bioconductor: Rsamtools | Projects

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 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

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1high memory phenotype CD4 T cells
Cited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: over 4 years ago

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.1186/s12864-015-2140-x

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 years ago

10.1186/s12864-018-4559-3

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 6 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

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: about 9 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: almost 7 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 7 years ago

10.1016/j.molcel.2019.03.024

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression
Cited by: 187
Author(s): Nadezda A. Fursova, Neil P. Blackledge, Manabu Nakayama, Shinsuke Ito, Haruhiko Koseki, Anca M. Farcas, Hamish W King, Haruhiko Koseki, Robert J. Klose
Software Mentions: 11
Published: over 5 years ago

10.1186/gb-2012-13-8-r77

ggbio: an R package for extending the grammar of graphics for genomic data
Cited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago

10.3390/ijms22083975

Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds
Cited by: 11
Author(s): Debosmita Sardar, Brittney Lozzi, Junsung Woo, Teng-Wei Huang, Caroline Cvetkovic, Chad J. Creighton, Robert Krencik, Benjamin Deneen
Software Mentions: 10
Published: over 3 years ago

10.3389/fnins.2020.00061

Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain
Cited by: 35
Author(s): Brittney Lozzi, Teng-Wei Huang, Debosmita Sardar, Anna Yu-Szu Huang, Benjamin Deneen
Software Mentions: 9
Published: almost 5 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

10.1186/s40478-019-0851-y

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas
Cited by: 12
Author(s): Ruslan Al‐Ali, Katharina Bauer, Jong‐Whi Park, Ruba Al-Abdulla, Valentina Fermi, Andreas von Deimling, Christel Herold‐Mende, Jan‐Philipp Mallm, Carl Herrmann, Wolfgang Wick, Şevin Turcan
Software Mentions: 9
Published: almost 5 years ago

10.3389/fncel.2021.648570

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
Cited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0066902

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
Cited by: 16
Author(s): Darragh G. McArt, Philip D. Dunne, Jaine K. Blayney, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Peter Hamilton, Shudong Zhang
Software Mentions: 9
Published: over 11 years ago

10.26508/lsa.202101108

Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo
Cited by: 11
Author(s): Karen N. McFarland, Carolina Wiesner Ceballos, Awilda M. Rosario, Thomas B. Ladd, Brenda D. Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilufer Ertekin‐Taner, Cory C. Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, Todd E. Golde
Software Mentions: 9
Published: over 3 years ago

10.1093/bioinformatics/bts477

easyRNASeq: a bioconductor package for processing RNA-Seq data
Cited by: 96
Author(s): Nicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong, Lars M. Steinmetz
Software Mentions: 9
Published: over 12 years ago

10.1186/1471-2164-15-284

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
Cited by: 743
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler
Software Mentions: 8
Published: almost 11 years ago

10.3390/ijms21103591

Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean
Cited by: 8
Author(s): Adrienne N. Moran Lauter, Lindsay Rutter, Dianne Cook, Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 8
Published: over 4 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

10.1186/1471-2164-14-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

10.1186/s12864-021-07735-7

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
Cited by: 11
Author(s): Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz‐Ferrer, Carolina Escobar, Tim De Meyer, Tina Kyndt
Software Mentions: 7
Published: over 3 years ago

10.1186/s13148-021-01129-y

Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD
Cited by: 22
Author(s): Nicholas Johnson, Xiumei Wu, Christopher D. Still, Xin Chu, Anthony Petrick, Glenn S. Gerhard, Karen N. Conneely, Johanna K. DiStefano
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: almost 8 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: almost 9 years ago

10.1186/1471-2164-15-702

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
Cited by: 58
Author(s): Adrienne N. Moran Lauter, Gregory A. Peiffer, Tao Yin, Steven A. Whitham, Dianne Cook, Randy C. Shoemaker, Michelle A. Graham
Software Mentions: 7
Published: over 10 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: almost 10 years ago

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: about 6 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: about 10 years ago

10.3390/microorganisms8020270

In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays
Cited by: 15
Author(s): Rossella Gratton, Paola Maura Tricarico, Almerinda Agrelli, Heverton Valentim Colaço da Silva, Lucas Coêlho Bernardo, Sérgio Crovella, Antônio Victor Campos Coelho, Ronald Moura, Lucas André Cavalcanti Brandão
Software Mentions: 7
Published: almost 5 years ago

10.3390/microorganisms9050996

Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions
Cited by: 1
Author(s): Karen Cristine Gonçalves dos Santos, G. Pelletier, Armand Séguin, François Guillemette, Jeffrey A. Hawkes, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 7
Published: over 3 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.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 8 years ago

10.3389/fgene.2017.00013

The Pancreatic Islet Regulome Browser
Cited by: 28
Author(s): Loris Mularoni, Mireia Ramos-Rodríguez, Lorenzo Pasquali
Software Mentions: 6
Published: almost 8 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

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.ppat.1008589

High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis
Cited by: 12
Author(s): Julián Naipauer, Daria Salyakina, Guy Journo, Santas Rosario, Siôn L. Williams, Martı́n C. Abba, Meir Shamay, Enrique A. Mesri
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms21197407

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression
Cited by: 14
Author(s): Martı́n C. Abba, Romina Canzoneri, Agustina Gurruchaga, Jae-Ho Lee, Pradeep Tatineni, Hyunsuk Kil, Ezequiel Lacunza, C. Marcelo Aldaz
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2016.00031

A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe
Cited by: 17
Author(s): Stefano Berto, Alvaro Perdomo‐Sabogal, Daniel Gerighausen, Jing Qin, Katja Nowick
Software Mentions: 6
Published: over 8 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

10.1186/1471-2164-15-353

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Cited by: 49
Author(s): Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel A. Keim, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 6
Published: over 10 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

10.3389/fpls.2017.01926

A Pectin Methylesterase ZmPme3 Is Expressed in Gametophyte factor1-s (Ga1-s) Silks and Maps to that Locus in Maize (Zea mays L.)
Cited by: 28
Author(s): Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott
Software Mentions: 6
Published: about 7 years ago

10.12688/f1000research.8964.1

RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
Cited by: 58
Author(s): Alexandra Popa, Kévin Lebrigand, Agnès Paquet, Nicolas Nottet, Karine Robbe-Sermesant, Rainer Waldmann, Pascal Barbry
Software Mentions: 6
Published: over 8 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

10.1186/s13059-017-1165-7

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Cited by: 20
Author(s): Inês de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 6
Published: over 7 years ago

10.3390/plants9040545

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)
Cited by: 3
Author(s): Cristina Gómez-Martín, Carmen Capel, Ana M. González, Ricardo Lebrón, Fernando J. Yuste‐Lisbona, Michael Hackenberg, José Luis Tejera Oliver, Marta Santalla, Rafael Lozano
Software Mentions: 6
Published: over 4 years ago

10.1242/dev.199604

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency
Cited by: 16
Author(s): Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-019-57214-z

5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation
Cited by: 14
Author(s): Santiago Uribe-Lewis, Thomas Carroll, Suraj Menon, Anna M. Nicholson, Piotr J. Manasterski, Douglas J. Winton, Simon Buczacki, Adele Murrell
Software Mentions: 6
Published: almost 5 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

10.1016/j.cell.2013.11.043

The Architecture of Parent-of-Origin Effects in Mice
Cited by: 79
Author(s): Richard Mott, Yuan Wei, Pamela J. Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, Jonathan Flint
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pone.0032724

Deep-Sequencing Protocols Influence the Results Obtained in Small-RNA Sequencing
Cited by: 33
Author(s): Joern Toedling, Nicolas Servant, Constance Ciaudo, Laurent Farinelli, Olivier Voinnet, Edith Heard, Emmanuel Barillot
Software Mentions: 6
Published: over 12 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-015-0605-5

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
Cited by: 61
Author(s): Santiago Uribe-Lewis, Rory Stark, Thomas Carroll, Mark J. Dunning, Martin Bachman, Yoko Itō, Lovorka Stojic, Silvia Halim, Sarah L. Vowler, Andy G. Lynch, Benjamin Delatte, Eric James de Bony, Laurence Colin, Matthieu Defrance, Felix Krueger, Ana Luísa Silva, Rogier ten Hoopen, Ashraf E.K. Ibrahim, François Fuks, Adele Murrell
Software Mentions: 5
Published: over 9 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

10.3390/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

10.1007/s00253-016-7588-3

Ploidy influences the functional attributes of de novo lager yeast hybrids
Cited by: 65
Author(s): Kristoffer Krogerus, Mikko Arvas, Matteo De Chiara, Frederico Magalhães, Laura Mattinen, Merja Oja, Virve Vidgren, Jia-Xing Yue, Gianni Liti, Brian Gibson
Software Mentions: 5
Published: over 8 years ago

10.1128/mSystems.00195-17

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome
Cited by: 8
Author(s): Kathy N. Lam, Eric C. Martens, Trevor C. Charles
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-019-5613-5

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes
Cited by: 25
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart, Philippe Glaser
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

10.1371/journal.ppat.1008221

PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment
Cited by: 23
Author(s): Julián Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Rolf Renne, Ho Lam Chan, Lluís Morey, Daria Salyakina, Martı́n C. Abba, Siôn L. Williams, Joshua M. Hare, Pascal J. Goldschmidt‐Clermont, Enrique A. Mesri
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-021-07552-y

Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential
Cited by: 20
Author(s): Juanita Engelbrecht, Tuan A. Duong, S. Prabhu, Mohamed Seedat, Noëlani van den Berg
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.11733

DMBA induced mouse mammary tumors display high incidence of activating Pik3caH1047 and loss of function Pten mutations
Cited by: 45
Author(s): Martı́n C. Abba, Yi Zhong, Jae-Ho Lee, Hyunsuk Kil, Yue Lu, Yoko Takata, Melissa S. Simper, Sally Gaddis, Jianjun Shen, C. Marcelo Aldaz
Software Mentions: 4
Published: about 8 years ago

10.1038/srep20064

Digital detection of endonuclease mediated gene disruption in the HIV provirus
Cited by: 21
Author(s): Ruth Hall Sedlak, Shu Liang, Nixon Niyonzima, Harshana S. De Silva Feelixge, Pavitra Roychoudhury, Alexander L. Greninger, Nicholas Weber, Sandrine Boissel, Andrew M. Scharenberg, Anqi Cheng, Amalia Magaret, Roger E. Bumgarner, Daniel Stone, Keith R. Jerome
Software Mentions: 4
Published: almost 9 years ago

10.1128/mSystems.00341-21

Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A
Cited by: 1
Author(s): Francesco Del Carratore, Marianna Iorio, Mercedes Pérez-Bonilla, Kamila Schmidt, Rosario Pérez‐Redondo, Margherita Sosio, Sandy MacDonald, Ivan Gyulev, Areti Tsigkinopoulou, Gavin H. Thomas, Olga Genilloud, Antonio Rodríguez‐García, Stefano Donadio, Rainer Breitling, Eriko Takano
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-015-2164-2

The direction of cross affects obesity after puberty in male but not female offspring
Cited by: 5
Author(s): Stefan Kärst, Danny Arends, Sebastian Heise, Jan Trost, Marie–Laure Yaspo, Vyacheslav Amstislavskiy, Thomas S. Risch, Hans Lehrach, Gudrun A. Brockmann
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-019-5998-1

Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants
Cited by: 8
Author(s): Marc‐André Lemay, Davoud Torkamaneh, Guillem Rigaill, Brian Boyle, Adrian O. Stec, Robert M. Stupar, François Belzile
Software Mentions: 4
Published: over 5 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

10.1016/j.molcel.2018.08.020

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures
Cited by: 206
Author(s): Thomas Clouaire, Vincent Rocher, Anahita Lashgari, Coline Arnould, Marion Aguirrebengoa, Anna Biernacka, Magdalena Skrzypczak, François Aymard, Bernard Fongang, Norbert Dojer, Jason S. Iacovoni, Maga Rowicka, Krzysztof Ginalski, Jacques Côté, Gaëlle Legube
Software Mentions: 4
Published: about 6 years ago

10.1186/s12974-019-1645-7

IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia
Cited by: 34
Author(s): Fátima Rivera-Escalera, Jonathan J. Pinney, Laura Owlett, Hoda A. Ahmed, Juilee Thakar, John A. Olschowka, Michael R. Elliott, M. Kerry O’Banion
Software Mentions: 4
Published: almost 5 years ago

10.1007/s00253-019-09904-x

Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25
Cited by: 30
Author(s): Małgorzata Ryngajłło, Paulina Jacek, Izabela Cielecka, Halina Kalinowska, Stanisław Bielecki
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007496

Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer
Cited by: 15
Author(s): Miranda D. Stobbe, Gian Andri Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P. Whalley, Emanuele Raineri, Marta Gut
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1004595

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
Cited by: 26
Author(s): Aamna K Kaul, Eugene F. Schuster, Barbara Jennings
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1008466

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Cited by: 59
Author(s): Barbara De Kegel, Colm J. Ryan
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0093846

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs
Cited by: 104
Author(s): Lei Shi, Zhe Zhang, Angela M Yu, Wei Wang, Zhi Wei, Ehtisham Akhter, Kelly Maurer, Patrícia Costa-Reis, Li Song, Michelle Petri, Kathleen E. Sullivan
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0088950

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells
Cited by: 68
Author(s): Jeannine Diesch, Elaine Sanij, Omer Gilan, Christopher G. Love, Hoanh Tran, Nicholas I. Fleming, Jason Ellul, Amalia Marcia, Izhak Haviv, Richard B. Pearson, Eugene Tulchinsky, John M. Mariadason, Oliver M. Sieber, Ross D. Hannan, Amardeep S. Dhillon
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0129350

Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection
Cited by: 0
Author(s): Thadeous J. Kacmarczyk, Caitlin Bourque, Xihui Zhang, Yanwen Jiang, Yariv Houvras, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-017-1549-4

BBCAnalyzer: a visual approach to facilitate variant calling
Cited by: 0
Author(s): Sarah Sandmann, Aniek O. de Graaf, Martin Dugas
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms22084267

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites
Cited by: 4
Author(s): Kristian Persson Hodén, Xinyi Hu, Gabriel García Martínez, Christina Dixelius
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-021-04153-0

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples
Cited by: 3
Author(s): Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange, Gerhard Schöfl
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.00854

New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data
Cited by: 7
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2018.02929

Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
Cited by: 11
Author(s): Agnès B Jousset, Isabelle Rosinski‐Chupin, Julie Takissian, Philippe Glaser, Rémy A. Bonnin, Thierry Naas
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2019.00079

Time to Treatment Prediction in Chronic Lymphocytic Leukemia Based on New Transcriptional Patterns
Cited by: 8
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, Ángeles Bendaña López, José Ángel Díaz Arias, Nicolas Varela, Marta Sonia González Pérez, Manuel Pérez‐Encinas, José Luis Bello López
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.119.400716

Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors
Cited by: 9
Author(s): Nik Susič, Sandra Janežič, Maja Rupnik, Barbara Gerič Stare
Software Mentions: 4
Published: over 4 years ago

10.1186/gb-2014-15-2-r21

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans
Cited by: 46
Author(s): Cristina González-Aguilera, Kohta Ikegami, Cristina de la Cruz Ayuso, Alberto de Luis, María Íñiguez, Juan Cabello, Jason D. Lieb, Peter Askjaer
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-015-0617-1

CopywriteR: DNA copy number detection from off-target sequence data
Cited by: 169
Author(s): Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P. Lolkema, Bauke Ylstra, Jos Jonkers, Sven Rottenberg, Lodewyk F.A. Wessels, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 4
Published: over 9 years ago

10.1093/gigascience/giy080

A workflow for simplified analysis of ATAC-cap-seq data in R
Cited by: 5
Author(s): Ram Krishna Shrestha, Pingtao Ding, Jonathan D. G. Jones, Dan MacLean
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.112.004994

Resequencing and Comparative Genomics of Stagonospora nodorum: Sectional Gene Absence and Effector Discovery
Cited by: 45
Author(s): Robert A. Syme, James K. Hane, Timothy L. Friesen, Richard P. Oliver
Software Mentions: 3
Published: over 11 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 4 years ago

10.1093/g3journal/jkab163

Nuku, a family of primate retrocopies derived from KU70
Cited by: 0
Author(s): Paul A. Rowley, Aisha Ellahi, Kyudong Han, Jagdish Suresh Patel, James T. Van Leuven, Sara L. Sawyer
Software Mentions: 3
Published: over 3 years ago

10.1111/mmi.14362

Mycobacterium tuberculosisrequires glyoxylate shunt and reverse methylcitrate cycle for lactate and pyruvate metabolism
Cited by: 66
Author(s): Agnese Serafini, Lendl Tan, Stuart Horswell, Steven Howell, Greenwood Dj, Deborah M. Hunt, Minh-Duy Phan, Mark A. Schembri, Mercedes Monteleone, Christine R Montague, Warwick J. Britton, Acely Garza-Garcia, Ambrosius P. Snijders, Brian C. VanderVen, Maximiliano G. Gutiérrez, Nicholas P. West, Luiz Pedro S. de Carvalho
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-017-3586-9

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
Cited by: 31
Author(s): Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Conrad Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim, Siegfried Scherer
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/eraa132

Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects
Cited by: 43
Author(s): Tom J. M. Van Dooren, Amanda Bortolini Silveira, Elodie Gilbault, José M. Jiménez‐Gómez, Antoine Martin, Liên Bach, Sébastien Tisné, Leandro Quadrana, Olivier Loudet, Vincent Colot
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-13-S8-S11

DFI: gene feature discovery in RNA-seq experiments from multiple sources
Cited by: 5
Author(s): Hatice Gülçin Özer, Jeffrey D. Parvin, Kun Huang
Software Mentions: 3
Published: almost 13 years ago

Projects: bioconductor: Rsamtools

Papers Mentioning Rsamtools 138