bioconductor: Rsamtools | Projects

10.1186/s12864-019-6313-x

Secretory RING finger proteins function as effectors in a grapevine galling insect
Cited by: 13
Author(s): Chaoyang Zhao, Claude Rispe, Paul D. Nabity
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-015-1583-4

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
Cited by: 44
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Odile Sismeiro, Adrien Villain, Violette Da Cunha, Marie-Elise Caliot, Marie‐Agnès Dillies, Patrick Trieu-Cuot, Philippe Bouloc, Marie‐Frédérique Lartigue, Philippe Glaser
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.46711

Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms
Cited by: 23
Author(s): Yoseop Yoon, Jeff Klomp, Inés Martín-Martín, Frank Criscione, Eric Calvo, José M. C. Ribeiro, Urs Schmidt‐Ott
Software Mentions: 3
Published: about 5 years ago

10.1016/j.cell.2021.03.012

Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions
Cited by: 126
Author(s): Ryan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Wei Jin, Mia Madel Alfajaro, Quanming Shi, Maxwell R. Mumbach, Aditi Limaye, Peter C DeWeirdt, Cameron O. Schmitz, Kevin R. Parker, Elizabeth Woo, Howard Y. Chang, Tamás L. Horváth, Jan E. Carette, Carolyn R. Bertozzi, Craig B. Wilen, Ansuman T. Satpathy
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2148-12-94

Uninformative polymorphisms bias genome scans for signatures of selection
Cited by: 131
Author(s): Marius Roesti, Walter Salzburger, Daniel Berner
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0247031

Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales
Cited by: 33
Author(s): M. Bradley Hanson, Candice K. Emmons, Michael J. Ford, Meredith V. Everett, Kim M. Parsons, Linda K. Park, Jennifer A. Hempelmann, Donald M. Van Doornik, Gregory S. Schorr, Jeffrey K Jacobsen, Mark F Sears, Maya S Sears, John G. Sneva, Robin W. Baird, Lynne Barrè
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-12084-1

DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated Disorders
Cited by: 36
Author(s): María Berdasco, Antonio Gómez, Marc Rubio, Jaume Català‐Mora, Vicente Zanón‐Moreno, Miguel López, Cristina Hernández, Shigeo Yoshida, Takahito Nakama, Keijiro Ishikawa, Tatsuro Ishibashi, Amina Boubekeur, Lotfi Louhibi, Miguel Ángel Pujana, Sergi Sayols, Fernando Setién, Dolores Corella, Carmen de Torres, Andreu Parareda, Ling Zhao, Kang Zhang, Matilde E. Lleonart, Javier Alonso, Rafael Simó, Josep M. Caminal, Manel Esteller
Software Mentions: 3
Published: about 7 years ago

10.3390/v13030437

viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results
Cited by: 1
Author(s): David F. Nieuwenhuijse, Bas B. Oude Munnink, Marion Koopmans
Software Mentions: 3
Published: over 3 years ago

10.3390/vaccines9060616

A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel
Cited by: 20
Author(s): Neta S. Zuckerman, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil, Yaniv Lustig, Ella Mendelson, Michal Mandelboim, Orna Mor, Neta S. Zuckerman
Software Mentions: 3
Published: over 3 years ago

10.1128/JVI.00571-17

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes
Cited by: 75
Author(s): Yasutsugu Suzuki, Lionel Frangeul, Laura B. Dickson, Hervé Blanc, Yann Verdier, Joëlle Vinh, Louis Lambrechts, Maria‐Carla Saleh
Software Mentions: 2
Published: over 7 years ago

10.1007/s00401-017-1714-x

Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease
Cited by: 49
Author(s): Arne De Roeck, Tobi Van den Bossche, Julie van der Zee, Jan Verheijen, Wouter De Coster, Jasper Van Dongen, Lubina Dillen, Yalda Baradaran-Heravi, Bavo Heeman, Raquel Sánchez‐Valle, Albert Lladó, Benedetta Nacmias, Sandro Sorbi, Ellen Gelpí, Oriol Grau‐Rivera, Estrella Gómez‐Tortosa, Pau Pástor, Sara Ortega‐Cubero, María A. Pastor, Caroline Graff, Håkan Thonberg, Luisa Benussi, Roberta Ghidoni, Giuliano Binetti, Alexandre de Mendonça, Madalena Martins, Barbara Borroni, Alessandro Padovani, Maria Rosário Almeida, Isabel Santana, Janine Diehl‐Schmid, Panagiotis Alexopoulos, Jordi Clarimón, Alberto Lleó, Juan Fortea, Magda Tsolaki, Maria Koutroumani, Radoslav Matěj, Zdeněk Rohan, Peter De Deyn, Sebastiaan Engelborghs, Patrick Cras, Christine Van Broeckhoven, Kristel Sleegers
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04060-4

Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers
Cited by: 6
Author(s): Pierre‐Julien Viailly, Vincent Sater, Mathieu Viennot, Élodie Bohers, Nicolas Vergne, Caroline Bérard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie‐Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, Fabrice Jardin
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-14-S11-S3

Efficient digest of high-throughput sequencing data in a reproducible report
Cited by: 4
Author(s): Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C. Perín, Hongbo Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White
Software Mentions: 2
Published: about 11 years ago

10.1186/s12859-020-3508-8

Origins and characterization of variants shared between databases of somatic and germline human mutations
Cited by: 10
Author(s): William Meyerson, John Leisman, Fábio C. P. Navarro, Mark Gerstein
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-6542-z

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets
Cited by: 4
Author(s): Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda, Itoshi Nikaido
Software Mentions: 2
Published: over 4 years ago

10.1186/s13104-015-1404-5

VING: a software for visualization of deep sequencing signals
Cited by: 20
Author(s): Marc Descrimes, Yousra Ben Zouari, Maxime Wéry, Rachel Legendre, Daniel Gautheret, Antonin Morillon
Software Mentions: 2
Published: about 9 years ago

10.1093/bioinformatics/btu419

RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy
Cited by: 26
Author(s): Kitty Lo, C. R. Boustred, Lyn S. Chitty, Vincent Plagnol
Software Mentions: 2
Published: over 10 years ago

10.3390/v13030511

Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a
Cited by: 2
Author(s): Kaho H. Tisthammer, Weiyan Dong, Jeffrey B. Joy, Pleuni S. Pennings
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0029002

Deep Sequencing Whole Transcriptome Exploration of the σE Regulon in Neisseria meningitidis
Cited by: 25
Author(s): Robert Antonius Gerhardus Huis in ‘t Veld, Antonius Marcellinus Willemsen, A. H. C. van Kampen, Edward J. Bradley, Frank Baas, Yvonne Pannekoek, Arie van der Ende
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0229449

Proteolysis and cartilage development are activated in the synovium after surgical induction of post traumatic osteoarthritis
Cited by: 10
Author(s): Ugur M. Ayturk, Jakob T. Sieker, Carla M. Haslauer, Benedikt L. Proffen, Manuela Weißenberger, Matthew L. Warman, Braden C. Fleming, Martha M. Murray
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0039359

Molecular Effects of Doxycycline Treatment on Pterygium as Revealed by Massive Transcriptome Sequencing
Cited by: 20
Author(s): Ignacio M. Larráyoz, Alberto de Luis, Óscar Rúa, Sara Velilla, Juan Cabello, Alfredo Martı́nez
Software Mentions: 2
Published: over 12 years ago

10.15252/emmm.202114060

rs41291957 controls miR‐143 and miR‐145 expression and impacts coronary artery disease risk
Cited by: 10
Author(s): Ignacio Fernando Hall, Montserrat Climent, Chiara Anselmi, Laura Papa, Vinicius Tragante, Luca Lambroia, Floriana Maria Farina, Marcus E. Kleber, Winfried März, Carlo Biguori, Gianluigi Condorelli, Leonardo Elia
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-015-0648-7

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
Cited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-019-1683-6

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean
Cited by: 13
Author(s): Jinyu Wang, Xianran Li, Kyung Do Kim, Michael J. Scanlon, Scott A. Jackson, Nathan M. Springer, Jianming Yu
Software Mentions: 2
Published: over 5 years ago

10.1111/jeb.13443

How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna
Cited by: 13
Author(s): Marinela Dukič, Daniel Berner, Christoph R. Haag, Dieter Ebert
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-94491-z

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe
Cited by: 20
Author(s): Adam B Rohrlach, Luka Papac, Ainash Childebayeva, Maïté Rivollat, Vanessa Villalba-Mouco, Gunnar U. Neumann, Sandra Penske, Eirini Skourtanioti, Marieke Sophia van de Loosdrecht, Murat Akar, Kamen Boyadzhiev, Yavor Boyadzhiev, Marie‐France Deguilloux, Miroslav Dobeš, Yılmaz Selim Erdal, Michal Ernée, Marcella Frangipane, Mirosław Furmanek, Susanne Friederich, Emmanuel Ghesquière, Agata Hałuszko, Svend Hansen, Mario Küßner, Marcello A. Mannino, Rana Özbal, Sabine Reinhold, Stéphane Rottier, Domingo C. Salazar‐García, Jorge Soler Díaz, Philipp W. Stockhammer, Consuelo Roca de Togores Muñoz, K. Aslıhan Yener, Cosimo Posth, Johannes Krause, Alexander Herbig, Wolfgang Haak
Software Mentions: 2
Published: over 3 years ago

10.1016/j.jmoldx.2018.07.005

Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients
Cited by: 75
Author(s): Bente Risberg, Dana W.Y. Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James A. Morris, Vincent Plagnol, Nitzan Rosenfeld, Carlos Caldas, James D. Brenton, Davina Gale
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms160922046

Identification of Conserved and Novel MicroRNAs during Tail Regeneration in the Mexican Axolotl
Cited by: 15
Author(s): Micah D. Gearhart, Jami R. Erickson, Andrew Walsh, Karen Echeverri
Software Mentions: 2
Published: about 9 years ago

10.1007/s00401-018-1841-z

An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s disease
Cited by: 64
Author(s): Arne De Roeck, Lena Duchateau, Jasper Van Dongen, Rita Cacace, Maria Bjerke, Tobi Van den Bossche, Patrick Cras, Rik Vandenberghe, Peter Paul De Deyn, Sebastiaan Engelborghs, Christine Van Broeckhoven, Kristel Sleegers
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2018.00185

Expression of the Circadian Clock Gene BMAL1 Positively Correlates With Antitumor Immunity and Patient Survival in Metastatic Melanoma
Cited by: 53
Author(s): Leonardo Vinícius Monteiro de Assis, Gabriela Sarti Kinker, Maria Nathália Moraes, Regina Pekelmann Markus, Pedro Augusto Carlos Magno Fernandes, Ana Maria de Lauro Castrucci
Software Mentions: 1
Published: over 6 years ago

10.12688/f1000research.7453.1

Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates
Cited by: 4
Author(s): Andy G. Lynch
Software Mentions: 1
Published: almost 9 years ago

10.1002/evl3.99

Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish
Cited by: 39
Author(s): Quiterie Haenel, Marius Roesti, Dario Moser, Andrew D. C. MacColl, Daniel Berner
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.cub.2020.06.057

Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti Ovaries
Cited by: 75
Author(s): Yasutsugu Suzuki, Artem Baidaliuk, Pascal Miesen, Lionel Frangeul, Anna B. Crist, Sarah H. Merkling, Albin Fontaine, Sébastian Lequime, Isabelle Moltini-Conclois, Hervé Blanc, Ronald P. van Rij, Louis Lambrechts, Maria-Carla Saleh
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pcbi.1003419

Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila
Cited by: 20
Author(s): Federico Comoglio, Renato Paro
Software Mentions: 1
Published: almost 11 years ago

10.3390/v12040468

Differential Small RNA Responses against Co-Infecting Insect-Specific Viruses in Aedes albopictus Mosquitoes
Cited by: 16
Author(s): Lionel Frangeul, Hervé Blanc, María-Carla Saleh, Yasutsugu Suzuki
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.01558-17

Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic Escherichia coli
Cited by: 39
Author(s): Kelvin G. K. Goh, Minh-Duy Phan, Brian M. Forde, Teik Min Chong, Wai‐Fong Yin, Kok‐Gan Chan, Glen C. Ulett, Matthew J. Sweet, Scott A. Beatson, Mark A. Schembri
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-15-236

De novo transcriptome analysis of Hevea brasiliensistissues by RNA-seq and screening for molecular markers
Cited by: 70
Author(s): Leonardo Rippel Salgado, Daniela Martins Koop, Daniel Guariz Pinheiro, Ronan Rivallan, Vincent Le Guen, Marisa Fabiana Nicolás, Luiz Gonzaga Paula de Almeida, Viviani Ribeiro Rocha, Milena Mangefeste Magalhães, Alexandra Lehmkuhl Gerber, Antônio Figueira, Júlio Cézar De Mattos Cascardo, Ana Tereza Ribeiro de Vasconcelos, Wilson A. Silva, Luiz Lehmann Coutinho, Dominique García
Software Mentions: 1
Published: over 10 years ago

Ecosyste.ms: Papers

Projects: bioconductor: Rsamtools

Papers Mentioning Rsamtools 138