bioconductor: bumphunter | Projects

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: almost 5 years ago

10.1186/s13059-021-02388-x

Gene set enrichment analysis for genome-wide DNA methylation data
Cited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago

10.12688/f1000research.12223.1

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
Cited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: about 7 years ago

10.1093/bioinformatics/bty713

Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: about 6 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: about 8 years ago

10.1186/s40246-019-0242-2

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis
Cited by: 4
Author(s): Carlos Ruiz‐Arenas, Alejandro Cáceres, Vı́ctor Moreno, Juan R. González
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13148-020-0824-9

Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population
Cited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: over 4 years ago

10.12688/f1000research.27868.3

WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
Cited by: 5
Author(s): Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Software Mentions: 9
Published: about 3 years ago

10.3389/fonc.2018.00100

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues
Cited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 6 years ago

10.1186/s13148-016-0230-5

Peripheral blood methylation profiling of female Crohn’s disease patients
Cited by: 40
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Jing Hua Zhao, Wouter J. de Jonge, Geert R. D’Haens, Marcel M.A.M. Mannens, Adri N. Mul, Anje A. te Velde, Peter Henneman
Software Mentions: 8
Published: over 8 years ago

10.1186/s13229-017-0119-y

Exaggerated CpH methylation in the autism-affected brain
Cited by: 30
Author(s): Shannon Ellis, Saloni Gupta, Anna Moes, Andrew B. West, Dan E. Arking
Software Mentions: 7
Published: over 7 years ago

10.1186/s13148-018-0453-8

Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C
Cited by: 55
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Cindy Skinner, Peter Ainsworth, Hanxin Lin, Guillaume Paré, David I. Rodenhiser, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 6 years ago

10.1186/s12918-015-0211-x

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential
Cited by: 41
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 6
Published: almost 9 years ago

10.1186/s13072-020-00346-8

DAMEfinder: a method to detect differential allele-specific methylation
Cited by: 8
Author(s): Stephany Orjuela, Dania Machlab, Mirco Menigatti, Giancarlo Marra, Mark D. Robinson
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-15-141

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Cited by: 17
Author(s): Martin A. Rijlaarsdam, Yvonne G. van der Zwan, Lambert C. J. Dorssers, Leendert H. J. Looijenga
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-019-5578-4

Genome-wide methylation is modified by caloric restriction in Daphnia magna
Cited by: 20
Author(s): Jack Hearn, Marianne Pearson, Mark Blaxter, Philip J. Wilson, Tom J. Little
Software Mentions: 5
Published: over 5 years ago

10.1007/s10522-019-09818-1

Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength
Cited by: 7
Author(s): Mette Soerensen, Weilong Li, Birgit Debrabant, Marianne Nygaard, Jonas Mengel‐From, Morten Frost, Kaare Christensen, Lene Christiansen, Qihua Tan
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-020-00779-6

Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
Cited by: 24
Author(s): Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López‐Isac, Alfredo Guillén‐Del‐Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar, Javier Martín
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-40786-1

Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures
Cited by: 18
Author(s): M. Schroêder, Lorenz Bastian, Cornelia Eckert, Nicola Gökbuget, Alva Rani James, Jutta Ortiz Tanchez, Cornelia Schlee, Konstandina Isaakidis, Björn Häupl, Katharina Baum, Oscar Arturo Migueles Lozano, Khouloud Kouidri, Kuan‐Ting Pan, Henning Urlaub, Stefan Schwartz, Thomas Burmeister, Arend von Stackelberg, Dieter Hoelzer, Heike Pfeiffer, Michael A. Rieger, Stefanie Göllner, Thomas Oellerich, Martin Horstman, Martin Schrappe, Jana Wolf, Renate Kirschner-Schwabe, Monika Brüggemann, Carsten Müller‐Tidow, Hubert Serve, Martin Neumann, Claudia D. Baldus
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-98614-4

Screening bioactive food compounds in honey bees suggests curcumin blocks alcohol-induced damage to longevity and DNA methylation
Cited by: 5
Author(s): Erik M. K. Rasmussen, Kristine L. Seier, Ingrid Kjelsberg Pedersen, Claus D. Kreibich, Gro V. Amdam, Daniel Münch, John Arne Dahl
Software Mentions: 5
Published: almost 3 years ago

10.18632/oncotarget.12204

Human PDE4D isoform composition is deregulated in primary prostate cancer and indicative for disease progression and development of distant metastases
Cited by: 21
Author(s): René Böttcher, Kalyan Dulla, Dianne van Strijp, Natasja F. Dits, Esther I. Verhoef, George S. Baillie, Geert J.L.H. van Leenders, Miles D. Houslay, Guido Jenster, Ralf Hoffmann
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13148-019-0749-3

A genome-wide DNA methylation signature for SETD1B-related syndrome
Cited by: 41
Author(s): Izabela M. Krzyzewska, Saskia M. Maas, Peter Henneman, Karin van der Lip, Andrea Venema, Kristin W. Barañano, Anna Chassevent, Erfan Aref‐Eshghi, Anthonie J. van Essen, Tokiko Fukuda, Hiroko Ikeda, Marie Line Jacquemont, H.-G. Kim, Audrey Labalme, Lewis Sm, Gaëtan Lesca, Irene Madrigal, Sonal Mahida, Naomichi Matsumoto, Raquel Rabionet, Evica Rajcan‐Separovic, Ying Qiao, Bekim Sadiković, Hirotomo Saitsu, David A. Sweetser, Mariëlle Alders, Marcel M.A.M. Mannens
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-021-01176-5

DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status
Cited by: 1
Author(s): Philipp Jurmeister, Karsten E. Weber, Sonia L. Villegas, Thomas Karn, Michael Untch, Anne Thieme, Volkmar Müller, Eliane Tabea Taube, Peter A. Fasching, Wolfgang Schmitt, Frederik Marmé, Elmar Stickeler, Bruno Valentin Sinn, Paul Jank, Christian Schem, Frederick Klauschen, Marion van Mackelenbergh, Carsten Denkert, Sibylle Loibl, David Capper
Software Mentions: 4
Published: almost 3 years ago

10.3389/fnmol.2021.672614

Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma
Cited by: 11
Author(s): Zac Chatterton, Natalia Mendelev, Sean Chen, Walter Carr, Gary H. Kamimori, Yongchao Ge, Andrew J. Dwork, Fatemeh Haghighi
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-019-1827-8

methylCC: technology-independent estimation of cell type composition using differentially methylated regions
Cited by: 12
Author(s): Stephanie Hicks, Rafael A. Irizarry
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41398-019-0548-9

Epigenome-wide association study of depression symptomatology in elderly monozygotic twins
Cited by: 44
Author(s): Anna Starnawska, Qihua Tan, Mette Soerensen, Matt McGue, Ole Mors, Anders D. Børglum, Kaare Christensen, Mette Nyegaard, Lene Christiansen
Software Mentions: 4
Published: about 5 years ago

10.1038/tp.2016.95

Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1
Cited by: 59
Author(s): Robert Kumsta, Sarah Marzi, Joana Viana, Emma Dempster, Bethany Crawford, Michael Rutter, Jonathan Mill, Edmund Sonuga‐Barke
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-015-0641-x

An evaluation of statistical methods for DNA methylation microarray data analysis
Cited by: 51
Author(s): Dongmei Li, Zidian Xie, Marc A. Le Pape, Timothy D. Dye
Software Mentions: 3
Published: about 9 years ago

10.1093/bioinformatics/btw691

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Cited by: 470
Author(s): Jean Philippe Fortin, Timothy J. Triche, Kasper D. Hansen
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13148-018-0457-4

Epigenome-wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation
Cited by: 42
Author(s): Namitha Mohandas, Sebastian Bass-Stringer, Jovana Maksimovic, Kylie Elizabeth Crompton, Yuk Jing Loke, Janet E. Walstab, Susan M Reid, David J. Amor, Dinah Reddihough, Jeffrey M. Craig
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-019-0764-4

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome
Cited by: 15
Author(s): Cecilie Bucher-Johannessen, Christian M. Page, Trine B. Haugen, Marcin W. Wojewodzic, Sophie D. Fosså, Tom Grotmol, Hege Sagstuen Haugnes, Trine B. Rounge
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0248429

Hypomethylation mediates genetic association with the major histocompatibility complex genes in Sjögren’s syndrome
Cited by: 4
Author(s): Calvin Chi, Kimberly E. Taylor, Hong Quach, Diana Quach, Lindsey A. Criswell, Lisa F. Barcellos
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-016-0238-x

Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction
Cited by: 49
Author(s): Maian Roifman, Sanaa Choufani, Andrei L. Turinsky, Sascha Drewlo, Sarah Keating, Michael Brudno, John Kingdom, Rosanna Weksberg
Software Mentions: 3
Published: about 8 years ago

10.1007/s00204-016-1879-4

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women
Cited by: 24
Author(s): Karin Engström, Tomasz K. Wojdacz, Francesco Marabita, Philip Ewels, Max Käller, Francesco Vezzi, Nicola Prezza, Joel Gruselius, Marie Vahter, Karin Broberg
Software Mentions: 3
Published: almost 8 years ago

10.1093/eep/dvv007

Prenatal lead exposure is associated with decreased cord blood DNA methylation of the glycoprotein VI gene involved in platelet activation and thrombus formation
Cited by: 28
Author(s): Karin Engström, Filip Rydbeck, Maria Kippler, Tomasz K. Wojdacz, Shams El Arifeen, Marie Vahter, Karin Broberg
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0206511

Increased DNA methylation of SLFN12 in CD4+ and CD8+ T cells from multiple sclerosis patients
Cited by: 32
Author(s): Brooke Rhead, Ina Skaara Brorson, Tone Berge, Crawford W. Adams, Hong Quach, Stine Marit Moen, Pål Berg‐Hansen, Elisabeth Gulowsen Celius, Dipen Sangurdekar, Paola G. Bronson, Rodney Arthur Lea, Sean M Burnard, Vicky Maltby, Rodney J. Scott, Jeannette Lechner‐Scott, Hanne F. Harbo, Steffan Daniël Bos, Lisa F. Barcellos
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0249002

An R package for divergence analysis of omics data
Cited by: 2
Author(s): Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-4594-0

Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain
Cited by: 32
Author(s): Brian R. Herb, Molly S. Shook, Christopher J. Fields, Gene E. Robinson
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-019-0602-8

Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis
Cited by: 13
Author(s): Tianyuan Lu, Kathleen Klein, Inés Colmegna, Maximilien Lora, Celia Greenwood, Marie Hudson
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-018-4450-2

Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine
Cited by: 32
Author(s): Zachary Gerring, Allan F. McRae, Grant W. Montgomery, Dale R. Nyholt
Software Mentions: 1
Published: over 6 years ago

10.1186/s13148-016-0172-y

Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs
Cited by: 28
Author(s): Leonie Roos, Jenny van Dongen, Christopher G. Bell, Andrea Burri, Panos Deloukas, Dorret I. Boomsma, Tim D. Spector, Jordana T. Bell
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-019-5906-8

A case of intraplacental gestational choriocarcinoma; characterised by the methylation pattern of the early placenta and an absence of driver mutations
Cited by: 14
Author(s): Philip Savage, David Gabriel Monk, José Ramón Hernández Mora, Nick van der Westhuizen, Jennifer Rauw, Anna V. Tinker, Wendy P. Robinson, Qisheng Song, Michael J. Seckl, Rosemary A. Fisher
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1004996

An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging
Cited by: 129
Author(s): Yuan Tian, Yinming Jiao, Simone de Jong, Roel A. Ophoff, Stephan Beck, Andrew E. Teschendorff
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2016.00510

Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study
Cited by: 24
Author(s): Anders Jørgen Svendsen, Kristina Gervin, Robert Lyle, Lene Christiansen, Kirsten Ohm Kyvik, Peter Junker, Christian Nielsen, Gunnar Houen, Qihua Tan
Software Mentions: 1
Published: almost 8 years ago

10.1080/15592294.2016.1145329

An epigenome-wide association meta-analysis of prenatal maternal stress in neonates: A model approach for replication
Cited by: 75
Author(s): Jolien Rijlaarsdam, Irene Pappa, Esther Walton, Marian J. Bakermans‐Kranenburg, Viara R. Mileva‐Seitz, Ralph C. A. Rippe, Sabine J. Roza, Vincent W.V. Jaddoe, Frank C. Verhulst, Janine F. Felix, Charlotte A.M. Cecil, Caroline L Relton, Tom R. Gaunt, Wendy L. McArdle, Jonathan Mill, Edward D. Barker, Henning Tiemeier, Marinus H. van IJzendoorn
Software Mentions: 1
Published: over 8 years ago

10.1186/gb-2013-14-8-r94

Measuring cell-type specific differential methylation in human brain tissue
Cited by: 94
Author(s): Carolina Montaño, Rafael A. Irizarry, Walter E. Kaufmann, Konrad Talbot, Raquel E. Gur, Andrew P. Feinberg, Margaret A. Taub
Software Mentions: 1
Published: over 11 years ago

Projects: bioconductor: bumphunter

Papers Mentioning bumphunter 46