bioconductor: Biostrings | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.3390/microorganisms9051094

Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance
Cited by: 16
Author(s): Alfredo Mari, Tim Roloff, Madlen Stange, Kirstine Kobberøe Søgaard, Erblin Asllanaj, Gerardo Tauriello, Leila T. Alexander, Michael Schweitzer, Karoline Leuzinger, Alexander Gensch, Aurélien Emmanuel Martinez, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Parham Sendi, Manuel Battegay, Catia Marzolini, Helena M. B. Seth-Smith, Torsten Schwede, Hans H. Hirsch, Adrian Egli
Software Mentions: 27
Published: over 3 years ago

10.1371/journal.pone.0243927

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: almost 4 years ago

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

10.1016/j.cell.2015.01.006

Enhancer Evolution across 20 Mammalian Species
Cited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 10 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.3389/fgene.2021.719204

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization
Cited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: over 3 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-015-0683-0

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Cited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: over 9 years ago

10.1371/journal.pcbi.1003118

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: over 11 years ago

10.1371/journal.pone.0225615

An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery
Cited by: 9
Author(s): Garrett C. McCarthy, Sydney Morgan, Jonathan T. Martiniuk, Brianne L. Newman, Stephanie McCann, Vivien Measday, Daniel M. Durall
Software Mentions: 14
Published: almost 4 years ago

10.7717/peerj.3472

Using high-throughput sequencing of ITS2 to describe <i>Symbiodinium</i> metacommunities in St. John, US Virgin Islands
Cited by: 50
Author(s): Ross Cunning, Ruth D. Gates, Peter J. Edmunds
Software Mentions: 14
Published: over 7 years ago

10.1186/s13068-019-1584-7

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock
Cited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: about 5 years ago

10.12688/f1000research.17082.2

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: over 5 years ago

10.1099/mgen.0.000524

BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
Cited by: 12
Author(s): Adrian Sven Geissler, Christian Anthon, Ferhat Alkan, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Anne Breüner, Stefan E. Seemann, Jeppe Vinther, Jan Gorodkin
Software Mentions: 12
Published: almost 4 years ago

10.7554/eLife.34409

General decapping activators target different subsets of inefficiently translated mRNAs
Cited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: almost 6 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: almost 14 years ago

10.3389/fimmu.2019.00827

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space
Cited by: 60
Author(s): Masato Ogishi, Hiroshi Yotsuyanagi
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: over 9 years ago

10.3389/fgene.2020.00548

Rcirc: An R Package for circRNA Analyses and Visualization
Cited by: 8
Author(s): Peisen Sun, Haoming Wang, Guanglin Li
Software Mentions: 11
Published: over 4 years ago

10.3390/plants8120547

New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences
Cited by: 12
Author(s): Hyoung Tae Kim, Ki-Byung Lim, Jung Sung Kim
Software Mentions: 11
Published: almost 5 years ago

10.1038/srep26929

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
Cited by: 43
Author(s): Fábio Pértille, Carlos Guerrero-Bosagna, Vinícius da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho
Software Mentions: 11
Published: over 8 years ago

10.3389/fmicb.2020.570985

Differently Pre-treated Rapeseed Meals Affect in vitro Swine Gut Microbiota Composition
Cited by: 8
Author(s): Long Cheng, S. de Vries, Koen Venema
Software Mentions: 11
Published: about 4 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: almost 10 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.7554/eLife.10421

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain
Cited by: 115
Author(s): Claudia Scheckel, Elodie Drapeau, María A. Frías, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell
Software Mentions: 10
Published: almost 9 years ago

10.1371/journal.pone.0041762

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Cited by: 7
Author(s): Matthew P Davis, Cei Abreu‐Goodger, Stijn van Dongen, Dong Lu, P. Täte, Nenad Bartoniček, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Software Mentions: 10
Published: almost 13 years ago

10.1093/gbe/evab028

sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R
Cited by: 14
Author(s): Kuan-Hao Chao, Kirston Barton, Sarah Palmer, Robert Lanfear
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: about 7 years ago

10.1038/srep46112

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing
Cited by: 31
Author(s): José de Ribamar da Silva Nunes, Shikai Liu, Fábio Pértille, Caio Augusto Perazza, Priscilla Marqui Schmidt Villela, Vera Maria Fonseca de Almeida-Val, Alexandre Wagner Silva Hilsdorf, Zhanjiang Liu, Luiz Lehmann Coutinho
Software Mentions: 9
Published: over 7 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2105-11-S12-S11

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
Cited by: 10
Author(s): Laurent Gautier
Software Mentions: 9
Published: almost 14 years ago

10.1186/s12859-020-3475-0

PACVr: plastome assembly coverage visualization in R
Cited by: 184
Author(s): Michael Gruenstaeudl, Nils Jenke
Software Mentions: 9
Published: over 4 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: about 6 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: about 4 years ago

10.3390/toxins12060414

Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia coli (STEC) Strains with Different Colonization Properties
Cited by: 4
Author(s): Stefanie A. Barth, M. Weber, Katharina Schaufler, Christian Berens, Lutz Geue, Christian Menge
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-017-07880-8

Global mapping of miRNA-target interactions in cattle (Bos taurus)
Cited by: 19
Author(s): Troels K. H. Scheel, Michael J. Moore, Joseph M. Luna, Eiko Nishiuchi, John Fak, Robert B. Darnell, Charles M. Rice
Software Mentions: 9
Published: over 7 years ago

10.1038/s42003-018-0171-y

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
Cited by: 33
Author(s): Stefan Reuscher, Tomohisa Furuta, Kanako Bessho‐Uehara, Michele Cosi, Kshirod K. Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari
Software Mentions: 9
Published: about 6 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0067048

Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes
Cited by: 40
Author(s): Christoph Fischer, Stephan Koblmüller, Christian Gülly, Christian Schlötterer, Christian Sturmbauer, Gerhard G. Thallinger
Software Mentions: 9
Published: over 11 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: about 5 years ago

10.3389/fonc.2021.575425

Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Shiqiang Zhang, Wenzhong Zheng, Donggen Jiang, Haiyun Xiong, Guolong Liao, Xiangwei Yang, He Ma, Jun Li, Miaojuan Qiu, Binbin Li, Chunhui Sun, Jing Zhao, Liling Wang, Jun Pang
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2164-14-S5-S9

Detection and classification of peaks in 5' cap RNA sequencing data
Cited by: 4
Author(s): Dario Strbenac, Nicola J. Armstrong, Jean Yee Hwa Yang
Software Mentions: 8
Published: about 11 years ago

10.7554/eLife.64919

Tissue-autonomous immune response regulates stress signaling during hypertrophy
Cited by: 11
Author(s): Robert Krautz, Dilan Khalili, Ulrich Theopold
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-018-29378-7

Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer
Cited by: 7
Author(s): Beatríz González, Ferran Fece de la Cruz, Johanna Samuelsson, Andreu Alibés, Sergio Alonso
Software Mentions: 8
Published: over 6 years ago

10.1038/s41598-019-44597-2

NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule
Cited by: 3
Author(s): Francisco Requena, Helena G Asenjo, Guillermo Barturen, Jordi Martorell-Marugán, Pedro Carmona-Sáez, David Landeira
Software Mentions: 8
Published: over 5 years ago

10.1186/1471-2105-16-S5-S10

Using epigenomics data to predict gene expression in lung cancer
Cited by: 40
Author(s): Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire
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: almost 13 years ago

10.1093/bioinformatics/bty088

SecretSanta: flexible pipelines for functional secretome prediction
Cited by: 10
Author(s): Anna Gogleva, Hajk-Georg Drost, Sebastián Schornack
Software Mentions: 7
Published: almost 7 years ago

10.3390/antiox10040627

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions
Cited by: 16
Author(s): Loes van Dam, Marc Pagès-Gallego, Paulien E. Polderman, Robert M. van Es, Boudewijn M.T. Burgering, Harmjan R. Vos, Tobias B. Dansen
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-018-26592-1

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pgen.1002704

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Cited by: 45
Author(s): Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew Knights, Cei Abreu‐Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartoniček, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
Software Mentions: 7
Published: over 12 years ago

10.1371/journal.pcbi.1006169

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Cited by: 115
Author(s): Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J N Groen, Thomas H. Gillingwater, Gabriella Viero
Software Mentions: 7
Published: over 6 years ago

10.1038/srep29033

Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data
Cited by: 130
Author(s): Susann Mönchgesang, Nadine Strehmel, Stephan Schmidt, Lore Westphal, Franziska Taruttis, E. Müller, Siska Herklotz, Steffen Neumann, Dierk Scheel
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-017-3662-1

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals
Cited by: 18
Author(s): Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
Software Mentions: 7
Published: over 7 years ago

10.1098/rstb.2019.0086

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Cited by: 22
Author(s): David M. Needham, Camille Poirier, Elisabeth Hehenberger, Valeria Jiménez, Jarred Swalwell, Alyson E. Santoro, Alexandra Z. Worden
Software Mentions: 7
Published: about 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: almost 7 years ago

10.1371/journal.pone.0097379

Direct Sequencing from the Minimal Number of DNA Molecules Needed to Fill a 454 Picotiterplate
Cited by: 12
Author(s): Mária Džunková, Marc García-Garcerá, Llúcia Martínez-Priego, Giussepe D’Auria, Francesc Calafell, Andrés Moya
Software Mentions: 6
Published: over 10 years ago

10.12688/f1000research.21763.1

vhcub: Virus-host codon usage co-adaptation analysis
Cited by: 12
Author(s): Ali Mostafa Anwar, Mohamed Soudy, Radwa Mohamed
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0086536

Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis
Cited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: almost 11 years ago

10.1186/s13073-017-0454-9

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
Cited by: 45
Author(s): Javier A. Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C. Boutros, Thomas Kislinger
Software Mentions: 6
Published: over 7 years ago

10.1128/mBio.00971-19

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages
Cited by: 48
Author(s): Travis N. Mavrich, Graham F. Hatfull
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-019-2961-8

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Cited by: 11
Author(s): Leandro Gabriel Roser, Fernán Agüero, Daniel O. Sánchez
Software Mentions: 6
Published: over 5 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: over 3 years ago

10.1289/ehp.1307297

Disruption of Aryl Hydrocarbon Receptor Homeostatic Levels during Embryonic Stem Cell Differentiation Alters Expression of Homeobox Transcription Factors that Control Cardiomyogenesis
Cited by: 46
Author(s): Qin Wang, Jing Chen, Chih‐Wei Ko, Yunxia Fan, Vinicius Carreira, Yinglei Chen, Ying Xia, Mario Medvedovic, Alvaro Puga
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pone.0157033

Pattern Recognition on Read Positioning in Next Generation Sequencing
Cited by: 0
Author(s): Boseon Byeon, Igor Kovalchuk
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pbio.3000559

Human sperm displays rapid responses to diet
Cited by: 102
Author(s): Daniel Nätt, Unn Kugelberg, Eduard Casas, Elizabeth Nedstrand, Stefan Zalavary, Pontus Henriksson, Carola Nijm, Julia Jäderquist, Johanna Sandborg, Eva Flinke, Rashmi Ramesh, Lovisa Örkenby, Filip Appelkvist, Thomas Lingg, Nicola Guzzi, Cristian Bellodi, Marie Löf, Tanya Vavouri, Anita Öst
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: almost 13 years ago

10.1186/s13073-017-0511-4

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells
Cited by: 6
Author(s): Snehangshu Kundu, Muhammad Akhtar-Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R. Wiśniewski, Per Artursson, Liqun He, Mats Hellström, Tobias Sjöblom
Software Mentions: 6
Published: almost 7 years ago

10.7554/eLife.33953

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins
Cited by: 84
Author(s): Nitzan Koppel, Jordan E. Bisanz, Maria-Eirini Pandelia, Peter J. Turnbaugh, Emily P. Balskus
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2164-15-925

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
Cited by: 23
Author(s): Antonella Federico, Davide Cirillo, Riccardo Delli Ponti, Gian Gaetano Tartaglia
Software Mentions: 5
Published: about 10 years ago

10.1186/s13059-019-1721-4

Chromatin accessibility plays a key role in selective targeting of Hox proteins
Cited by: 35
Author(s): Damiano Porcelli, Bettina Fischer, Steven Russell, Robert A. White
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02386-z

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Cited by: 4
Author(s): Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior Pachter
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: over 6 years ago

10.1186/s13068-021-01975-1

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Cited by: 14
Author(s): Monika Tõlgo, Silvia Hüttner, Peter Rugbjerg, Nguyễn Thanh Thủy, Vu Nguyen Thanh, Johan Larsbrink, Lisbeth Olsson
Software Mentions: 5
Published: over 3 years ago

10.1016/j.gdata.2015.07.002

RNAome sequencing delineates the complete RNA landscape
Cited by: 1
Author(s): Kasper Derks, Joris Pothof
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-014-0494-z

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach
Cited by: 31
Author(s): Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P. Fairfax, Kenneth Chan, Katharine Plant, Julian C. Knight
Software Mentions: 5
Published: about 10 years ago

10.1186/s12859-021-04240-2

Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
Cited by: 4
Author(s): Hiroaki Kato, Mitsuhiro Shimizu, Takeshi Urano
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22157928

A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups
Cited by: 3
Author(s): Daniel J. Goodall, Katie H. Jameson, Michelle Hawkins, Christian J. Rudolph
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0208371

Genetic resistance to DEHP-induced transgenerational endocrine disruption
Cited by: 17
Author(s): Ludwig Stenz, Rita Rahban, Julien Prados, Serge Nef, Ariane Paoloni-Giacobino
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0164463

A Tale of Tails: Dissecting the Enhancing Effect of Tailed Primers in Real-Time PCR
Cited by: 6
Author(s): Frank Vandenbussche, Élisabeth Mathijs, David Lefebvre, Kris De Clercq, Steven Van Borm
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.03703

Selection of chromosomal DNA libraries using a multiplex CRISPR system
Cited by: 298
Author(s): Owen Ryan, Jeffrey M. Skerker, Matthew J. Maurer, Xin Li, Jordan C. Tsai, Snigdha Poddar, Michael E. Lee, Will DeLoache, John E. Dueber, Adam P. Arkin, Jamie H. D. Cate
Software Mentions: 5
Published: over 10 years ago

10.3389/fpls.2016.01225

TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity
Cited by: 29
Author(s): Niklas Schandry, Orlando de Lange, Philippe Prior, Thomas Lahaye
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1008917

Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites
Cited by: 23
Author(s): Élodie Gazanion, Laurent Lacroix, Patrizia Alberti, Pratima Gurung, Sharon Wein, Ming Cheng, Jean‐Louis Mergny, Ana Gomes, José-Juan Lopez-Rubio
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.03346

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network
Cited by: 82
Author(s): Carine Gubelmann, Petra Schwalie, Sunil K. Raghav, Eva Röder, Tenagne Delessa, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudofsky, Didier Trono, Christian Wolfrum, Bart Deplancke
Software Mentions: 5
Published: about 10 years ago

10.1073/pnas.2008281117

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
Cited by: 192
Author(s): Bethany L. Dearlove, Éric Lewitus, Hongjun Bai, Yifan Li, Daniel B. Reeves, Michael Joyce, Paul T. Scott, Mihret F. Amare, Sandhya Vasan, Nelson L. Michael, Kayvon Modjarrad, Morgane Rolland
Software Mentions: 5
Published: about 4 years ago

10.1534/g3.116.032276

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in<i>Saccharomyces cerevisiae</i>
Cited by: 39
Author(s): Benjamin Neymotin, Victoria M. Ettorre, David Gresham
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-015-1820-x

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
Cited by: 19
Author(s): Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James, Jean Yee Hwa Yang
Software Mentions: 5
Published: over 9 years ago

10.3389/fbioe.2020.598392

Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance
Cited by: 6
Author(s): Maryna Vasylkivska, Barbora Branská, Karel Sedlář, Katerina Jureckova, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: about 4 years ago

10.15252/msb.20209885

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function
Cited by: 12
Author(s): Wim J. de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-017-17408-9

Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli
Cited by: 7
Author(s): Peter Großmann, Anja Lück, Christoph Kaleta
Software Mentions: 5
Published: almost 7 years ago

10.1007/978-1-4939-9074-0_25

Sharing Programming Resources Between Bio* Projects
Cited by: 4
Author(s): Raoul Jean Pierre Bonnal, Andy Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher J. Fields, Toshiaki Katayama, Pjotr Prins
Software Mentions: 4
Published: almost 6 years ago

10.26508/lsa.202000825

The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells
Cited by: 13
Author(s): Maria Inês Alvelos, Mirko Brüggemann, F. X. Reymond Sutandy, Jonàs Juan-Mateu, Máikel Luís Colli, Anke Busch, Miguel Lopes, Ângela Castela, Annemieke Aartsma‐Rus, Julian König, Kathi Zarnack, Décio L. Eizirik
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12711-021-00643-0

Genetic variation in recombination rate in the pig
Cited by: 15
Author(s): Martin Johnsson, Andrew Whalen, Roger Ros‐Freixedes, Gregor Gorjanc, Ching-Yi Chen, William Herring, Dirk-Jan de Koning, John M. Hickey
Software Mentions: 4
Published: over 3 years ago

10.1155/2013/340620

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
Cited by: 79
Author(s): Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele Calogero
Software Mentions: 4
Published: almost 12 years ago

10.1155/2014/736798

Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA
Cited by: 2
Author(s): Xiaoyong Sun, Simon Lin, Xiaoyan Yan
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0107259

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
Cited by: 48
Author(s): Melanie Spornraft, Benedikt Kirchner, Bettina Haase, Vladimı́r Beneš, Michael W. Pfaffl, Irmgard Riedmaier
Software Mentions: 4
Published: about 10 years ago

Projects: bioconductor: Biostrings

Papers Mentioning Biostrings 220