Lista de obras - Marc A. Marti-Renom - Dominio Público Uruguay

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

artículo científico publicado en 2020

A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

artículo científico publicado en 2013

A composite score for predicting errors in protein structure models

artículo científico publicado en 2006

A kernel for open source drug discovery in tropical diseases

artículo científico publicado en 2009

A kernel for the Tropical Disease Initiative

artículo científico publicado en 2009

A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

artículo científico publicado en 2021

ASAP: analysis of peptide composition

article

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

artículo científico publicado en 2006

Alignment of multiple protein structures based on sequence and structure features.

artículo científico publicado en 2009

Alignment of protein sequences by their profiles

artículo científico publicado en 2004

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

artículo científico publicado en 2011

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

artículo científico publicado en 2015

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

artículo científico

Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution

artículo científico publicado en 2019

Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution

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

artículo científico publicado en 2011

CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

artículo científico publicado en 2020

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

artículo científico publicado en 2020

Challenges and guidelines toward 4D nucleome data and model standards

artículo científico publicado en 2018

Challenges for visualizing three-dimensional data in genomic browsers

artículo científico publicado en 2017

Characterization of protein hubs by inferring interacting motifs from protein interactions

artículo científico publicado en 2007

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

Classification of protein disulphide-bridge topologies.

artículo científico publicado en 2001

Comparative protein structure modeling using Modeller

artículo científico publicado en 2006

Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

artículo científico publicado en 2022

DBAli tools: mining the protein structure space

artículo científico publicado en 2007

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

artículo científico publicado en 2017

Detecting remotely related proteins by their interactions and sequence similarity

artículo científico publicado en 2005

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

scientific article published on 04 June 2018

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

artículo científico publicado en 2014

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

artículo científico publicado en 2021

EVA: Evaluation of protein structure prediction servers.

artículo científico publicado en 2003

Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B

article

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs.

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

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

scientific article published on 28 June 2019

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

artículo científico publicado en 2011

Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains

artículo científico publicado en 2018

LifeTime and improving European healthcare through cell-based interceptive medicine

artículo científico publicado en 2020

Ligand-target prediction by structural network biology using nAnnoLyze

artículo científico publicado en 2015

Localization of binding sites in protein structures by optimization of a composite scoring function

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 2004

Mating type specific chromosome conformation in Saccharomyces cerevisiae

Membrane protein integration into the endoplasmic reticulum

artículo científico publicado en 2011

ModLink+: improving fold recognition by using protein-protein interactions

artículo científico publicado en 2009

ModView, visualization of multiple protein sequences and structures

artículo científico publicado en 2003

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

artículo científico publicado en 2020

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

artículo científico publicado en 2011

On the demultiplexing of chromosome capture conformation data

artículo científico publicado en 2015

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

artículo científico publicado en 2018

Open Source Research — the Power of Us

artículo científico publicado en 2006

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

artículo científico publicado en 2015

Parallel sequencing lives, or what makes large sequencing projects successful

Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing.

artículo científico publicado en 2012

Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

artículo científico publicado en 2021

Prediction of enzyme function by combining sequence similarity and protein interactions

artículo científico publicado en 2008

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

scientific article published on 17 September 2018

Protein similarities beyond disulphide bridge topology

artículo científico publicado en 1998

Protein translocation into peroxisomes by ring-shaped import receptors

artículo científico publicado en 2007

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

artículo científico publicado en 2021

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

artículo científico publicado en 2010

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

scientific article published on 01 July 2019

RNA structure alignment by a unit-vector approach

artículo científico publicado en 2008

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

artículo científico publicado en 2000

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

artículo científico publicado en 2006

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints a aEdited by A. R. Fersht

article

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery

artículo científico publicado en 2015

Reliability of assessment of protein structure prediction methods.

artículo científico publicado en 2002

Reply to Moult et al

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

artículo científico publicado en 2015

SARA: a server for function annotation of RNA structures

artículo científico publicado en 2009

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

artículo científico publicado en 2021

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

artículo científico publicado en 2017

Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling

scholarly article published 15 January 2016

Structure determination of genomic domains by satisfaction of spatial restraints

artículo científico publicado en 2011

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

artículo científico publicado en 2004

Structure-based statistical analysis of transmembrane helices

artículo científico publicado en 2012

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

artículo científico publicado en 2000

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

article

TADs enriched in histone H1.2 strongly overlap with the B compartment, inaccessible chromatin and AT-rich Giemsa bands

artículo científico publicado en 2020

TADs without borders

artículo científico publicado en 2020

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

artículo científico publicado en 2013

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

artículo científico publicado en 2007

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

artículo científico publicado en 2005

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

artículo científico publicado en 2015

The impact of chromosomal fusions on 3D genome folding and recombination in the germ line

artículo científico publicado en 2021

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

scientific article published on 21 May 2018

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

artículo científico publicado en 2011

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

artículo científico publicado en 2010

Tools for comparative protein structure modeling and analysis

artículo científico publicado en 2003

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

artículo científico publicado en 2018

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

scientific article published on 22 May 2020

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

artículo científico publicado en 2008

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

artículo científico publicado en 2002

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package

artículo científico publicado en 2013

Variable gap penalty for protein sequence-structure alignment

artículo científico publicado en 2006

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

artículo científico publicado en 2018

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

artículo científico publicado en 2013

Lista de obras de Marc A. Marti-Renom

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

A Novel Family of Soluble Minimal Scaffolds Provides Structural Insight into the Catalytic Domains of Integral Membrane Metallopeptidases

A composite score for predicting errors in protein structure models

A kernel for open source drug discovery in tropical diseases

A kernel for the Tropical Disease Initiative

A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

ASAP: analysis of peptide composition

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

Alignment of multiple protein structures based on sequence and structure features.

Alignment of protein sequences by their profiles

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

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

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

Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution

Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution

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

CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

Challenges and guidelines toward 4D nucleome data and model standards

Challenges for visualizing three-dimensional data in genomic browsers

Characterization of protein hubs by inferring interacting motifs from protein interactions

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

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

Classification of protein disulphide-bridge topologies.

Comparative protein structure modeling using Modeller

Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

DBAli tools: mining the protein structure space

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Detecting remotely related proteins by their interactions and sequence similarity

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

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

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

EVA: Evaluation of protein structure prediction servers.

Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs.

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

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

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

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

Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains

LifeTime and improving European healthcare through cell-based interceptive medicine

Ligand-target prediction by structural network biology using nAnnoLyze

Localization of binding sites in protein structures by optimization of a composite scoring function

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

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

Mating type specific chromosome conformation in Saccharomyces cerevisiae

Membrane protein integration into the endoplasmic reticulum

ModLink+: improving fold recognition by using protein-protein interactions

ModView, visualization of multiple protein sequences and structures

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

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

On the demultiplexing of chromosome capture conformation data

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Open Source Research — the Power of Us

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

Parallel sequencing lives, or what makes large sequencing projects successful

Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing.

Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

Prediction of enzyme function by combining sequence similarity and protein interactions

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

Protein similarities beyond disulphide bridge topology

Protein translocation into peroxisomes by ring-shaped import receptors

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

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

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

RNA structure alignment by a unit-vector approach

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

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

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints a aEdited by A. R. Fersht

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery

Reliability of assessment of protein structure prediction methods.

Reply to Moult et al

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

SARA: a server for function annotation of RNA structures

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

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

Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling

Structure determination of genomic domains by satisfaction of spatial restraints