
10.1186/s12864-015-1391-x
Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy
Cited by: 73
Author(s): Christian Schrøder Kaas, Claus Kristensen, Michael J Betenbaugh, Mikael Rørdam Andersen
Software Mentions: 4
Published: about 9 years ago
10.1074/mcp.RA118.000877
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*
Cited by: 86
Author(s): Roman Mylonas, Ilan Beer, Christian Iseli, Chloé Chong, Hui Song Pak, David Gfeller, George Coukos, Ioannis Xénarios, Markus Müller, Michal Bassani-Sternberg
Software Mentions: 4
Published: over 5 years ago
10.1007/s13205-014-0231-z
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae
Cited by: 15
Author(s): Mohd Shahbaaz, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 4
Published: almost 10 years ago
10.1016/j.dib.2015.11.063
Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods
Cited by: 29
Author(s): Claire Ramus, Agnès Hovasse, Marlène Marcellin, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, David Bouyssié, Sebastian Vaca, Christine Carapito, Karima Chaoui, Christophe Bruley, Jérôme Garin, Sarah Cianférani, Myriam Ferro, Alain Van Dorssaeler, Odile Burlet‐Schiltz, Christine Schaeffer, Yohann Couté, Anne Gonzalez de Peredo
Software Mentions: 4
Published: about 8 years ago
10.1186/1471-2105-9-537
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
Cited by: 28
Author(s): Fan Mo, Hong Xu, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin
Software Mentions: 4
Published: over 15 years ago
10.1371/journal.pone.0237715
Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties
Cited by: 4
Author(s): Stephanie A. Bruggeman, David P. Horvath, Anne Fennell, Jose L. Gonzalez-Hernandez, Sharon A. Clay
Software Mentions: 4
Published: over 3 years ago
10.1186/s13100-019-0166-3
Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew
Cited by: 17
Author(s): Sonja M. Dunemann, James D. Wasmuth
Software Mentions: 4
Published: almost 5 years ago
10.1186/s13100-018-0123-6
Extensive exchange of transposable elements in the Drosophila pseudoobscura group
Cited by: 25
Author(s): Tom Hill, Andrea J. Betancourt
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0211285
Taxonomical over splitting in the Rhodnius prolixus (Insecta: Hemiptera: Reduviidae) clade: Are R. taquarussuensis (da Rosa et al., 2017) and R. neglectus (Lent, 1954) the same species?
Cited by: 44
Author(s): Juliana Damieli Nascimento, João Aristeu da Rosa, Fabian C. Salgado-Roa, Carolina Hernández, Carolina Pardo‐Díaz, Kaio Cesar Chaboli Alevi, Amanda Ravazi, Jader de Oliveira, Maria Tercília Vilela de Azeredo-Oliveira, Camilo Salazar, Juan David Ramírez
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0249695
Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT
Cited by: 5
Author(s): Xinming Zhuo, Qun Wang, Liesbeth Vossaert, Roseen Salman, Adriel Kim, Ignatia Van den Veyver, Amy M. Breman, Arthur L. Beaudet
Software Mentions: 4
Published: about 3 years ago
10.1186/s13100-019-0150-y
RepetDB: a unified resource for transposable element references
Cited by: 37
Author(s): Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michaël Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon, Hadi Quesneville
Software Mentions: 4
Published: over 5 years ago
10.1186/s13100-018-0144-1
Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification
Cited by: 200
Author(s): Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas
Software Mentions: 4
Published: over 5 years ago
10.1186/1471-2164-11-432
Bcheck: a wrapper tool for detecting RNase P RNA genes
Cited by: 24
Author(s): Dilmurat Yusuf, Manja Marz, Peter F. Stadler, Ivo L. Hofacker
Software Mentions: 4
Published: almost 14 years ago
10.1371/journal.pone.0004229
Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing
Cited by: 19
Author(s): Xiangqin Cui, Ann E. Loraine
Software Mentions: 4
Published: over 15 years ago