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A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer

2023 | Other
Contributors: Rendo, Veronica; Schubert, Michael; Khuu, Nicholas; Suarez Peredo Rodriguez, Maria; Huang, Kaimeng; Swift, Michelle; He, Yizhou; Zerbib, Johanna; Smith, Ross; Raaijmakers, Jonne et al.
Source: Self-asserted source
Maria Colome Tatche

ARID1A Mutations Protect Follicular Lymphoma from FAS-dependent Immune Surveillance by Reducing RUNX3/ETS1-Driven FAS-Expression

2023 | Other
Contributors: Antoniolli, Martina; Solovey, Maria; Strobl, Carolin Dorothea; Bararia, Deepak; Keay, William David; Hildebrand, Johannes Adrian; Adolph, Louisa; Heide, Michael; Passerini, Verena; Freyholdt, Tabea et al.
Source: Self-asserted source
Maria Colome Tatche

CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data

Development (Cambridge, England)
2023 | Journal article
Part of ISSN: 0950-1991
Contributors: Lubatti, Gabriele; Stock, Marco; Iturbide, Ane; Ruiz Tejada Segura, Mayra L; Riepl, Melina; Tyser, Richard C V; Danese, Anna; Colomé-Tatché, Maria; Theis, Fabian J; Srinivas, Shankar et al.
Source: Self-asserted source
Maria Colome Tatche

CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition

HemaSphere
2023 | Journal article
Part of ISSN: 2572-9241
Contributors: Swoboda, Anja S; Arfelli, Vanessa C; Danese, Anna; Windisch, Roland; Kerbs, Paul; Redondo Monte, Enric; Bagnoli, Johannes W; Chen-Wichmann, Linping; Caroleo, Alessandra; Cusan, Monica et al.
Source: Self-asserted source
Maria Colome Tatche

epiAneufinder identifies copy number alterations from single-cell ATAC-seq data

Nature communications
2023 | Journal article
Part of ISSN: 2041-1723
Contributors: Ramakrishnan, Akshaya; Symeonidi, Aikaterini; Hanel, Patrick; Schmid, Katharina T; Richter, Maria L; Schubert, Michael; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche

Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge

Genome biology
2023 | Journal article
Part of ISSN: 1474-7596
Contributors: Sanchez-Quant, Eva; Richter, Maria Lucia; Colomé-Tatché, Maria; Martinez-Jimenez, Celia Pilar
Source: Self-asserted source
Maria Colome Tatche

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
2022 | Journal article
Part of ISSN: 1058-4838
Contributors: Walker, Andreas; Houwaart, Torsten; Finzer, Patrick; Ehlkes, Lutz; Tyshaieva, Alona; Damagnez, Maximilian; Strelow, Daniel; Duplessis, Ashley; Nicolai, Jessica; Wienemann, Tobias et al.
Source: Self-asserted source
Maria Colome Tatche

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
2022 | Journal article
Part of ISSN: 1025-496X
Contributors: Houwaart, Torsten; Belhaj, Samir; Tawalbeh, Emran; Nagels, Dirk; Fröhlich, Yara; Finzer, Patrick; Ciruela, Pilar; Sabrià, Aurora; Herrero, Mercè; Andrés, Cristina et al.
Source: Self-asserted source
Maria Colome Tatche

Brief homogeneous TCR signals instruct common iNKT progenitors whose effector diversification is characterized by subsequent cytokine signaling

Immunity
2021 | Journal article
Part of ISSN: 1074-7613
Contributors: Bortoluzzi, Sabrina; Dashtsoodol, Nyambayar; Engleitner, Thomas; Drees, Christoph; Helmrath, Sabine; Mir, Jonas; Toska, Albulena; Flossdorf, Michael; Öllinger, Rupert; Solovey, Maria et al.
Source: Self-asserted source
Maria Colome Tatche

Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo

2021 | Other
Contributors: Schubert, Michael; Hong, Christy; Jilderda, Laura; Rueda, Marta Requesens; Tijhuis, Andréa; Simon, Judith; Bakker, Petra; Cooper, Jon; Damaskou, Aristi; Wardenaar, René et al.
Source: Self-asserted source
Maria Colome Tatche

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Genome medicine
2021 | Journal article
Part of ISSN: 1756-994X
Contributors: Aschenbrenner, Anna C; Mouktaroudi, Maria; Krämer, Benjamin; Oestreich, Marie; Antonakos, Nikolaos; Nuesch-Germano, Melanie; Gkizeli, Konstantina; Bonaguro, Lorenzo; Reusch, Nico; Baßler, Kevin et al.
Source: Self-asserted source
Maria Colome Tatche

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Immunity
2021 | Journal article
Part of ISSN: 1074-7613
Contributors: Krämer, Benjamin; Knoll, Rainer; Bonaguro, Lorenzo; ToVinh, Michael; Raabe, Jan; Astaburuaga-García, Rosario; Schulte-Schrepping, Jonas; Kaiser, Kim Melanie; Rieke, Gereon J; Bischoff, Jenny et al.
Source: Self-asserted source
Maria Colome Tatche

EpiScanpy: integrated single-cell epigenomic analysis

Nature communications
2021 | Journal article
Part of ISSN: 2041-1723
Contributors: Danese, Anna; Richter, Maria L; Chaichoompu, Kridsadakorn; Fischer, David S; Theis, Fabian J; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche

Region-level epimutation rates in Arabidopsis thaliana

Heredity
2021 | Journal article
Part of ISSN: 0018-067X
Contributors: Denkena, Johanna; Johannes, Frank; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche

Swarm Learning for decentralized and confidential clinical machine learning

Nature
2021 | Journal article
Part of ISSN: 0028-0836
Contributors: Warnat-Herresthal, Stefanie; Schultze, Hartmut; Shastry, Krishnaprasad Lingadahalli; Manamohan, Sathyanarayanan; Mukherjee, Saikat; Garg, Vishesh; Sarveswara, Ravi; Händler, Kristian; Pickkers, Peter; Aziz, N Ahmad et al.
Source: Self-asserted source
Maria Colome Tatche

Benchmarking atlas-level data integration in single-cell genomics.

Nature methods
2021-12-23 | Journal article
Contributors: Malte D Luecken; Maren Büttner; Kridsadakorn Chaichoompu; Anna Danese; Marta Interlandi; Mueller MF; Strobl DC; Luke Zappia; Dugas M; Colomé-Tatché M et al.
Source: Self-asserted source
Maria Colome Tatche

Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy

Nature Communications
2021-07-12 | Journal article | Author
Part of ISSN: 2041-1723
Contributors: Maria L. Richter; I. K. Deligiannis; K. Yin; Anna Danese; E. Lleshi; Paul Coupland; Catalina Vallejos; Kylie P Matchett; Neil Henderson; Maria Colome Tatche et al.
Source: Self-asserted source
Maria Colome Tatche

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.

Heliyon
2021-05-28 | Journal article
Contributors: Yogesh Singh; Christoph Trautwein; Rolf Fendel; Krickeberg N; Georgy Berezhnoy; Bissinger R; Ossowski S; Salker MS; Nicolas Lougi Pascal Casadei; Riess O et al.
Source: Self-asserted source
Maria Colome Tatche

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Genome biology
2020 | Journal article
Part of ISSN: 1474-7596
Contributors: Hofmeister, Brigitte T; Denkena, Johanna; Colomé-Tatché, Maria; Shahryary, Yadollah; Hazarika, Rashmi; Grimwood, Jane; Mamidi, Sujan; Jenkins, Jerry; Grabowski, Paul P; Sreedasyam, Avinash et al.
Source: Self-asserted source
Maria Colome Tatche

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Genome biology
2020 | Journal article
Part of ISSN: 1474-7596
Contributors: Shahryary, Yadollah; Symeonidi, Aikaterini; Hazarika, Rashmi R; Denkena, Johanna; Mubeen, Talha; Hofmeister, Brigitte; van Gurp, Thomas; Colomé-Tatché, Maria; Verhoeven, Koen J F; Tuskan, Gerald et al.
Source: Self-asserted source
Maria Colome Tatche

Altering microtubule dynamics is synergistically toxic with spindle assembly checkpoint inhibition

Life science alliance
2020 | Journal article
Part of ISSN: 2575-1077
Contributors: Schukken, Klaske M; Lin, Yu-Chih; Bakker, Petra L; Schubert, Michael; Preuss, Stephanie F; Simon, Judith E; van den Bos, Hilda; Storchova, Zuzana; Colomé-Tatché, Maria; Bastians, Holger et al.
Source: Self-asserted source
Maria Colome Tatche

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data

Bioinformatics (Oxford, England)
2020 | Journal article
Part of ISSN: 1367-4803
Contributors: Porubsky, David; Sanders, Ashley D; Taudt, Aaron; Colomé-Tatché, Maria; Lansdorp, Peter M; Guryev, Victor
Source: Self-asserted source
Maria Colome Tatche

Gene networks in cancer are biased by aneuploidies and sample impurities

Biochimica et biophysica acta. Gene regulatory mechanisms
2020 | Journal article
Part of ISSN: 1874-9399
Contributors: Schubert, Michael; Colomé-Tatché, Maria; Foijer, Floris
Source: Self-asserted source
Maria Colome Tatche

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Cell
2020 | Journal article
Part of ISSN: 0092-8674
Contributors: Schulte-Schrepping, Jonas; Reusch, Nico; Paclik, Daniela; Baßler, Kevin; Schlickeiser, Stephan; Zhang, Bowen; Krämer, Benjamin; Krammer, Tobias; Brumhard, Sophia; Bonaguro, Lorenzo et al.
Source: Self-asserted source
Maria Colome Tatche

Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

Genome biology
2019 | Journal article
Part of ISSN: 1474-7596
Contributors: Hanna, Courtney W; Pérez-Palacios, Raquel; Gahurova, Lenka; Schubert, Michael; Krueger, Felix; Biggins, Laura; Andrews, Simon; Colomé-Tatché, Maria; Bourc'his, Deborah; Dean, Wendy et al.
Source: Self-asserted source
Maria Colome Tatche

Quantification of Aneuploidy in Mammalian Systems

Methods in molecular biology (Clifton, N.J.)
2019 | Journal article
Part of ISSN: 1064-3745
Contributors: van den Bos, Hilda; Bakker, Bjorn; Taudt, Aaron; Guryev, Victor; Colomé-Tatché, Maria; Lansdorp, Peter M; Foijer, Floris; Spierings, Diana C J
Source: Self-asserted source
Maria Colome Tatche

Widespread long-range cis-regulatory elements in the maize genome

Nature plants
2019 | Journal article
Part of ISSN: 2055-0278
Contributors: Ricci, William A; Lu, Zefu; Ji, Lexiang; Marand, Alexandre P; Ethridge, Christina L; Murphy, Nathalie G; Noshay, Jaclyn M; Galli, Mary; Mejía-Guerra, María Katherine; Colomé-Tatché, Maria et al.
Source: Self-asserted source
Maria Colome Tatche

METHimpute: imputation-guided construction of complete methylomes from WGBS data

BMC genomics
2018 | Journal article
Part of ISSN: 1471-2164
Contributors: Taudt, Aaron; Roquis, David; Vidalis, Amaryllis; Wardenaar, René; Johannes, Frank; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

Nature structural & molecular biology
2018 | Journal article
Part of ISSN: 1545-9993
Contributors: Hanna, Courtney W; Taudt, Aaron; Huang, Jiahao; Gahurova, Lenka; Kranz, Andrea; Andrews, Simon; Dean, Wendy; Stewart, A Francis; Colomé-Tatché, Maria; Kelsey, Gavin
Source: Self-asserted source
Maria Colome Tatche

Statistical single cell multi-omics integration

Current Opinion in Systems Biology
2018-02 | Journal article
Part of ISSN: 2452-3100
Contributors: M. Colomé-Tatché; F.J. Theis
Source: Self-asserted source
Maria Colome Tatche

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

2017 | Other
Contributors: Richards, Christina; Alonso, Conchita; Becker, Claude; Bossdorf, Oliver; Bucher, Etienne; Colomé-Tatché, Maria; Durka, Walter; Engelhardt, Jan; Gaspar, Bence; Gogol-Döring, Andreas et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Ecology letters
2017 | Journal article
Part of ISSN: 1461-023X
Contributors: Richards, Christina L; Alonso, Conchita; Becker, Claude; Bossdorf, Oliver; Bucher, Etienne; Colomé-Tatché, Maria; Durka, Walter; Engelhardt, Jan; Gaspar, Bence; Gogol-Döring, Andreas et al.
Source: Self-asserted source
Maria Colome Tatche

Histone propionylation is a mark of active chromatin

Nature structural & molecular biology
2017 | Journal article
Part of ISSN: 1545-9993
Contributors: Kebede, Adam F; Nieborak, Anna; Shahidian, Lara Zorro; Le Gras, Stephanie; Richter, Florian; Gómez, Diana Aguilar; Baltissen, Marijke P; Meszaros, Gergo; Magliarelli, Helena de Fatima; Taudt, Aaron et al.
Source: Self-asserted source
Maria Colome Tatche

METHimpute: Imputation-guided construction of complete methylomes from WGBS data

2017 | Other
Contributors: Taudt, Aaron; Roquis, David; Vidalis, Amaryllis; Wardenaar, René; Johannes, Frank; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient

Annals of Oncology
2017-04-11 | Journal article
Contributors: P. Ferronika; H. van den Bos; A. Taudt; D. C. J. Spierings; A. Saber; T. J. N. Hiltermann; K. Kok; D. Porubsky; A. J. van der Wekken; W. Timens et al.
Source: Self-asserted source
Maria Colome Tatche via Crossref Metadata Search

chromstaR: Tracking combinatorial chromatin state dynamics in space and time

2016 | Other
Contributors: Taudt, Aaron; Nguyen, Minh Anh; Heinig, Matthias; Johannes, Frank; Colomé-Tatché, Maria
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Erratum to: Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons

Genome biology
2016 | Journal article
Part of ISSN: 1474-7596
Contributors: van den Bos, Hilda; Spierings, Diana C J; Taudt, Aaron; Bakker, Bjorn; Porubský, David; Falconer, Ester; Novoa, Carolina; Halsema, Nancy; Kazemier, Hinke G; Hoekstra-Wakker, Karina et al.
Source: Self-asserted source
Maria Colome Tatche

Genetic sources of population epigenomic variation

Nature reviews. Genetics
2016 | Journal article
Part of ISSN: 1471-0056
Contributors: Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Signatures of Dobzhansky-Muller Incompatibilities in the Genomes of Recombinant Inbred Lines

Genetics
2016 | Journal article
Part of ISSN: 0016-6731
Contributors: Colomé-Tatché, Maria; Johannes, Frank
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies

Genome biology
2016 | Journal article
Part of ISSN: 1474-7596
Contributors: Bakker, Bjorn; Taudt, Aaron; Belderbos, Mirjam E; Porubsky, David; Spierings, Diana C J; de Jong, Tristan V; Halsema, Nancy; Kazemier, Hinke G; Hoekstra-Wakker, Karina; Bradley, Allan et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons

Genome biology
2016 | Journal article
Part of ISSN: 1474-7596
Contributors: van den Bos, Hilda; Spierings, Diana C J; Taudt, Aaron S; Bakker, Bjorn; Porubský, David; Falconer, Ester; Novoa, Carolina; Halsema, Nancy; Kazemier, Hinke G; Hoekstra-Wakker, Karina et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Erratum to: Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

Genome biology
2016-06 | Journal article
Source: Self-asserted source
Maria Colome Tatche via Europe PubMed Central

histoneHMM: Differential analysis of histone modifications with broad genomic footprints

BMC bioinformatics
2015 | Journal article
Part of ISSN: 1471-2105
Contributors: Heinig, Matthias; Colomé-Tatché, Maria; Taudt, Aaron; Rintisch, Carola; Schafer, Sebastian; Pravenec, Michal; Hubner, Norbert; Vingron, Martin; Johannes, Frank
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

Proceedings of the National Academy of Sciences of the United States of America
2015 | Journal article
Part of ISSN: 0027-8424
Contributors: van der Graaf, Adriaan; Wardenaar, René; Neumann, Drexel A; Taudt, Aaron; Shaw, Ruth G; Jansen, Ritsert C; Schmitz, Robert J; Colomé-Tatché, Maria; Johannes, Frank
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip

Methods in molecular biology (Clifton, N.J.)
2014 | Journal article
Part of ISSN: 1064-3745
Contributors: Cortijo, Sandra; Wardenaar, René; Colomé-Tatché, Maria; Johannes, Frank; Colot, Vincent
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Mapping the epigenetic basis of complex traits

Science (New York, N.Y.)
2014 | Journal article
Part of ISSN: 0036-8075
Contributors: Cortijo, Sandra; Wardenaar, René; Colomé-Tatché, Maria; Gilly, Arthur; Etcheverry, Mathilde; Labadie, Karine; Caillieux, Erwann; Hospital, Fréderic; Aury, Jean-Marc; Wincker, Patrick et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Natural variation of histone modification and its impact on gene expression in the rat genome

Genome research
2014 | Journal article
Part of ISSN: 1088-9051
Contributors: Rintisch, Carola; Heinig, Matthias; Bauerfeind, Anja; Schafer, Sebastian; Mieth, Christin; Patone, Giannino; Hummel, Oliver; Chen, Wei; Cook, Stuart; Cuppen, Edwin et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis

Methods in molecular biology (Clifton, N.J.)
2013 | Journal article
Part of ISSN: 1064-3745
Contributors: Wardenaar, René; Liu, Haiyin; Colot, Vincent; Colomé-Tatché, Maria; Johannes, Frank
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

Proceedings of the National Academy of Sciences of the United States of America
2012 | Journal article
Part of ISSN: 0027-8424
Contributors: Colomé-Tatché, Maria; Cortijo, Sandra; Wardenaar, René; Morgado, Lionel; Lahouze, Benoit; Sarazin, Alexis; Etcheverry, Mathilde; Martin, Antoine; Feng, Suhua; Duvernois-Berthet, Evelyne et al.
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎

MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays

Bioinformatics (Oxford, England)
2012 | Journal article
Part of ISSN: 1367-4803
Contributors: Seifert, Michael; Cortijo, Sandra; Colomé-Tatché, Maria; Johannes, Frank; Roudier, François; Colot, Vincent
Source: Self-asserted source
Maria Colome Tatche
grade
Preferred source (of 2)‎
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Peer review (7 reviews for 5 publications/grants)

Review activity for Communications biology. (1)
Review activity for Genome medicine. (2)
Review activity for Nature biotechnology. (1)
Review activity for Nature communications (2)
Review activity for Nature methods. (1)