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: pypi: fasta

https://packages.ecosyste.ms/registries/pypi.org/packages/fasta

The fasta python package enables you to deal with biological sequence files easily.
20 versions
Latest release: almost 2 years ago
1 dependent package
190 downloads last month

Papers Mentioning fasta 848

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: 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: almost 4 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: over 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: over 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: almost 6 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: over 8 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: over 10 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: over 11 years ago
10.1371/journal.pone.0198773
When old metagenomic data meet newly sequenced genomes, a case study
Cited by: 9
Author(s): Xin Li, Saleh A. Naser, Annette R. Khaled, Haiyan Hu, Xiaoman Li
Software Mentions: 4
Published: over 6 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: almost 7 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: almost 16 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: over 4 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: over 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: over 6 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: almost 4 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: almost 6 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: almost 6 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: over 14 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: over 8 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: over 5 years ago
10.1186/s12859-017-1906-3
fLPS: Fast discovery of compositional biases for the protein universe
Cited by: 57
Author(s): Paul M. Harrison
Software Mentions: 4
Published: about 7 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: 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: over 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: about 9 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: almost 7 years ago
10.1186/s12864-020-07072-1
B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes
Cited by: 18
Author(s): Syed Farhan Ahmad, Maryam Jehangir, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Vladimir Pavan Margarido, Diogo Cavalcanti Cabral-de-Mello, Rachel J. O’Neill, Guilherme Targino Valente, Cesar Martins
Software Mentions: 4
Published: about 4 years ago
10.1186/1471-2164-15-989
Evaluation of viral genome assembly and diversity estimation in deep metagenomes
Cited by: 31
Author(s): Daniel Aguirre de Cárcer, Florent E. Angly, Antonio Alcamı́
Software Mentions: 4
Published: almost 11 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: about 8 years ago
10.1186/2042-5783-3-2
Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Cited by: 109
Author(s): D.J. Edwards, Kathryn E. Holt
Software Mentions: 4
Published: over 11 years ago
10.1186/1471-2164-14-283
Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: over 11 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: almost 14 years ago
10.1371/journal.pone.0166721
A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing
Cited by: 3
Author(s): Chuan-Kang Ting, Chun-Shin Lin, Ming-Tsai Chan, Jeremy J.W. Chen, Sheng-Yu Chuang, Yao‐Ting Huang
Software Mentions: 4
Published: about 8 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: over 8 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: over 4 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: almost 13 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: over 8 years ago
10.3390/ijms21165847
Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer Therapies
Cited by: 11
Author(s): Oliver Snow, Nada Lallous, Martin Ester, Artem Cherkasov
Software Mentions: 4
Published: over 4 years ago
10.1186/1471-2164-14-471
Analysis and annotation of the hexaploid oat seed transcriptome
Cited by: 60
Author(s): Juan J. Gutiérrez-González, Zheng Jin Tu, David F. Garvin
Software Mentions: 3
Published: over 11 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
10.1186/s12864-021-07971-x
Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Cited by: 2
Author(s): Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang
Software Mentions: 3
Published: about 3 years ago
10.1186/s12859-020-3515-9
Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions
Cited by: 12
Author(s): Hailin Chen, Ruiyu Guo, Guanghui Li, Wei Zhang, Zuping Zhang
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-021-03980-5
ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Cited by: 7
Author(s): Elisa Pischedda, Cristina M. Crava, Martina Carlassara, Susanna Zucca, Laila Gasmi, Mariangela Bonizzoni
Software Mentions: 3
Published: almost 4 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
10.1186/s12864-019-5815-x
Transcriptome Analysis of Gene Families Involved in Chemosensory Function in Spodoptera littoralis (Lepidoptera: Noctuidae)
Cited by: 53
Author(s): William B. Walker, Amit Roy, Peter Anderson, Fredrik Schlyter, Bill S. Hansson, Mattias C. Larsson
Software Mentions: 3
Published: over 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
10.1186/1471-2164-10-486
KAIKObase: An integrated silkworm genome database and data mining tool
Cited by: 114
Author(s): Michihiko Shimomura, Hiroshi Minami, Yoshitaka Suetsugu, Hajime Ohyanagi, Chikatada Satoh, Baltazar A. Antonio, Yoshiaki Nagamura, Keiko Kadono-Okuda, Hideyuki Kajiwara, Hideki Sezutsu, Javaregowda Nagaraju, Marian R. Goldsmith, Qingyou Xia, Kimiko Yamamoto, Kazuei Mita
Software Mentions: 3
Published: about 15 years ago
10.1186/s12859-020-03764-3
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information
Cited by: 8
Author(s): Ralf Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard Kuo, Robert H. S. Kraus
Software Mentions: 3
Published: about 4 years ago
10.1186/s12859-021-04174-9
SAUTE: sequence assembly using target enrichment
Cited by: 8
Author(s): Alexandre Souvorov, Richa Agarwala
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-017-4344-8
Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex
Cited by: 15
Author(s): Gina L. Conte, Kathryn A. Hodgins, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Loren H. Rieseberg, Michael C. Whitlock
Software Mentions: 3
Published: almost 7 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
10.1186/s12864-018-5399-x
Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum
Cited by: 18
Author(s): Rodrigo A. Olarte, Jon Menke, Ying Zhang, Shawn Sullivan, Jason C. Slot, Yinyin Huang, Jonathan P. Badalamenti, C. Alisha Quandt, Joseph W. Spatafora, Kathryn E. Bushley
Software Mentions: 3
Published: almost 6 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
10.1155/2014/462135
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
10.1186/1471-2164-10-472
Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes
Cited by: 132
Author(s): Sylvain Forêt, Robert Kucharski, Yvonne Pittelkow, Gabrielle A. Lockett, Ryszard Maleszka
Software Mentions: 3
Published: about 15 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
10.1155/2014/187105
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
10.1186/1471-2164-12-104
Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
Cited by: 176
Author(s): José Blanca, Joaquı́n Cañizares, Cristina Roig, Peio Ziarsolo, F. Nuez, Belén Picó
Software Mentions: 3
Published: almost 14 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/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
10.1186/s12859-015-0677-y
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species
Cited by: 13
Author(s): Aram Avila-Herrera, Katherine S. Pollard
Software Mentions: 3
Published: about 9 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
10.1186/s12864-015-2112-1
Sequencing-based high throughput mutation detection in bread wheat
Cited by: 12
Author(s): Gaganjot Sidhu, Amita Mohan, Ping Zheng, Amandeep Kaur Dhaliwal, Dorrie Main, Kulvinder S. Gill
Software Mentions: 3
Published: about 9 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
10.1186/1471-2105-13-S14-S8
GapFiller: a de novo assembly approach to fill the gap within paired reads
Cited by: 281
Author(s): Francesca Nadalin, Francesco Vezzi, Alberto Policriti
Software Mentions: 3
Published: about 12 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/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
10.12688/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
10.1093/bioinformatics/btab048
<i>De novo</i> genome assembly of <i>Solanum sitiens</i> 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
10.1186/s12863-019-0754-8
Genetic diversity of Bm86 sequences in Rhipicephalus (Boophilus) microplus ticks from Mexico: analysis of haplotype distribution patterns
Cited by: 9
Author(s): Saúl G. Martínez-Arzate, J. C. Sánchez-Bermúdez, S. Sotelo-Gómez, Héctor Díaz-Albiter, Wael Hegazy-Hassan, Esvieta Tenorio-Borroto, Alberto Barbabosa‐Pliego, Juan Carlos Vázquez-Chagoyan
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2105-10-357
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
Cited by: 200
Author(s): Surendra Kumar, Åsmund Skjæveland, Russell J. S. Orr, Pål Enger, Torgeir A. Ruden, Bjørn-Helge Mevik, Fabien Burki, Andreas Botnen, Kamran Shalchian-Tabrizi
Software Mentions: 3
Published: about 15 years ago
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
10.1186/s12863-017-0568-5
IntroMap: a signal analysis based method for the detection of genomic introgressions
Cited by: 3
Author(s): Daniel J. Shea, Mitsuru Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12859-015-0860-1
Treelink: data integration, clustering and visualization of phylogenetic trees
Cited by: 9
Author(s): Christian Allende, Erik Sohn, Cedric Little
Software Mentions: 3
Published: almost 9 years ago
10.1186/s12859-016-1300-6
AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments
Cited by: 9
Author(s): Thomas Shafee, Ira Cooke
Software Mentions: 3
Published: about 8 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
10.3897/BDJ.8.e55137
The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera
Cited by: 7
Author(s): Sónia Ferreira, José Manuel Tierno de Figueroa, Filipa M. S. Martins, Joana Veríssimo, Lorenzo Quaglietta, José Manuel Grosso-Silva, Pedro Lopes, Pedro Sousa, Joana Paupério, Nuno A. Fonseca, Pedro Beja
Software Mentions: 3
Published: over 4 years ago
10.3897/BDJ.3.e4078
PASSIFOR: A reference library of DNA barcodes for French saproxylic beetles (Insecta, Coleoptera)
Cited by: 19
Author(s): Rodolphe Rougerie, Carlos Lopez‐Vaamonde, Thomas Barnouin, Julien Delnatte, Nicolas Moulin, Thierry Noblecourt, Benoît Nusillard, Guilhem Parmain, Fabien Soldati, Christophe Bouget
Software Mentions: 3
Published: over 9 years ago
10.1186/s13040-016-0095-3
Visual programming for next-generation sequencing data analytics
Cited by: 13
Author(s): Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Software Mentions: 3
Published: over 8 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
10.1186/1752-0509-4-3
Deciphering chemotaxis pathways using cross species comparisons
Cited by: 66
Author(s): Rebecca Hamer, Pao‐Yang Chen, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane
Software Mentions: 3
Published: almost 15 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
10.1002/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
10.1186/s12859-014-0403-1
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
Cited by: 11
Author(s): Joseph P. Salisbury, Qian Liu, Jeffrey N. Agar
Software Mentions: 3
Published: almost 10 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
10.1186/s12870-020-02483-4
Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress
Cited by: 32
Author(s): Ai‐Nong Yu, Jinfeng Zhao, Zhenhua Wang, Kai Chen, Peng Zhang, Gang Tian, Xin Liu, Erhu Guo, Yan-Wei Du, Yuwen Wang
Software Mentions: 3
Published: over 4 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.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
10.1093/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
10.1371/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
10.1093/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
10.1371/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
10.1093/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
10.1371/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.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
10.1186/s12870-014-0333-0
A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants
Cited by: 64
Author(s): Patrick Favre, Laure Bapaume, Eligio Bossolini, Mauro Delorenzi, Laurent Falquet, Didier Reinhardt
Software Mentions: 3
Published: almost 10 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
10.1186/1756-0500-4-48
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities
Cited by: 7
Author(s): Peter V Troshin, Vincent L. G. Postis, Denise Ashworth, Stephen A. Baldwin, Michael J. McPherson, Geoffrey J. Barton
Software Mentions: 3
Published: over 13 years ago
10.1186/1471-2148-10-90
Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes
Cited by: 56
Author(s): Chenhong Li, Jean-Jack M. Riethoven, Lan Ma
Software Mentions: 3
Published: almost 15 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
10.3389/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