Fidel Ramírez

发表

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains

Thomas Lengauer, F. Ramírez, J. Walter, 2018, Genome Biology.

Partially methylated domains are hallmarks of a cell specific epigenome topology

Thomas Lengauer, F. Ramírez, J. Walter, 2018, bioRxiv.

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.

Ho-Ryun Chung, Fidel Ramírez, Thomas Manke, 2015, Molecular cell.

Novel approaches to the integration and analysis of systems biology data

Fidel Ramírez, F. Ramírez, Fidel Ramírez, 2011 .

The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells.

F. Ramírez, B. van Steensel, R. Schneider, 2013, Cell reports.

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramírez, Thomas Manke, Vivek Bhardwaj, 2016, Nucleic Acids Res..

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramírez, Sarah Diehl, Thomas Manke, 2014, Nucleic Acids Res..

Computing topological parameters of biological networks

Fidel Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, 2008, Bioinform..

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

F. Ramírez, Gina Renschler, G. Richard, 2019, bioRxiv.

Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.

J. Martens, T. Jenuwein, F. Ramírez, 2014, Molecular cell.

pyGenomeTracks: reproducible plots for multivariate genomic datasets

Fidel Ramírez, Rolf Backofen, Thomas Manke, 2020, Bioinform..

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

Fidel Ramírez, Rolf Backofen, Thomas Manke, 2018, Nucleic Acids Res..

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Kin Chung Lam, B. Habermann, F. Ramírez, 2017, bioRxiv.

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

GOATOOLS: A Python library for Gene Ontology analyses

Brent S. Pedersen, P. Flick, C. Mungall, 2018, Scientific Reports.

CAPRI enables comparison of evolutionarily conserved RNA interacting regions

F. Ramírez, A. Akhtar, T. Manke, 2019, Nature Communications.

MOF-associated complexes ensure stem cell identity and Xist repression

Fidel Ramírez, Rolf Backofen, Thomas Manke, 2014, eLife.

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Irene Papatheodorou, Rolf Backofen, Anton Nekrutenko, 2020, GigaScience.

Community-driven data analysis training for biology

Anthony Bretaudeau, Fidel Ramírez, Rolf Backofen, 2017, bioRxiv.

RELACS nuclei barcoding enables high-throughput ChIP-seq

Fidel Ramírez, Thomas Manke, Laura Arrigoni, 2018, Communications Biology.

DASMI: exchanging, annotating and assessing molecular interaction data

Hagen Blankenburg, Robert D. Finn, Andreas Prlic, 2009, Bioinform..

Functional evaluation of domain-domain interactions and human protein interaction networks

Fidel Ramírez, Thomas Lengauer, Mario Albrecht, 2007, Bioinform..

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.

Thomas Lengauer, K. Rohr, H. Erfle, 2011, Cell host & microbe.

DASMIweb: online integration, analysis and assessment of distributed protein interaction data

Hagen Blankenburg, Fidel Ramírez, Joachim Büch, 2009, Nucleic Acids Res..

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains

Thomas Lengauer, F. Ramírez, J. Walter, 2018, Genome Biology.

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation

L. Steinmetz, N. Luscombe, F. Ramírez, 2016, Nature Structural &Molecular Biology.

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Kin Chung Lam, B. Habermann, F. Ramírez, 2017, Nature Communications.

Computational analysis of human protein interaction networks

Thomas Lengauer, M. Albrecht, Y. Assenov, 2007, Proteomics.

CAPRI enables comparison of evolutionarily conserved RNA interacting regions

F. Ramírez, A. Akhtar, T. Manke, 2019, Nature Communications.

Functional characterization of human genes from exon expression and RNA interference results.

M. Albrecht, D. Emig, H. Blankenburg, 2012, Methods in molecular biology.

Supplemental Information Recruitment and Activation of a Lipid Kinase by Hepatitis C Virus NS 5 A Is Essential for Integrity of the Membranous Replication Compartment

Thomas Lengauer, K. Rohr, H. Erfle, 2010 .

Ultra-parallel ChIP-seq by barcoding of intact nuclei

F. Ramírez, L. Arrigoni, T. Manke, 2018, bioRxiv.

Novel search method for the discovery of functional relationships

Fidel Ramírez, Mario Albrecht, Glenn Lawyer, 2011, Bioinform..

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Irene Papatheodorou, Rolf Backofen, Anton Nekrutenko, 2020, bioRxiv.

Functional interplay between MSL 1 and CDK 7 controls RNA polymerase II Ser 5 phosphorylation

L. Steinmetz, N. Luscombe, F. Ramírez, 2016 .

GOATOOLS: Tools for Gene Ontology

Patrick Flick, Brent S. Pedersen, Christopher J. Mungall, 2015 .

MOF-associated complexes ensure stem cell identity and Xist repression

Patrick R. Wright, R. Backofen, E. Heard, 2014, eLife.

GOATOOLS: A Python library for Gene Ontology analyses

Patrick Flick, Fidel Ramírez, Aurélien Naldi, 2018, Scientific Reports.