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: bumphunter
https://packages.ecosyste.ms/registries/bioconductor.org/packages/bumphunter
Bump Hunter
1 version
Latest release: about 1 year ago
15 dependent packages
361,694 downloads total
Papers Mentioning bumphunter 46
10.1186/s13059-019-1805-1
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylationCited 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: about 5 years ago
10.1186/s13059-021-02388-x
Gene set enrichment analysis for genome-wide DNA methylation dataCited 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 BioconductorCited 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 datasetsCited 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 analysesCited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: over 8 years ago
10.1186/s40246-019-0242-2
Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosisCited 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 populationCited 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 dataCited 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: over 3 years ago
10.3389/fonc.2018.00100
Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate TissuesCited 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 patientsCited 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 brainCited 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 KDM5CCited 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 potentialCited by: 41
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 6
Published: about 9 years ago
10.1186/s13072-020-00346-8
DAMEfinder: a method to detect differential allele-specific methylationCited 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 profilesCited 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 magnaCited 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 strengthCited 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: over 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 lociCited 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: about 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 signaturesCited 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 methylationCited 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: about 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 metastasesCited 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: about 8 years ago
10.1186/s13148-019-0749-3
A genome-wide DNA methylation signature for SETD1B-related syndromeCited 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: about 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 statusCited 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: about 3 years ago
10.3389/fnmol.2021.672614
Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood PlasmaCited 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: over 3 years ago
10.1186/s13059-019-1827-8
methylCC: technology-independent estimation of cell type composition using differentially methylated regionsCited 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 twinsCited 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 CYP2E1Cited 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 analysisCited by: 51
Author(s): Dongmei Li, Zidian Xie, Marc A. Le Pape, Timothy D. Dye
Software Mentions: 3
Published: over 9 years ago
10.1093/bioinformatics/btw691
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfiCited 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 methylationCited 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 epigenomeCited 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 syndromeCited 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 restrictionCited 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: over 8 years ago
10.1007/s00204-016-1879-4
Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed womenCited 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 formationCited by: 28
Author(s): Karin Engström, Filip Rydbeck, Maria Kippler, Tomasz K. Wojdacz, Shams El Arifeen, Marie Vahter, Karin Broberg
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0206511
Increased DNA methylation of SLFN12 in CD4+ and CD8+ T cells from multiple sclerosis patientsCited 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: about 6 years ago
10.1371/journal.pone.0249002
An R package for divergence analysis of omics dataCited 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 brainCited 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 pathogenesisCited by: 13
Author(s): Tianyuan Lu, Kathleen Klein, Inés Colmegna, Maximilien Lora, Celia Greenwood, Marie Hudson
Software Mentions: 1
Published: about 5 years ago
10.1186/s12864-018-4450-2
Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraineCited by: 32
Author(s): Zachary Gerring, Allan F. McRae, Grant W. Montgomery, Dale R. Nyholt
Software Mentions: 1
Published: almost 7 years ago
10.1186/s13148-016-0172-y
Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairsCited 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: almost 9 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 mutationsCited 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: over 5 years ago
10.1371/journal.pgen.1004996
An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in AgingCited 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 StudyCited 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 replicationCited 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: almost 9 years ago
10.1186/gb-2013-14-8-r94
Measuring cell-type specific differential methylation in human brain tissueCited 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: almost 12 years ago