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
10.1002/pmic.201400392
Visualization of proteomics data using R and BioconductorCited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago
10.1371/journal.pone.0243927
A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequencesCited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago
10.1371/journal.pgen.1009538
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiaeCited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 3 years ago
10.3389/fmicb.2015.00104
Long-term forest soil warming alters microbial communities in temperate forest soilsCited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: over 9 years ago
10.1099/mgen.0.000225
Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogenyCited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: over 5 years ago
10.1186/1471-2105-13-133
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scalingCited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago
10.12688/f1000research.51477.2
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebratesCited by: 2
Author(s): Ann Mc Cartney, Medhat Mahmoud, Michael D. Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K. Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M. Khayat, Maximillian G. Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jimin Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. Sedlazeck
Software Mentions: 14
Published: about 3 years ago
10.1093/molbev/msab063
Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte GenusCited by: 42
Author(s): Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, C. Schluechter, P. Lamkowski, Jeremy Schmutz, Adam Healey, Bryan Piatkowski, A. Jonathan Shaw, David J. Weston, Kjell Ivar Flatberg, Péter Szövényi, Kristian Hassel, Hans K. Stenøien
Software Mentions: 14
Published: over 3 years ago
10.1186/s13059-021-02349-4
PEPPRO: quality control and processing of nascent RNA profiling dataCited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 years ago
10.1111/eva.12965
Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster <i>Crassostrea gigas</i> throughout the Northern HemisphereCited by: 11
Author(s): Ben J. G. Sutherland, Claire Rycroft, Anne‐Laure Ferchaud, Rob Saunders, Li Li, Sheng Liu, Amy M. Chan, Sarah P. Otto, Curtis A. Suttle, Kristina M. Miller
Software Mentions: 13
Published: over 4 years ago
10.1186/s12859-021-04057-z
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing dataCited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: over 3 years ago
10.1007/s00248-020-01635-1
Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral CompositionCited by: 12
Author(s): Irina Tanuwidjaja, Cordula Vogel, Geertje Johanna Pronk, Anne Schöler, Susanne Kublik, Gisle Vestergaard, Ingrid Kögel‐Knabner, Mirna Mrkonjić Fuka, Michael Schloter, Stefanie Schulz
Software Mentions: 13
Published: almost 4 years ago
10.1099/mgen.0.000131
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing readsCited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago
10.12688/f1000research.12874.2
Measuring evolutionary rates of proteins in a structural contextCited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: over 6 years ago
10.1371/journal.pcbi.1008991
Memes: A motif analysis environment in R using tools from the MEME SuiteCited by: 22
Author(s): Spencer L. Nystrom, Daniel J. McKay
Software Mentions: 12
Published: about 3 years ago
10.1099/mgen.0.000499
A comprehensive and high-quality collection of Escherichia coli genomes and their genesCited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: almost 4 years ago
10.1371/journal.pone.0169662
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: almost 8 years ago
10.3390/cells10020322
Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation RegionCited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: over 3 years ago
10.12688/f1000research.18458.2
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: over 5 years ago
10.1177/1176934320956575
Vesicle Transport in Plants: A Revised Phylogeny of SNARE ProteinsCited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: almost 5 years ago
10.3389/fimmu.2016.00372
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell TranscriptsCited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: about 8 years ago
10.3389/fmicb.2018.01095
CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference SoftwareCited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 6 years ago
10.1002/1878-0261.12850
High‐throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype‐specific serologically relevant biomarkersCited by: 13
Author(s): Thilde Terkelsen, Maria Pernemalm, Pavel Gromov, Anna‐Lise Børresen‐Dale, Anders Krogh, Vilde Drageset Haakensen, Janne Lethiö, Elena Papaleo, Irina Gromova
Software Mentions: 10
Published: almost 4 years ago
10.1186/1471-2164-13-462
NG6: Integrated next generation sequencing storage and processing environmentCited by: 54
Author(s): Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas, Christophe Klopp
Software Mentions: 10
Published: almost 13 years ago
10.3390/cancers13020230
A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human TumorsCited by: 10
Author(s): Bárbara Costa, Michael Fletcher, Pavle Boskovic, Ekaterina Ivanova, Tanja Eisemann, Sabrina Lohr, Lukas Bunse, Martin Löwer, Stefanie Burchard, Andrey Korshunov, Nadia Coltella, Melania Cusimano, Luigi Naldini, Hai-Kun Liu, Michael Platten, Bernhard Radlwimmer, Peter Angel, Heike Peterziel
Software Mentions: 10
Published: almost 4 years ago
10.1093/molbev/msaa218
Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate<i>Cis</i>-Regulatory Alleles Underlying Rapid Craniofacial DivergenceCited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: about 4 years ago
10.1371/journal.pone.0245280
rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA familiesCited by: 0
Author(s): Lara Sellés Vidal, Rafael Ayala, Guy‐Bart Stan, Rodrigo Ledesma-Amaro
Software Mentions: 10
Published: almost 4 years ago
10.3390/microorganisms8121887
A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and FunctionCited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: almost 4 years ago
10.1186/s12862-021-01806-9
The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)Cited by: 8
Author(s): Polina Drozdova, Alena Kizenko, Alexandra Saranchina, Anton Gurkov, Maria Firulyova, E. B. Govorukhina, Maxim A. Timofeyev
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.60188
Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cellsCited by: 42
Author(s): Kristen L. Wells, Corey N. Miller, Andreas R. Gschwind, Wei Wu, Jonah D Phipps, Mark S. Anderson, Lars M. Steinmetz
Software Mentions: 9
Published: almost 4 years ago
10.1371/journal.pcbi.1008982
Predicting mean ribosome load for 5’UTR of any length using deep learningCited by: 14
Author(s): Alexander Karollus, Žiga Avsec, Julien Gagneur
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pone.0226694
AlleleProfileR: A versatile tool to identify and profile sequence variants in edited genomesCited by: 4
Author(s): Arne A.N. Bruyneel, Alexandre R. Colas, Ioannis Karakikes, Mark Mercola
Software Mentions: 9
Published: almost 5 years ago
10.1186/s12859-019-2799-0
FastqPuri: high-performance preprocessing of RNA-seq dataCited by: 22
Author(s): Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
Software Mentions: 9
Published: over 5 years ago
10.1371/journal.pone.0204877
Rare haplotype load as marker for lethal mutagenesisCited by: 7
Author(s): Josep Gregori, María Eugenia Soria, Isabel Gallego, Mercedes Guerrero-Murillo, Juan Ignacio Esteban, Josep Quer, Celia Perales, Esteban Domingo
Software Mentions: 9
Published: about 6 years ago
10.1371/journal.pone.0199274
Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in ratsCited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: almost 6 years ago
10.1371/journal.pone.0152747
The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findErCited by: 32
Author(s): Jürgen Behr, Andreas Geißler, Jonas Schmid, Anja Zehe, Rudi F. Vogel
Software Mentions: 9
Published: over 8 years ago
10.1186/s13059-021-02374-3
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycleCited by: 18
Author(s): Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, Augusto César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven Wingett, Peter Fraser
Software Mentions: 9
Published: over 3 years ago
10.1186/s13059-020-02141-w
Improved reference genome of the arboviral vector Aedes albopictusCited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: about 4 years ago
10.3389/fgene.2019.00981
CircCode: A Powerful Tool for Identifying circRNA Coding AbilityCited by: 49
Author(s): Peisen Sun, Guanglin Li
Software Mentions: 9
Published: about 5 years ago
10.1534/g3.118.200892
Isolation by Distance, Source-Sink Population Dynamics and Dispersal Facilitation by Trade Routes: Impact on Population Genetic Structure of a Stored Grain PestCited by: 14
Author(s): Erick M. G. Cordeiro, James F. Campbell, Thomas W. Phillips, Eduard Akhunov
Software Mentions: 8
Published: over 5 years ago
10.3390/biom10010026
Graph Theory-Based Sequence Descriptors as Remote Homology PredictorsCited by: 12
Author(s): Guillermı́n Agüero-Chapin, Deborah Galpert Cañizares, Reinaldo Molina Ruiz, Evys Ancede-Gallardo, Gisselle Pérez-Machado, G Riva, Agostinho Antunes
Software Mentions: 8
Published: almost 5 years ago
10.3389/fmicb.2018.00570
SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP ExperimentsCited by: 37
Author(s): Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 8
Published: over 6 years ago
10.1186/s13072-019-0305-6
CGGBP1 regulates CTCF occupancy at repeatsCited by: 12
Author(s): Divyesh Patel, Manthan Patel, Subhamoy Datta, Uma Singh
Software Mentions: 8
Published: about 5 years ago
10.1186/s40168-018-0434-3
Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencingCited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: over 6 years ago
10.3389/fgene.2015.00172
FAST: FAST Analysis of Sequences ToolboxCited by: 28
Author(s): Travis J Lawrence, Kyle T. Kauffman, Katherine C. H. Amrine, Dana L. Carper, Raymond S. Lee, Peter J. Becich, Claudia J. Canales, David H. Ardell
Software Mentions: 8
Published: over 9 years ago
10.12688/f1000research.19675.1
Large-scale sequence comparisons with sourmashCited by: 103
Author(s): Pierce Nt, Luiz Irber, Taylor Reiter, Phillip T. Brooks, Brown Ct
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pbio.3001007
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inferenceCited by: 180
Author(s): Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas
Software Mentions: 8
Published: almost 4 years ago
10.1093/molbev/msaa135
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral MicrobiomeCited by: 25
Author(s): Jaelle C. Brealey, Henrique G. Leitão, Tom van der Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski
Software Mentions: 8
Published: over 4 years ago
10.1186/s12864-020-07123-7
Illuminating the dark side of the human transcriptome with long read transcript sequencingCited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: about 4 years ago
10.1038/s41598-019-40949-0
Extensive conservation of the proneuropeptide and peptide prohormone complement in mollusksCited by: 17
Author(s): André Luiz de Oliveira, Andrew Calcino, Andreas Wanninger
Software Mentions: 8
Published: over 5 years ago
10.1186/s13073-017-0428-y
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patientsCited by: 378
Author(s): Janis R. Bedarf, Falk Hildebrand, Luís Pedro Coelho, Shinichi Sunagawa, Mohammad Bahram, Felix Goeser, Peer Bork, Ullrich Wüllner
Software Mentions: 8
Published: over 7 years ago
10.1186/s13059-020-02223-9
Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarityCited by: 17
Author(s): Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser, Athina Vidaki
Software Mentions: 8
Published: almost 4 years ago
10.3389/fpls.2021.693039
Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral TransitionCited by: 5
Author(s): Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
Software Mentions: 7
Published: about 3 years ago
10.1186/s12859-017-1942-z
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativaCited by: 17
Author(s): Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs
Software Mentions: 7
Published: almost 7 years ago
10.1534/g3.114.012526
Polymorphism Identification and Improved Genome Annotation of <i>Brassica rapa</i> Through Deep RNA SequencingCited by: 30
Author(s): Upendra Kumar Devisetty, Michaeal F. Covington, An V. Tat, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 7
Published: about 10 years ago
10.1186/1745-6150-9-4
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq dataCited by: 48
Author(s): Ngoc Tam L. Tran, Chun-Hsi Huang
Software Mentions: 7
Published: almost 11 years ago
10.1186/1471-2105-10-325
Riboswitch Detection Using Profile Hidden Markov ModelsCited by: 33
Author(s): Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, Annangarachari Krishnamachari, Supratim Sengupta
Software Mentions: 7
Published: about 15 years ago
10.3389/fmicb.2014.00601
The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence dataCited by: 8
Author(s): Alban Ramette, Pier Luigi Buttigieg
Software Mentions: 7
Published: almost 10 years ago
10.3389/fgene.2012.00287
Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and ChallengesCited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: almost 13 years ago
10.1371/journal.pone.0209589
A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nestsCited by: 12
Author(s): Oliver Quinn, Monica A. M. Gruber, Robert L. Brown, James W. Baty, Mariana Bulgarella, Philip J. Lester
Software Mentions: 7
Published: almost 6 years ago
10.1186/s13293-020-00312-9
Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq dataCited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: over 4 years ago
10.1186/1471-2164-12-227
Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencingCited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: over 13 years ago
10.7717/peerj.642
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse<i>Peromyscus eremicus</i>Cited by: 34
Author(s): Matthew D. MacManes, Michael B. Eisen
Software Mentions: 7
Published: about 10 years ago
10.12688/f1000research.18866.2
MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic dataCited by: 12
Author(s): Mike W.C. Thang, Xin-Yi Chua, Gareth Price, D. Gorse, Matthew A. Field
Software Mentions: 7
Published: about 5 years ago
10.3389/fgene.2021.664424
Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and TissuesCited by: 5
Author(s): Eliah Overbey, Theros T Ng, Pietro Catini, Lisa Griggs, Paul A. Stewart, Suzana Tkalčić, R. David Hawkins, Yvonne Drechsler
Software Mentions: 7
Published: over 3 years ago
10.1186/s13007-019-0440-x
Comparing time series transcriptome data between plants using a network module finding algorithmCited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: over 5 years ago
10.1016/j.omtn.2017.08.010
Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAsCited by: 2
Author(s): Pantazis Theotokis, Louise Usher, Christopher K. Kortschak, Ed C. Schwalbe, Sterghios A. Moschos
Software Mentions: 7
Published: almost 7 years ago
10.1177/1176934319843130
OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer DesignerCited by: 1
Author(s): Vivek Bhakta Mathema, Arjen M. Dondorp, Mallika Imwong
Software Mentions: 7
Published: almost 6 years ago
10.3389/fgene.2020.00082
SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference GenomesCited by: 6
Author(s): Yue Xing, Alan R. Dabney, Xiao Li, Guosong Wang, C. A. Gill, Claudio Casola
Software Mentions: 7
Published: over 4 years ago
10.1186/s12864-015-1270-5
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophagesCited by: 43
Author(s): Aiping Mao, Jun Shen, Zhixiang Zuo
Software Mentions: 7
Published: over 9 years ago
10.1186/s12859-019-2684-x
From trash to treasure: detecting unexpected contamination in unmapped NGS dataCited by: 42
Author(s): Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino
Software Mentions: 7
Published: over 5 years ago
10.7554/eLife.28440
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activityCited by: 37
Author(s): Pierre Khoueiry, Charles Girardot, Lucia Ciglar, Pei-Chen Peng, E. Hilary Gustafson, Saurabh Sinha, Eileen E. M. Furlong
Software Mentions: 7
Published: about 7 years ago
10.1038/sdata.2018.148
Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequencesCited by: 5
Author(s): Soo-Yon Rhee, Robert W. Shafer
Software Mentions: 7
Published: over 6 years ago
10.1038/srep29042
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thalianaCited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: over 8 years ago
10.1371/journal.pone.0242943
Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategyCited by: 7
Author(s): Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar
Software Mentions: 7
Published: almost 4 years ago
10.1186/s12859-018-2074-9
BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelinesCited by: 11
Author(s): Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy C. Vargas, William D. McCaig, Girish Ramrattan, Saymon Akther, Amanda M. Larracuente, Lia Di, Filipe Garrett Vieira, Wang Qiu
Software Mentions: 7
Published: over 6 years ago
10.1186/1471-2164-14-204
RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptomeCited by: 63
Author(s): Yvan Wenger, Brigitte Galliot
Software Mentions: 7
Published: almost 12 years ago
10.1371/journal.pone.0071515
Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticusCited by: 21
Author(s): Susan Bullman, Alan Lucid, Daniel Corcoran, Roy D. Sleator, Brigid Lucey
Software Mentions: 7
Published: about 11 years ago
10.1371/journal.pone.0226527
Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sortingCited by: 22
Author(s): Kevin K. Beentjes, Arjen G.C.L. Speksnijder, Menno Schilthuizen, Marten Hoogeveen, Rob Pastoor, Berry B. van der Hoorn
Software Mentions: 7
Published: almost 5 years ago
10.1186/1471-2164-13-683
Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexingCited by: 24
Author(s): Enrique Ramos, Benjamin T. Levinson, Sara E. Chasnoff, Andrew Hughes, Andrew L. Young, Katherine A. Thornton, Allie Li, Francesco Vallania, Michael Province, Todd E. Druley
Software Mentions: 7
Published: almost 12 years ago
10.1128/mSystems.00086-17
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal MicrobiotaCited by: 8
Author(s): Eric J. de Muinck, Knut E.A. Lundin, Pål Trosvik
Software Mentions: 7
Published: about 7 years ago
10.1099/mgen.0.000211
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species levelCited by: 35
Author(s): Guilhem Royer, Jean‐Winoc Decousser, Catherine Branger, Mathieu Dubois, Claudine Médigue, Erick Denamur, David Vallenet
Software Mentions: 6
Published: about 6 years ago
10.1371/journal.pgen.1009691
Induction of a chromatin boundary in vivo upon insertion of a TAD borderCited by: 11
Author(s): Andréa Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pntd.0003240
Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene FragmentsCited by: 13
Author(s): Katrine Whiteson, Vladimir Lazarević, Manuela Tangomo-Bento, Myriam Girard, Heather Maughan, Didier Pittet, Patrice François, Jacques Schrenzel
Software Mentions: 6
Published: almost 10 years ago
10.1371/journal.pgen.1008632
Evolution of Ty1 copy number control in yeast by horizontal transfer and recombinationCited by: 24
Author(s): Wioletta Czaja, Douda Bensasson, Hyo Won Ahn, David Garfinkel, Casey M. Bergman
Software Mentions: 6
Published: over 4 years ago
10.3389/fmicb.2015.00277
Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil CrustCited by: 44
Author(s): Ulisses Nunes da Rocha, Hinsby Cadillo‐Quiroz, Ulaş Karaöz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin P. Bowen, Ferrán García-Pichel, Aindrila Mukhopadhyay, Trent Northen, Eoin L. Brodie
Software Mentions: 6
Published: over 9 years ago
10.3389/fmicb.2015.01038
Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, BrazilCited by: 10
Author(s): Ana Paula B. Moreira, Pedro Milet Meirelles, Eidy de Oliveira Santos, Gilberto M. Amado‐Filho, Ronaldo B. Francini‐Filho, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 6
Published: about 9 years ago
10.3389/fmicb.2020.591093
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency TestCited by: 8
Author(s): David Dylus, Trestan Pillonel, Onya Opota, Daniel Wüthrich, Helena M. B. Seth-Smith, Adrian Egli, Stefano Leo, Vladimir Lazarević, Jacques Schrenzel, Sacha Laurent, Claire Bertelli, Dominique Blanc, Stefan Neuenschwander, Alban Ramette, Laurent Falquet, Frank Imkamp, Peter M. Keller, André Kahles, Simone Oberhaensli, Valérie Barbié, Christophe Dessimoz, Gilbert Greub, Aitana Lebrand
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12859-017-1594-z
Identification of long non-coding transcripts with feature selection: a comparative studyCited by: 20
Author(s): Giovanna Maria Ventola, Teresa Maria Rosaria Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 6
Published: over 7 years ago
10.1186/s12864-016-2381-3
Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicidaCited by: 40
Author(s): Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque, Steve J. Charette
Software Mentions: 6
Published: almost 9 years ago
10.1186/1471-2164-12-619
A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparationCited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: almost 13 years ago
10.1093/g3journal/jkab189
Long-read transcriptome and other genomic resources for the angiosperm <i>Silene noctiflora</i>Cited by: 7
Author(s): Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B Sloan
Software Mentions: 6
Published: over 3 years ago
10.7717/peerj.4013
PBxplore: a tool to analyze local protein structure and deformability with Protein BlocksCited by: 26
Author(s): Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern, Pierre Poulain
Software Mentions: 6
Published: almost 7 years ago
10.1186/1756-0500-7-68
Simulating a population genomics data set using FlowSimCited by: 2
Author(s): Ketil Malde
Software Mentions: 6
Published: almost 11 years ago
10.1093/bioinformatics/btz855
Improved linking of motifs to their TFs using domain informationCited by: 1
Author(s): Nina Baumgarten, Florian Schmidt, Marcel H. Schulz
Software Mentions: 6
Published: almost 5 years ago
10.3389/fcimb.2021.609160
Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human CellsCited by: 27
Author(s): Ying Yin, Xiaozhao Liu, Ximiao He, Li-Quan Zhou
Software Mentions: 6
Published: over 3 years ago
10.3390/pathogens10091109
Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA StructureCited by: 6
Author(s): Priyanka Mehta, Shanmukh Alle, Anusha Chaturvedi, Aparna Swaminathan, Sheeba Saifi, Ranjeet Maurya, Partha Chattopadhyay, Priti Devi, Ruchi Chauhan, Akshay Kanakan, Janani Srinivasa Vasudevan, Ramanathan Sethuraman, Subramanian Chidambaram, Mashrin Srivastava, Avinash Chakravarthi, Johnny Jacob, Madhuri Namagiri, Varma Konala, Sujeet Jha, U. Deva Priyakumar, P. K. Vinod, Rajesh Pandey
Software Mentions: 6
Published: about 3 years ago
10.7717/peerj.484
The mitochondrial genome of<i>Paragonimus westermani</i>(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: about 10 years ago
10.1093/database/baaa082
Siberian sturgeon multi-tissue reference transcriptome databaseCited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12915-019-0731-8
The round goby genome provides insights into mechanisms that may facilitate biological invasionsCited by: 28
Author(s): Irene Adrian‐Kalchhauser, Anders Blomberg, Tomas Larsson, Zuzana Musilová, Claire R. Peart, Martin Pippel, Monica Hongrø Solbakken, Jaanus Suurväli, Jean‐Claude Walser, Joanna Y. Wilson, Magnus Alm Rosenblad, Demián Burguera, Silvia Gutnik, Nico K. Michiels, Mats Töpel, Kirill Pankov, Siegfried Schloissnig, Sylke Winkler
Software Mentions: 6
Published: almost 5 years ago