bioconductor: LOLA | Projects | Ecosyste.ms: Papers

10.1186/s13148-021-01173-8

Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism
Cited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: almost 3 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-019-1664-9

RnBeads 2.0: comprehensive analysis of DNA methylation data
Cited by: 188
Author(s): Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Software Mentions: 8
Published: over 5 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12859-020-03652-w

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Cited by: 22
Author(s): Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov
Software Mentions: 7
Published: about 4 years ago

10.1186/s13059-021-02440-w

Bedshift: perturbation of genomic interval sets
Cited by: 5
Author(s): Aaron Gu, Hyun-Jae Cho, Nathan C. Sheffield
Software Mentions: 6
Published: almost 3 years ago

10.1186/s12967-018-1751-9

Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Cited by: 37
Author(s): Raúl Fernández Pérez, Pablo Santamarina, Juan Ramón Tejedor, Rocío G. Urdinguio, Julio Álvarez, P. Redon, Agustín F. Fernández, Mario F. Fraga, Empar Lurbe
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1006940

CNEr: A toolkit for exploring extreme noncoding conservation
Cited by: 15
Author(s): Ge Tan, Dimitris Polychronopoulos, Boris Lenhard
Software Mentions: 6
Published: almost 5 years ago

10.3390/ijms22010078

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts
Cited by: 10
Author(s): Paulina Kołodziej-Wojnar, Joanna Borkowska, Zofia Wicik, Anna Domaszewska-Szostek, Jacek Połosak, Marta Cąkała-Jakimowicz, Olga Bujanowska, Monika Puzianowska-Kuźnicka
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2018.09.040

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Cited by: 116
Author(s): Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayón, S. Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M. Luscombe, James Briscoe
Software Mentions: 6
Published: over 5 years ago

10.1016/j.celrep.2015.11.024

Differential DNA Methylation Analysis without a Reference Genome
Cited by: 35
Author(s): Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock
Software Mentions: 6
Published: over 8 years ago

10.1016/j.stem.2018.06.014

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Cited by: 137
Author(s): Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-020-02139-4

COCOA: coordinate covariation analysis of epigenetic heterogeneity
Cited by: 10
Author(s): John T. Lawson, Jason P. Smith, Stefan Bekiranov, Francine E. Garrett-Bakelman, Nathan C. Sheffield
Software Mentions: 5
Published: almost 4 years ago

10.1093/bioinformatics/btx099

DeepBlueR: large-scale epigenomic analysis in R
Cited by: 6
Author(s): Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Software Mentions: 5
Published: over 7 years ago

10.1172/JCI94509

STAT5BN642H is a driver mutation for T cell neoplasia
Cited by: 52
Author(s): Hà Phạm, Barbara Maurer, Michaela Prchal-Murphy, Reinhard Grausenburger, Eva Grundschober, Tahereh Javaheri, Harini Nivarthi, Auke Boersma, Thomas Kolbe, Mohamed Elabd, Florian Halbritter, Jan Pěnčík, Zahra Kazemi, Florian Grebien, Markus Hengstschläger, Lukas Kenner, Stefan Kubicek, Matthias Farlik, Christoph Bock, Peter Valent, Mathias Müller, Thomas Rülicke, Veronika Sexl, Richard Moriggl
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00158

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains
Cited by: 32
Author(s): Kellen Garrison Cresswell, Mikhail G. Dozmorov
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-020-3443-8

MethylNet: an automated and modular deep learning approach for DNA methylation analysis
Cited by: 61
Author(s): Joshua Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas, Brock C. Christensen
Software Mentions: 4
Published: over 4 years ago

10.3390/genes11010034

Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions
Cited by: 3
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1007737

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
Cited by: 0
Author(s): Kunal Kathuria, Aakrosh Ratan
Software Mentions: 4
Published: over 4 years ago

10.3389/fphar.2019.00126

Making Sense of the Epigenome Using Data Integration Approaches
Cited by: 46
Author(s): Emma Cazaly, Joseph Saad, Wenyu Wang, Caroline A. Heckman, Miina Ollikainen, Jing Tang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-021-01156-9

DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker
Cited by: 6
Author(s): Nasim Azizgolshani, Curtis L. Petersen, Youdinghuan Chen, Joshua Levy, Lucas A. Salas, Laurent Praly, Lananh N. Nguyen, Brock C. Christensen
Software Mentions: 4
Published: almost 3 years ago

10.3389/fgene.2020.00003

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Cited by: 13
Author(s): Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil K. Raghav
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-020-00724-7

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
Cited by: 14
Author(s): Justyna A. Wierzbińska, Réka Tóth, Naveed Ishaque, Karsten Rippe, Jan‐Philipp Mallm, Lara Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert, John C. Byrd, Christopher C. Oakes, Christoph Plass, Daniel B. Lipka
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/btv612

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Cited by: 315
Author(s): Nathan C. Sheffield, Christoph Bock
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12915-020-00822-3

Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps
Cited by: 22
Author(s): Fabrice Legeai, Bernardo F. Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca B. Dikow, Claire Lemaitre, Véronique Jouan, Marc Ravallec, Jean‐Michel Drezen, Denis Tagu, Frédéric Baudat, Gábor Gyapay, Xin Zhou, Shanlin Liu, Bruce A. Webb, Seán G. Brady, Anne Nathalie Volkoff
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0184120

Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition
Cited by: 25
Author(s): Xuan Tao, Yan Liang, Xuemei Yang, Jianhui Pang, Zhijun Zhong, Xiaohui Chen, Yuekui Yang, Kai Zeng, Runming Kang, Yongjia Lei, Sancheng Ying, Jing Gong, Yiren Gu, Xuebin Lv
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms20194822

Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection
Cited by: 4
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 3
Published: almost 5 years ago

10.1093/humrep/deab137

Association of medically assisted reproduction with offspring cord blood DNA methylation across cohorts
Cited by: 14
Author(s): Doretta Caramaschi, James Jungius, Christian M. Page, Boris Novakovic, Richard Saffery, Jane Halliday, Sharon Lewis, Maria C Magnus, Stephanie J. London, Siri Eldevik Håberg, Caroline L Relton, Debbie A. Lawlor, Hannah R Elliott
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-021-87457-8

Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level
Cited by: 21
Author(s): Chloe D. Goldsmith, Jesús Rafael Rodríguez‐Aguilera, Ines El-Rifai, Adrien Jarretier-Yuste, Valérie Hervieu, Olivier Raineteau, Pierre Saintigny, Victoria Chagoya de Sánchez, Robert Dante, Gabriel Ichim, Héctor Hernández-Vargas
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-020-00785-8

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes
Cited by: 44
Author(s): Charles E. Mordaunt, Julia M. Jianu, Benjamin I. Laufer, Yihui Zhu, Keith W. Dunaway, Kelly M. Bakulski, Jason I. Feinberg, Heather E. Volk, Kristen Lyall, Lisa Croen, Craig J. Newschaffer, Sally J Ozonoff, Irva Hertz‐Picciotto, M. Daniele Fallin, Rebecca J. Schmidt, Janine M. LaSalle
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40478-021-01177-8

Sex-specific DNA methylation differences in Alzheimer’s disease pathology
Cited by: 23
Author(s): Lanyu Zhang, Juan I. Young, Lissette Gomez, Tiago C. Silva, Michael A. Schmidt, Jesse Cai, Xi Chen, Eden R. Martin, Lily Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-14-70

A novel method for cross-species gene expression analysis
Cited by: 40
Author(s): Erik Kristiansson, Tobias Österlund, Lars Gunnarsson, Gabriella Arne, D. G. Joakim Larsson, Olle Nerman
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-10-411

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery
Cited by: 32
Author(s): Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto, Yasushi Okuno
Software Mentions: 2
Published: almost 15 years ago

10.1093/bioinformatics/bty083

MIRA: an R package for DNA methylation-based inference of regulatory activity
Cited by: 18
Author(s): John T. Lawson, Eleni M. Tomazou, Christoph Bock, Nathan C. Sheffield
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-017-0873-y

Normal breast tissue DNA methylation differences at regulatory elements are associated with the cancer risk factor age
Cited by: 51
Author(s): Kevin C. Johnson, E. Andrés Houseman, Jessica E. King, Brock C. Christensen
Software Mentions: 2
Published: about 7 years ago

10.1016/j.stem.2016.10.019

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation
Cited by: 189
Author(s): Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur, Rakesh Uppal, Hendrik G. Stunnenberg, Willem H. Ouwehand, Elisa Laurenti, Thomas Lengauer, Mattia Frontini, Christoph Bock
Software Mentions: 2
Published: over 7 years ago

10.3390/cells9061484

Targeting Nuclear NOTCH2 by Gliotoxin Recovers a Tumor-Suppressor NOTCH3 Activity in CLL
Cited by: 7
Author(s): Rainer Hubmann, Susanne Schnabl, Mohammad Araghi, Christian Schmidl, André F. Rendeiro, Martin Hilgarth, Dita Demirtas, Farghaly Ali, Philipp B. Staber, Peter Valent, Christoph Zielinski, Ulrich Jaeger, Medhat Shehata
Software Mentions: 2
Published: about 4 years ago

10.1186/s12711-020-00546-6

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB
Cited by: 17
Author(s): Marina Naval-Sánchez, Laércio R. Porto-Neto, Diércles Francisco Cardoso, Ben J. Hayes, Hans D. Daetwyler, James W. Kijas, Antônio Reverter
Software Mentions: 2
Published: about 4 years ago

10.1007/s00432-020-03349-w

DNA CpG methylation in sequential glioblastoma specimens
Cited by: 6
Author(s): Zoltán Krabóth, Bence Gálik, Márton Tompa, Béla Kajtár, Péter Urbán, Attila Gyenesei, Attila Miseta, Bernadette Kálmán
Software Mentions: 2
Published: almost 4 years ago

10.1007/s00384-016-2636-0

Laparoscopic lavage is superior to colon resection for perforated purulent diverticulitis—a meta-analysis
Cited by: 40
Author(s): Eva Angenete, David Bock, Jacob Rosenberg, Eva Haglind
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2020.00532

Cross-Species Annotation of Expressed Genes and Detection of Different Functional Gene Modules Between 10 Cold- and 10 Hot-Propertied Chinese Herbal Medicines
Cited by: 2
Author(s): Arong Li, Aqian Li, Zhiping Deng, Jiewen Guo, Haishan Wu
Software Mentions: 1
Published: about 4 years ago

10.1093/gigascience/gix032

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
Cited by: 20
Author(s): Boris Simovski, Daniel Vodák, Sveinung Gundersen, Diana Domańska, Abdulrahman Azab, Lars Holden, Matthew T. G. Holden, Ivar Grytten, Knut Dagestad Rand, Finn Drabløs, Morten Johansen, Antonio M. Mora, Christin Lund-Andersen, Bastian Fromm, Ragnhild Eskeland, Odd S. Gabrielsen, Egil Ferkingstad, Sigve Nakken, Mads Bengtsen, Alexander Johan Nederbragt, Hildur Sif Thorarensen, Johannes Andreas Akse, Ingrid K. Glad, Eivind Hovig, Geir Kjetil Sandve
Software Mentions: 1
Published: over 7 years ago

10.1007/s11084-017-9536-3

Cataclysm No More: New Views on the Timing and Delivery of Lunar Impactors
Cited by: 75
Author(s): N. E. B. Zellner
Software Mentions: 1
Published: about 7 years ago

10.1186/s12968-018-0502-7

Simultaneous multi slice (SMS) balanced steady state free precession first-pass myocardial perfusion cardiovascular magnetic resonance with iterative reconstruction at 1.5 T
Cited by: 32
Author(s): Muhummad Sohaib Nazir, Radhouène Neji, Peter Speier, Fiona Reid, Daniel Stäb, Michaela Schmidt, Christoph Forman, Reza Razavi, Sven Plein, Tevfik F Ismail, Amedeo Chiribiri, Sébastien Roujol
Software Mentions: 1
Published: over 5 years ago

10.12688/f1000research.23390.2

Seqpare: a novel metric of similarity between genomic interval sets
Cited by: 0
Author(s): Selena C. Feng, Nathan C. Sheffield, Jianglin Feng
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-46165-0

A universal approach for drainage basins
Cited by: 7
Author(s): Erneson A. Oliveira, R. S. Pires, Rubens S. Oliveira, Vasco Furtado, Hans J. Herrmann, José S. Andrade
Software Mentions: 1
Published: about 5 years ago

10.1186/s13072-019-0255-z

Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers
Cited by: 32
Author(s): Charles E. Mordaunt, Dorothy A. Kieffer, Noreene M. Shibata, Anna Członkowska, Tomasz Litwin, Karl-Heinz Weiss, Yihui Zhu, Christopher L. Bowlus, Souvik Sarkar, Stewart Cooper, Yu‐Jui Yvonne Wan, Mohamed R. Ali, Janine M. LaSalle, Valentina Medici
Software Mentions: 1
Published: over 5 years ago

10.3390/s21165359

A Flexible Multimodal Sole Sensor for Legged Robot Sensing Complex Ground Information during Locomotion
Cited by: 4
Author(s): Yingtian Xu, Ziya Wang, Wanjun Hao, Wenyu Zhao, Waner Lin, Bingchen Jin, Ning Ding
Software Mentions: 1
Published: almost 3 years ago

10.1186/s13072-021-00387-7

Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature
Cited by: 10
Author(s): Benjamin I. Laufer, Jessica Gómez, Julia M. Jianu, Janine M. LaSalle
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.0030134

Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning
Cited by: 102
Author(s): Poramate Manoonpong, Tao Geng, Tomas Kulvičius, Bernd Porr, Florentin Wörgötter
Software Mentions: 1
Published: about 17 years ago

10.1186/1550-2783-7-40

Nine weeks of supplementation with a multi-nutrient product augments gains in lean mass, strength, and muscular performance in resistance trained men
Cited by: 26
Author(s): Stephen Schmitz, Jennifer E Hofheins, Robert Lemieux
Software Mentions: 1
Published: over 14 years ago

10.1186/s13148-021-01027-3

DNA methylation of blood cells is associated with prevalent type 2 diabetes in a meta-analysis of four European cohorts
Cited by: 34
Author(s): Diana L. Juvinao-Quintero, Riccardo E. Marioni, Carolina Ochoa‐Rosales, Tom C. Russ, Ian J. Deary, Joyce B. J. van Meurs, Trudy Voortman, Marie‐France Hivert, Gemma C Sharp, Caroline L Relton, Hannah R Elliott
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0054979

A Data Similarity-Based Strategy for Meta-analysis of Transcriptional Profiles in Cancer
Cited by: 4
Author(s): Qingchao Qiu, Pengcheng Lu, Yuzhu Xiang, Yu Shyr, Xi Chen, Brian D. Lehmann, Daniel Joseph Viox, Alfred L. George, Yajun Yi
Software Mentions: 1
Published: over 11 years ago

10.2196/jmir.2001

De-identification Methods for Open Health Data: The Case of the Heritage Health Prize Claims Dataset
Cited by: 52
Author(s): Khaled El Emam, Luk Arbuckle, Güneş Koru, Benjamin Eze, Lisa Gaudette, Emilio Neri, Sean Rose, Jeremy Howard, Jonathan Gluck
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2007-8-7-r133

Strategy for encoding and comparison of gene expression signatures
Cited by: 24
Author(s): Yajun Yi, Chun Li, Clay R. Miller, Alfred L. George
Software Mentions: 1
Published: about 17 years ago

10.3389/fgene.2020.00053

epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis
Cited by: 12
Author(s): Yao Zhou, Yongzheng Sun, Dandan Huang, Dariusz Plewczynski
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: LOLA

Papers Mentioning LOLA 56