Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: rtracklayer
https://packages.ecosyste.ms/registries/bioconductor.org/packages/rtracklayer
R interface to genome annotation files and the UCSC genome browser
2 versions
Latest release: about 1 year ago
237 dependent packages
3,529,318 downloads total
Papers Mentioning rtracklayer 107
10.12688/f1000research.22259.1
Fluent genomics with plyranges and tximetaCited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago
10.15252/msb.20209539
Predictive features of gene expression variation reveal mechanistic link with differential expressionCited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago
10.1155/2021/8020879
Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network MechanismCited by: 10
Author(s): Jin Zhang, Fei Xiao, Guangliang Qiang, Zhenrong Zhang, Qianli Ma, Hao Yang, H. Rosie Xing, Chaoyang Liang
Software Mentions: 22
Published: about 3 years ago
10.12688/f1000research.13577.2
Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studiesCited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago
10.1016/j.molcel.2021.05.023
Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infectionCited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago
10.1186/1471-2105-11-237
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dataCited 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
10.1186/s12864-015-2140-x
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction dataCited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 years ago
10.1371/journal.pone.0256196
Finding differentially expressed sRNA-Seq regions with srnadiffCited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago
10.3390/cells8111321
Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding DatasetsCited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: about 5 years ago
10.1007/s00401-021-02343-x
Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseasesCited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: over 3 years ago
10.1186/s13059-018-1484-3
CTCF maintains regulatory homeostasis of cancer pathwaysCited by: 39
Author(s): Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni, Duncan T. Odom
Software Mentions: 14
Published: over 6 years ago
10.1186/s13059-021-02264-8
GeneWalk identifies relevant gene functions for a biological context using network representation learningCited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: almost 4 years ago
10.12688/f1000research.12223.1
recount workflow: Accessing over 70,000 human RNA-seq samples with BioconductorCited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: about 7 years ago
10.1371/journal.pcbi.1003118
Software for Computing and Annotating Genomic RangesCited 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
10.1038/s41598-021-97362-9
N6-methylandenosine-related lncRNAs play an important role in the prognosis and immune microenvironment of pancreatic ductal adenocarcinomaCited by: 5
Author(s): Yuhai Hu, Yiping Chen
Software Mentions: 14
Published: about 3 years ago
10.1099/mgen.0.000524
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information accessCited 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
10.1186/gb-2012-13-8-r77
ggbio: an R package for extending the grammar of graphics for genomic dataCited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago
10.1038/s41598-019-41601-7
Characteristics and homogeneity of N6-methylation in human genomesCited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: over 5 years ago
10.1371/journal.pone.0016432
An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-SeqCited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: almost 14 years ago
10.1186/s13059-014-0413-3
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulatorsCited by: 19
Author(s): Laurence D. Hurst, Oxana Sachenkova, Carsten O. Daub, Alistair R.R. Forrest, Łukasz Huminiecki
Software Mentions: 10
Published: over 10 years ago
10.1371/journal.pgen.1007102
Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-contentCited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: almost 7 years ago
10.12688/f1000research.8759.2
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experimentsCited by: 16
Author(s): Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Software Mentions: 10
Published: over 8 years ago
10.1186/s13059-018-1432-2
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter mapCited by: 57
Author(s): Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Software Mentions: 10
Published: over 6 years ago
10.1038/s41598-017-06110-5
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding lociCited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: over 7 years ago
10.1186/s41065-021-00196-8
Dynamic co-expression modular network analysis in nonalcoholic fatty liver diseaseCited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: over 3 years ago
10.3389/fgene.2015.00339
Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X ChromosomeCited by: 23
Author(s): Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie‐Agnès Dillies, Stephan Beck, Jean‐Yves Coppée, Pascale Cossart, Hélène Bierne
Software Mentions: 9
Published: almost 9 years ago
10.1371/journal.pcbi.1006596
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancerCited by: 43
Author(s): Deena M.A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra E. Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Pinjiang Cao, Lincoln Stein, Julie M. Wilson, John M.S. Bartlett, Ming‐Sound Tsao, Neesha C. Dhani, David W. Hedley, Steven Gallinger, Benjamin Haibe‐Kains
Software Mentions: 9
Published: almost 6 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 speciesCited 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
10.1186/s13059-015-0702-5
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq dataCited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: over 9 years ago
10.1038/s41598-020-59516-z
Variability in estimated gene expression among commonly used RNA-seq pipelinesCited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: almost 5 years ago
10.1186/s13059-018-1597-8
plyranges: a grammar of genomic data transformationCited by: 62
Author(s): Stuart Lee, Dianne Cook, Michael C. Lawrence
Software Mentions: 9
Published: almost 6 years ago
10.3390/toxins12060414
Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia coli (STEC) Strains with Different Colonization PropertiesCited 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
10.1186/1471-2164-14-S5-S9
Detection and classification of peaks in 5' cap RNA sequencing dataCited by: 4
Author(s): Dario Strbenac, Nicola J. Armstrong, Jean Yee Hwa Yang
Software Mentions: 8
Published: about 11 years ago
10.3390/ijms21103591
Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant SoybeanCited 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
10.1186/1471-2164-15-284
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databasesCited by: 743
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler
Software Mentions: 8
Published: almost 11 years ago
10.1038/tp.2015.169
Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brainCited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: about 9 years ago
10.1371/journal.pgen.1005930
Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional DefectsCited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 8 years ago
10.1186/s13059-018-1582-2
Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesisCited by: 77
Author(s): Anna R. Poetsch, Simon J. Boulton, Nicholas M. Luscombe
Software Mentions: 7
Published: almost 6 years ago
10.1186/s13059-021-02450-8
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variantsCited by: 3
Author(s): Chenyang Dong, Shane P. Simonett, Sun‐Young Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Huan Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller, Sündüz Keleş
Software Mentions: 7
Published: about 3 years ago
10.7554/eLife.51529
Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stabilityCited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: almost 5 years ago
10.3390/cancers13061296
Candidate Markers of Olaparib Response from Genomic Data Analyses of Human Cancer Cell LinesCited by: 3
Author(s): Setor Amuzu, Eurı́dice Carmona, Anne-Marie Mes-Masson, Celia M.T. Greenwood, Patricia N. Tonin, Jiannis Ragoussis
Software Mentions: 7
Published: over 3 years ago
10.3390/cancers13163929
Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AMLCited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: over 3 years ago
10.1136/jitc-2020-001335
Druggable epigenetic suppression of interferon-induced chemokine expression linked to <i>MYCN</i> amplification in neuroblastomaCited by: 15
Author(s): Johanna A Seier, Julia Reinhardt, Kritika Saraf, Susanna S. Ng, Julian Philipp Layer, Dillon Corvino, Kristina Althoff, Frank A. Giordano, Alexander Schramm, Matthias Fischer, Michael Hölzel
Software Mentions: 7
Published: over 3 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 leavesCited 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/s12864-021-07735-7
Non-coding RNAs in the interaction between rice and Meloidogyne graminicolaCited 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
10.3389/fnbeh.2019.00157
Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in AdulthoodCited by: 37
Author(s): Jordan Marrocco, Jason D. Gray, Joshua F. Kogan, Nathan R. Einhorn, Emma M. O’Cinneide, Todd G. Rubin, Thomas Carroll, Eric F. Schmidt, Bruce S. McEwen
Software Mentions: 7
Published: over 5 years ago
10.3389/fgene.2019.01372
4See: A Flexible Browser to Explore 4C DataCited by: 12
Author(s): Yousra Ben Zouari, Angeliki Platania, Anne Molitor, Tom Sexton
Software Mentions: 7
Published: almost 5 years ago
10.1038/s41598-021-93509-w
Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activationCited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: over 3 years ago
10.3390/genes11091107
Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticinaCited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: about 4 years ago
10.1186/s12859-015-0742-6
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics dataCited by: 60
Author(s): Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker, Mattia Pelizzola
Software Mentions: 7
Published: about 9 years ago
10.7554/eLife.45672
Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determinationCited by: 27
Author(s): Lee Langer, James M. Ward, Trevor Archer
Software Mentions: 6
Published: over 5 years ago
10.1186/s13059-017-1335-7
Regulatory remodeling in the allo-tetraploid frog Xenopus laevisCited by: 27
Author(s): Dei M. Elurbe, Sarita S. Paranjpe, Γεώργιος Γεωργίου, Ila van Kruijsbergen, Ozren Bogdanović, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra
Software Mentions: 6
Published: about 7 years ago
10.1016/j.cell.2013.11.043
The Architecture of Parent-of-Origin Effects in MiceCited 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.pgen.1009645
An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencingCited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: over 3 years ago
10.1186/s12943-017-0691-y
Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studiesCited by: 212
Author(s): Kaja Christine Graue Berg, Peter W. Eide, Ina A. Eilertsen, Bjarne Johannessen, Jarle Bruun, Stine A. Danielsen, Merete Bjørnslett, Leonardo A. Meza‐Zepeda, Mette Eknæs, Guro Elisabeth Lind, Ola Myklebost, Rolf Inge Skotheim, Anita Sveen, Ragnhild Lothe
Software Mentions: 6
Published: over 7 years ago
10.1093/icb/icaa138
Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a SongbirdCited by: 11
Author(s): Kees van Oers, Bernice Sepers, William Sies, Fleur Gawehns, Koen Verhoeven, Veronika N. Laine
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0075136
Synergistic Re-Activation of Epigenetically Silenced Genes by Combinatorial Inhibition of DNMTs and LSD1 in Cancer CellsCited by: 31
Author(s): Han Han, Xiaojing Yang, Kurinji Pandiyan, Gangning Liang
Software Mentions: 6
Published: about 11 years ago
10.3390/pathogens10091109
Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA StructureCited by: 6
Author(s): Priyanka Mehta, Shanmukh Alle, Anusha Chaturvedi, Aparna Swaminathan, Sheeba Saifi, Ranjeet Maurya, Partha Chattopadhyay, Priti Devi, Ruchi Chauhan, Akshay Kanakan, Janani Srinivasa Vasudevan, Ramanathan Sethuraman, Subramanian Chidambaram, Mashrin Srivastava, Avinash Chakravarthi, Johnny Jacob, Madhuri Namagiri, Varma Konala, Sujeet Jha, U. Deva Priyakumar, P. K. Vinod, Rajesh Pandey
Software Mentions: 6
Published: about 3 years ago
10.3389/fgene.2017.00013
The Pancreatic Islet Regulome BrowserCited by: 28
Author(s): Loris Mularoni, Mireia Ramos-Rodríguez, Lorenzo Pasquali
Software Mentions: 6
Published: almost 8 years ago
10.1186/s13059-015-0741-y
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic dataCited by: 222
Author(s): Jean Philippe Fortin, Kasper D. Hansen
Software Mentions: 6
Published: about 9 years ago
10.1371/journal.pgen.1008917
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasitesCited 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
10.15252/emmm.202013162
The NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cellsCited by: 23
Author(s): Federica Zilli, Pedro Marques Ramos, Priska Auf der Maur, Charly Jehanno, Atul Sethi, Marie–May Coissieux, Tobias Eichlisberger, Loïc Sauteur, Adelin Rouchon, Laura Bonapace, Joana Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael Stadler, Mohamed Bentires‐Alj
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-018-5411-5
Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell lineCited by: 6
Author(s): Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka, Matthias Schweizer
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.ppat.1009346
Epigenomic characterization of latent HIV infection identifies latency regulating transcription factorsCited by: 27
Author(s): Stuart R. Jefferys, Samuel D. Burgos, Jackson J Peterson, Sara R. Selitsky, Anne-Marie W. Turner, Lindsey I. James, Yi-Hsuan Tsai, Alisha R. Coffey, David M. Margolis, Joel S. Parker, Edward P. Browne
Software Mentions: 5
Published: over 3 years ago
10.1016/j.xpro.2021.100483
Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancerCited by: 2
Author(s): A. Gordon Robertson, Christina Yau, Jian Carrot‐Zhang, Jeffrey S. Damrauer, Theo Knijnenburg, Nyasha Chambwe, Katherine A. Hoadley, Anab Kemal, Jean C. Zenklusen, Andrew D. Cherniack, Rameen Beroukhim, Wanding Zhou
Software Mentions: 5
Published: over 3 years ago
10.1186/s12935-020-01243-6
Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinomaCited by: 24
Author(s): Wanqing Weng, Zhongjing Zhang, Weiguo Huang, Xiangxiang Xu, Boda Wu, Tingbo Ye, Yunfeng Shan, Ke–Qing Shi, Zhuo Lin
Software Mentions: 5
Published: over 4 years ago
10.1186/s13073-016-0315-y
The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3pCited by: 34
Author(s): Zsolt Czimmerer, Tamás Varga, Máté Kiss, Cesaré Ovando Vázquez, Quang Minh Doan‐Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna Nagy, Bence Dániel, Szilárd Póliska, Attila Horváth, Gergely Nagy, Éva Várallyay, Matthew N. Poy, Judith E. Allen, Zsolt Bacsó, Cei Abreu‐Goodger, László Nagy
Software Mentions: 5
Published: over 8 years ago
10.1186/s12859-021-04112-9
NoRCE: non-coding RNA sets cis enrichment toolCited by: 4
Author(s): Gülden Olgun, Afshan Nabi, Öznur Taştan
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-021-07552-y
Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potentialCited 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
10.1186/gb-2012-13-10-r95
Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkersCited by: 60
Author(s): Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H. Schulte, Rosa Noguera, Raymond Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 13 years ago
10.1242/dev.131664
Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β‑catenin recruitmentCited by: 99
Author(s): Yukio Nakamura, Eduardo Rodrigues Alves, Gert Jan C. Veenstra, Stefan Hoppler
Software Mentions: 5
Published: almost 9 years ago
10.1186/s13059-020-02013-3
FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencingCited by: 33
Author(s): Magali Hennion, Jean‐Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stéfan Engelen, Arnaud Lemainque, Benjamin Audit, Olivier Hyrien
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-019-6088-0
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsCited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: about 5 years ago
10.1186/s12864-018-4800-0
Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traitsCited by: 20
Author(s): Min Wang, Tim Hancock, Amanda J. Chamberlain, Christy J. Vander Jagt, J.E. Pryce, Benjamin G. Cocks, Michael E. Goddard, Ben J. Hayes
Software Mentions: 4
Published: over 6 years ago
10.1038/s42003-020-01516-w
miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1Cited by: 17
Author(s): Mitsuo Kato, Maryam Abdollahi, Ragadeepthi Tunduguru, Walter Tsark, Zhuo Chen, Xiwei Wu, Jinhui Wang, Zhen Bouman Chen, Feng‐Mao Lin, Linda Lanting, Mei Wang, Janice M. Huss, Patrick T. Fueger, David C. Chan, Rama Natarajan
Software Mentions: 4
Published: almost 4 years ago
10.1016/j.devcel.2020.09.002
Combinatorial Action of Temporally Segregated Transcription FactorsCited by: 38
Author(s): Julien Charest, Thomas Daniele, Jingkui Wang, Aleksandr Bykov, Ariane Mandlbauer, Mila Asparuhova, Josef Röhsner, Paula Gutiérrez-Pérez, Luisa Cochella
Software Mentions: 4
Published: about 4 years ago
10.1186/s12864-021-07627-w
Draft genome of a biparental beetle species, Lethrus apterusCited by: 0
Author(s): Nikolett Nagy, R. Rácz, Oliver Rimington, Szilárd Póliska, Pablo Orozco‐terWengel, Michael William Bruford, Zoltán Barta
Software Mentions: 4
Published: over 3 years ago
10.12688/f1000research.51143.1
periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNACited by: 5
Author(s): Jacques Serizay, Julie Ahringer
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2019.01178
Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic TwinsCited by: 7
Author(s): Ronaldo da Silva Francisco, Cristina dos Santos Ferreira, Juan Carlo Santos e Silva, Douglas Terra Machado, Yasmmin Martins, Víctor Ramos, Gustavo Simões Carnivali, Anice Garcia, Enrique Medina‐Acosta
Software Mentions: 4
Published: almost 5 years ago
10.3389/fmed.2021.737007
Severe SARS-CoV-2 Breakthrough Reinfection With Delta Variant After Recovery From Breakthrough Infection by Alpha Variant in a Fully Vaccinated Health WorkerCited by: 64
Author(s): Jayanthi Shastri, Swapneil Parikh, Veena Aggarwal, Sachee Agrawal, Nirjhar Chatterjee, Rajit Shah, Priti Devi, Priyanka Mehta, Rajesh Pandey
Software Mentions: 4
Published: over 3 years ago
10.1186/s12915-018-0556-x
Evolutionary stability of topologically associating domains is associated with conserved gene regulationCited by: 108
Author(s): Jan Krefting, Miguel A. Andrade‐Navarro, Jonas Ibn-Salem
Software Mentions: 4
Published: over 6 years ago
10.1186/s12859-021-04208-2
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomesCited by: 12
Author(s): Maxim Ivanov, Albin Sandelin, Sebastian Marquardt
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-019-44877-x
A catalog of single nucleotide changes distinguishing modern humans from archaic homininsCited by: 55
Author(s): Martin Kuhlwilm, Cédric Boeckx
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-020-75400-2
A systems genomics approach to uncover the molecular properties of cancer genesCited by: 0
Author(s): Felix Graßmann, Yudi Pawitan, Kamila Czene
Software Mentions: 4
Published: about 4 years ago
10.1093/molbev/msz105
Altered Localization of Hybrid Incompatibility Proteins in DrosophilaCited by: 8
Author(s): Jacob C. Cooper, A. Lukacs, Shelley Reich, Tamás Schauer, Axel Imhof, Nitin Phadnis
Software Mentions: 3
Published: over 5 years ago
10.1038/srep22851
An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity DisorderCited by: 17
Author(s): Leandro Lima, Ana Cecília Feio-dos-Santos, Síntia Belangero, Ary Gadelha, Rodrigo A. Bressan, Giovanni Abrahão Salum, Pedro Mário Pan, Tais Moriyama, Ana Soledade Graeff‐Martins, Ana Carina Tamanaha, Pedro Gomes de Alvarenga, Fernanda Valle Krieger, Bacy Fleitlich-Bilyk, Andrea Parolin Jackowski, Elisa Brietzke, João Ricardo Sato, Guilherme Polanczyk, Jair de Jesus Mari, Gisele Gus Manfro, Maria Conceição do Rosário, Eurípedes Constantino Miguel, Renato Puga, Ana Carolina Tahira, Viviane Neri Souza, Thais Chile, Gisele Rodrigues Gouveia, Sérgio Nery Simões, Xiao Chang, Renata Pellegrino, Lifeng Tian, Joseph T. Glessner, Ronaldo Fumio Hashimoto, Luís Augusto Rohde, Patrick Sleiman, Hákon Hákonarson, Helena Brentani
Software Mentions: 3
Published: over 8 years ago
10.1038/srep37536
The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyleCited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: almost 8 years ago
10.1186/s12864-015-1700-4
Read count-based method for high-throughput allelic genotyping of transposable elements and structural variantsCited by: 0
Author(s): Aléxandre Kuhn, Yao Min Ong, Stephen R. Quake, William F. Burkholder
Software Mentions: 3
Published: over 9 years ago
10.3390/genes12091442
Tensor-Decomposition-Based Unsupervised Feature Extraction in Single-Cell Multiomics Data AnalysisCited by: 6
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 3
Published: about 3 years ago
10.3390/genes6041140
COBRA-Seq: Sensitive and Quantitative Methylome ProfilingCited by: 9
Author(s): Hilal Varinli, Aaron L. Statham, Susan J. Clark, Peter L. Molloy, Jason P. Ross
Software Mentions: 3
Published: about 9 years ago
10.1186/s12864-019-5900-1
Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic dataCited by: 5
Author(s): Fernando Carazo, Marian Gimeno, Juan A Ferrer-Bonsoms, Ángel Rubio
Software Mentions: 3
Published: over 5 years ago
10.1073/pnas.2104758118
Dynamic chromatin regulatory landscape of human CAR T cell exhaustionCited by: 26
Author(s): David Gennert, Rachel C. Lynn, Jeff M. Granja, Evan W. Weber, Maxwell R. Mumbach, Yang Zhao, Zhana Duren, Elena Sotillo, William J. Greenleaf, Wing Hung Wong, Ansuman T. Satpathy, Crystal L. Mackall, Howard Y. Chang
Software Mentions: 3
Published: over 3 years ago
10.1038/sdata.2018.240
Meta-mining of copy number profiles of high-risk neuroblastoma tumorsCited by: 26
Author(s): Pauline Depuydt, Jan Koster, Valentina Boeva, Toby Dylan Hocking, Frank Speleman, Gudrun Schleiermacher, Katleen De Preter
Software Mentions: 3
Published: about 6 years ago
10.7554/eLife.22767
A high-resolution map of transcriptional repressionCited by: 43
Author(s): Ziwei Liang, Karen E. Brown, Thomas Carroll, Benjamin Taylor, Isabel Ferreirós-Vidal, Brian Hendrich, David Rueda, Amanda G. Fisher, Matthias Merkenschlager
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-017-1756-z
Identifying and mitigating batch effects in whole genome sequencing dataCited by: 37
Author(s): Jennifer Tom, Jens Reeder, William F. Forrest, Robert Graham, Julie Hunkapiller, Timothy W. Behrens, Tushar Bhangale
Software Mentions: 2
Published: over 7 years ago
10.7554/eLife.59201
A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatinCited by: 32
Author(s): Morgan E. Levine, Ross A. McDevitt, Margarita Meer, Kathy A Perdue, Andrea Di Francesco, Theresa Meade, Colin Farrell, Kyra Thrush, Meng Wang, Christopher Dunn, Matteo Pellegrini, Rafael de Cabo, Luigi Ferrucci
Software Mentions: 2
Published: about 4 years ago
10.1186/s13059-019-1621-7
Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screensCited by: 34
Author(s): Jean‐Philippe Fortin, Jenille Tan, Karen E. Gascoigne, Peter M. Haverty, William F. Forrest, Michael R. Costa, Scott E. Martin
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0150427
Information Thermodynamics of Cytosine DNA MethylationCited by: 13
Author(s): Robersy Sánchez, Sally A. Mackenzie
Software Mentions: 2
Published: over 8 years ago
10.1186/s13029-015-0032-8
LocusTrack: Integrated visualization of GWAS results and genomic annotationCited by: 28
Author(s): Gabriel Cuéllar-Partida, Miguel E. Renteriá, Stuart MacGregor
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12864-020-6542-z
Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasetsCited by: 4
Author(s): Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda, Itoshi Nikaido
Software Mentions: 2
Published: over 4 years ago