List of works - Marc A. Martí‐Renom

Comparative protein structure modeling using Modeller

scientific article (publication date: October 2006)

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

scientific article

Tools for comparative protein structure modeling and analysis

scientific article

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

scientific article

MODBASE, a database of annotated comparative protein structure models, and associated resources

scientific article

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation

scientific article published on October 2011

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis

scientific article published on July 2013

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

scientific article published on October 2014

Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition

scientific article published in June 2004

MODBASE, a database of annotated comparative protein structure models and associated resources

scientific article published on 23 October 2008

Alignment of protein sequences by their profiles

scientific article

A composite score for predicting errors in protein structure models

scientific article

EVA: continuous automatic evaluation of protein structure prediction servers

scientific article published on December 1, 2001

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting

scientific article

EVA: Evaluation of protein structure prediction servers

scientific article

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

scientific article published on 19 July 2017

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

scientific article published on 15 January 2018

Reliability of assessment of protein structure prediction methods

scientific article

The C-type lectin fold as an evolutionary solution for massive sequence variation

scientific article

Bridging the resolution gap in structural modeling of 3D genome organization

scientific article

Restraint-based three-dimensional modeling of genomes and genomic domains

scientific article

Chromatin globules: a common motif of higher order chromosome structure?

scientific article published on 12 April 2011

Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies

scientific article published in December 2002

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

scientific article

Alignment of multiple protein structures based on sequence and structure features

scientific article

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

scientific article published on 26 December 2018

RNA structure alignment by a unit-vector approach

scientific article

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.

scientific article published on 24 November 2017

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

scientific article

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

scientific article

Variable gap penalty for protein sequence-structure alignment

scientific article published on 19 January 2006

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

scientific article

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon

scientific article

Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824.

scientific article published on 19 September 2011

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.

scientific article published on 28 December 2015

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

scientific article published on 21 May 2018

Structure determination of genomic domains by satisfaction of spatial restraints

scientific article published on January 2011

SARA: a server for function annotation of RNA structures

scientific article published on 29 May 2009

All-atom knowledge-based potential for RNA structure prediction and assessment

scientific article

Structure-based statistical analysis of transmembrane helices

scientific article published on May 16, 2012

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans

scientific article published in January 2008

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

scientific article published on 17 September 2018

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis

scientific article (publication date: 2013)

Characterization of protein hubs by inferring interacting motifs from protein interactions

scientific article

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

scientific article

Protein similarities beyond disulphide bridge topology

scientific article published on 01 December 1998

A kernel for open source drug discovery in tropical diseases

scientific article

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

scientific article published on 28 June 2019

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

scientific article

List of works by Marc A. Martí‐Renom

Comparative protein structure modeling using Modeller

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

Tools for comparative protein structure modeling and analysis

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

MODBASE, a database of annotated comparative protein structure models, and associated resources

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition

MODBASE, a database of annotated comparative protein structure models and associated resources

Alignment of protein sequences by their profiles

A composite score for predicting errors in protein structure models

EVA: continuous automatic evaluation of protein structure prediction servers

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting

EVA: Evaluation of protein structure prediction servers

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

Reliability of assessment of protein structure prediction methods

The C-type lectin fold as an evolutionary solution for massive sequence variation

Bridging the resolution gap in structural modeling of 3D genome organization

Restraint-based three-dimensional modeling of genomes and genomic domains

Chromatin globules: a common motif of higher order chromosome structure?

Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Alignment of multiple protein structures based on sequence and structure features

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

RNA structure alignment by a unit-vector approach

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

Variable gap penalty for protein sequence-structure alignment

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon

Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824.

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

Structure determination of genomic domains by satisfaction of spatial restraints

SARA: a server for function annotation of RNA structures

All-atom knowledge-based potential for RNA structure prediction and assessment

Structure-based statistical analysis of transmembrane helices

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis

Characterization of protein hubs by inferring interacting motifs from protein interactions

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

Protein similarities beyond disulphide bridge topology

A kernel for open source drug discovery in tropical diseases

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae