cran: fasta | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: about 9 years ago

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: over 3 years ago

10.1371/journal.pgen.1009538

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Cited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: about 3 years ago

10.3389/fmicb.2015.00104

Long-term forest soil warming alters microbial communities in temperate forest soils
Cited 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: about 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 phylogeny
Cited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: about 5 years ago

10.1186/1471-2105-13-133

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Cited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: almost 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 vertebrates
Cited 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: over 2 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 Genus
Cited 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: about 3 years ago

10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: almost 3 years ago

10.1111/eva.12965

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere
Cited 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: about 4 years ago

10.1186/s12859-021-04057-z

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Cited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: about 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 Composition
Cited 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: over 3 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited 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: over 6 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pcbi.1008991

Memes: A motif analysis environment in R using tools from the MEME Suite
Cited by: 22
Author(s): Spencer L. Nystrom, Daniel J. McKay
Software Mentions: 12
Published: over 2 years ago

10.1099/mgen.0.000499

A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Cited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: over 3 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: over 7 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited 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: about 5 years ago

10.1177/1176934320956575

Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: over 4 years ago

10.3389/fimmu.2016.00372

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts
Cited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: over 7 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited 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: almost 6 years ago

10.1002/1878-0261.12850

High‐throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype‐specific serologically relevant biomarkers
Cited 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: over 3 years ago

10.1186/1471-2164-13-462

NG6: Integrated next generation sequencing storage and processing environment
Cited by: 54
Author(s): Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas, Christophe Klopp
Software Mentions: 10
Published: over 12 years ago

10.3390/cancers13020230

A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human Tumors
Cited 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: over 3 years ago

10.1093/molbev/msaa218

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal CandidateCis-Regulatory Alleles Underlying Rapid Craniofacial Divergence
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0245280

rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families
Cited by: 0
Author(s): Lara Sellés Vidal, Rafael Ayala, Guy‐Bart Stan, Rodrigo Ledesma-Amaro
Software Mentions: 10
Published: over 3 years ago

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited 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: over 3 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: almost 3 years ago

10.7554/eLife.60188

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells
Cited 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: over 3 years ago

10.1371/journal.pcbi.1008982

Predicting mean ribosome load for 5’UTR of any length using deep learning
Cited by: 14
Author(s): Alexander Karollus, Žiga Avsec, Julien Gagneur
Software Mentions: 9
Published: almost 3 years ago

10.1371/journal.pone.0226694

AlleleProfileR: A versatile tool to identify and profile sequence variants in edited genomes
Cited by: 4
Author(s): Arne A.N. Bruyneel, Alexandre R. Colas, Ioannis Karakikes, Mark Mercola
Software Mentions: 9
Published: over 4 years ago

10.1186/s12859-019-2799-0

FastqPuri: high-performance preprocessing of RNA-seq data
Cited by: 22
Author(s): Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0204877

Rare haplotype load as marker for lethal mutagenesis
Cited 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: over 5 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited 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: over 5 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 findEr
Cited by: 32
Author(s): Jürgen Behr, Andreas Geißler, Jonas Schmid, Anja Zehe, Rudi F. Vogel
Software Mentions: 9
Published: about 8 years ago

10.1186/s13059-021-02374-3

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Cited 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: almost 3 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited 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: over 3 years ago

10.3389/fgene.2019.00981

CircCode: A Powerful Tool for Identifying circRNA Coding Ability
Cited by: 49
Author(s): Peisen Sun, Guanglin Li
Software Mentions: 9
Published: over 4 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 Pest
Cited by: 14
Author(s): Erick M. G. Cordeiro, James F. Campbell, Thomas W. Phillips, Eduard Akhunov
Software Mentions: 8
Published: about 5 years ago

10.3390/biom10010026

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors
Cited 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: over 4 years ago

10.3389/fmicb.2018.00570

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments
Cited by: 37
Author(s): Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 8
Published: about 6 years ago

10.1186/s13072-019-0305-6

CGGBP1 regulates CTCF occupancy at repeats
Cited by: 12
Author(s): Divyesh Patel, Manthan Patel, Subhamoy Datta, Uma Singh
Software Mentions: 8
Published: over 4 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 sequencing
Cited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: about 6 years ago

10.3389/fgene.2015.00172

FAST: FAST Analysis of Sequences Toolbox
Cited 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: almost 9 years ago

10.12688/f1000research.19675.1

Large-scale sequence comparisons with sourmash
Cited by: 103
Author(s): Pierce Nt, Luiz Irber, Taylor Reiter, Phillip T. Brooks, Brown Ct
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pbio.3001007

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
Cited by: 180
Author(s): Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas
Software Mentions: 8
Published: over 3 years ago

10.1093/molbev/msaa135

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Cited 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: almost 4 years ago

10.1186/s12864-020-07123-7

Illuminating the dark side of the human transcriptome with long read transcript sequencing
Cited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-40949-0

Extensive conservation of the proneuropeptide and peptide prohormone complement in mollusks
Cited by: 17
Author(s): André Luiz de Oliveira, Andrew Calcino, Andreas Wanninger
Software Mentions: 8
Published: about 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 patients
Cited 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: about 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 dissimilarity
Cited 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: over 3 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 Transition
Cited 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: over 2 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 sativa
Cited by: 17
Author(s): Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs
Software Mentions: 7
Published: over 6 years ago

10.1534/g3.114.012526

Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing
Cited by: 30
Author(s): Upendra Kumar Devisetty, Michaeal F. Covington, An V. Tat, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 7
Published: over 9 years ago

10.1186/1745-6150-9-4

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
Cited by: 48
Author(s): Ngoc Tam L. Tran, Chun-Hsi Huang
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2105-10-325

Riboswitch Detection Using Profile Hidden Markov Models
Cited by: 33
Author(s): Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, Annangarachari Krishnamachari, Supratim Sengupta
Software Mentions: 7
Published: over 14 years ago

10.3389/fmicb.2014.00601

The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data
Cited by: 8
Author(s): Alban Ramette, Pier Luigi Buttigieg
Software Mentions: 7
Published: over 9 years ago

10.3389/fgene.2012.00287

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges
Cited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: over 12 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 nests
Cited 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: over 5 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 data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: almost 4 years ago

10.1186/1471-2164-12-227

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Cited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: almost 13 years ago

10.7717/peerj.642

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mousePeromyscus eremicus
Cited by: 34
Author(s): Matthew D. MacManes, Michael B. Eisen
Software Mentions: 7
Published: over 9 years ago

10.12688/f1000research.18866.2

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
Cited by: 12
Author(s): Mike W.C. Thang, Xin-Yi Chua, Gareth Price, D. Gorse, Matthew A. Field
Software Mentions: 7
Published: over 4 years ago

10.3389/fgene.2021.664424

Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues
Cited 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: almost 3 years ago

10.1186/s13007-019-0440-x

Comparing time series transcriptome data between plants using a network module finding algorithm
Cited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.omtn.2017.08.010

Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs
Cited by: 2
Author(s): Pantazis Theotokis, Louise Usher, Christopher K. Kortschak, Ed C. Schwalbe, Sterghios A. Moschos
Software Mentions: 7
Published: over 6 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 Designer
Cited by: 1
Author(s): Vivek Bhakta Mathema, Arjen M. Dondorp, Mallika Imwong
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2020.00082

SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes
Cited by: 6
Author(s): Yue Xing, Alan R. Dabney, Xiao Li, Guosong Wang, C. A. Gill, Claudio Casola
Software Mentions: 7
Published: about 4 years ago

10.1186/s12864-015-1270-5

Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages
Cited 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 data
Cited by: 42
Author(s): Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.28440

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity
Cited 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: over 6 years ago

10.1038/sdata.2018.148

Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
Cited by: 5
Author(s): Soo-Yon Rhee, Robert W. Shafer
Software Mentions: 7
Published: almost 6 years ago

10.1038/srep29042

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pone.0242943

Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy
Cited by: 7
Author(s): Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-018-2074-9

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines
Cited 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: about 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 transcriptome
Cited by: 63
Author(s): Yvan Wenger, Brigitte Galliot
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0071515

Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus
Cited by: 21
Author(s): Susan Bullman, Alan Lucid, Daniel Corcoran, Roy D. Sleator, Brigid Lucey
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0226527

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting
Cited 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: over 4 years ago

10.1186/1471-2164-13-683

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing
Cited 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: over 11 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 Microbiota
Cited by: 8
Author(s): Eric J. de Muinck, Knut E.A. Lundin, Pål Trosvik
Software Mentions: 7
Published: over 6 years ago

10.1099/mgen.0.000211

PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Cited by: 35
Author(s): Guilhem Royer, Jean‐Winoc Decousser, Catherine Branger, Mathieu Dubois, Claudine Médigue, Erick Denamur, David Vallenet
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009691

Induction of a chromatin boundary in vivo upon insertion of a TAD border
Cited by: 11
Author(s): Andréa Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo
Software Mentions: 6
Published: almost 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 Fragments
Cited 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: over 9 years ago

10.1371/journal.pgen.1008632

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination
Cited by: 24
Author(s): Wioletta Czaja, Douda Bensasson, Hyo Won Ahn, David Garfinkel, Casey M. Bergman
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2015.00277

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
Cited 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: about 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, Brazil
Cited 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: over 8 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 Test
Cited 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: over 3 years ago

10.1186/s12859-017-1594-z

Identification of long non-coding transcripts with feature selection: a comparative study
Cited by: 20
Author(s): Giovanna Maria Ventola, Teresa Maria Rosaria Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 6
Published: about 7 years ago

10.1186/s12864-016-2381-3

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
Cited 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: over 8 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 preparation
Cited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: over 12 years ago

10.1093/g3journal/jkab189

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora
Cited by: 7
Author(s): Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B Sloan
Software Mentions: 6
Published: almost 3 years ago

10.7717/peerj.4013

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Cited 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: over 6 years ago

10.1186/1756-0500-7-68

Simulating a population genomics data set using FlowSim
Cited by: 2
Author(s): Ketil Malde
Software Mentions: 6
Published: over 10 years ago

10.1093/bioinformatics/btz855

Improved linking of motifs to their TFs using domain information
Cited by: 1
Author(s): Nina Baumgarten, Florian Schmidt, Marcel H. Schulz
Software Mentions: 6
Published: over 4 years ago

10.3389/fcimb.2021.609160

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells
Cited by: 27
Author(s): Ying Yin, Xiaozhao Liu, Ximiao He, Li-Quan Zhou
Software Mentions: 6
Published: about 3 years ago

10.3390/pathogens10091109

Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure
Cited 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: over 2 years ago

10.7717/peerj.484

The mitochondrial genome ofParagonimus westermani(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: over 9 years ago

10.1093/database/baaa082

Siberian sturgeon multi-tissue reference transcriptome database
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: over 4 years ago

10.1186/s12915-019-0731-8

The round goby genome provides insights into mechanisms that may facilitate biological invasions
Cited 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: over 4 years ago

Projects: cran: fasta

Papers Mentioning fasta 848