List of works - Debora Marks

3D RNA and Functional Interactions from Evolutionary Couplings

scientific article

A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data

scientific article published on 01 January 2018

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

scholarly article by Eran Kotler published in September 2018

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

scientific article published on 01 July 2018

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

scientific article (publication date: 28 April 2015)

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

scientific article (publication date: 13 January 2015)

Antiparallel protocadherin homodimers use distinct affinity- and specificity mediating regions in cadherin repeats 1-4

Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

scientific article (publication date: 29 July 2016)

Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development

scientific article

CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy

scientific article published on 21 December 2020

Combining Evolutionary Covariance and NMR Data for Protein Structure Determination

scientific article published on 23 December 2018

Computational analysis of mouse piRNA sequence and biogenesis ⬇️

scientific article (publication date: November 2007)

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

scientific article

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

article

Correction: Human MicroRNA Targets

scientific article

Cryo-electron microscopy structure of the lipid droplet-formation protein seipin

scientific article published on 16 October 2018

Deep generative models of genetic variation capture the effects of mutations

scientific article published on 24 September 2018

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

scientific article

Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis

scientific article

FreeContact: fast and free software for protein contact prediction from residue co-evolution

scientific article (publication date: 26 March 2014)

Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

scientific article published on 11 September 2018

Gene expression. MicroRNA control of protein expression noise

scientific article

Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings

scientific article published on 03 December 2018

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013

scientific article (publication date: 15 November 2016)

Granulocyte transfusions for preventing infections in patients with neutropenia or neutrophil dysfunction

scientific article

Human MicroRNA targets

scientific article

Identification of virus-encoded microRNAs

scientific article

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

scientific article (publication date: July 2015)

Inferring protein 3D structure from deep mutation scans

scientific article published on 17 June 2019

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

scientific article published on 20 August 2019

MicroRNA profiling of the murine hematopoietic system

scientific article

MicroRNA targets in Drosophila

scientific article

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

scientific article published on 11 May 2020

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

scientific article published on 01 September 2020

Mutation effects predicted from sequence co-variation

scientific article published on 16 January 2017

Noise control is a primary function of microRNAs and post-transcriptional regulation

Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2

scientific article (publication date: 14 March 2011)

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

PconsFold: improved contact predictions improve protein models

scientific article (publication date: September 2014)

Population-specific design of de-immunized protein biotherapeutics.

scientific article published on 2 March 2018

Prediction of human microRNA targets

scientific article published on January 2006

Protein 3D structure computed from evolutionary sequence variation

scientific article published in 2011

Protein Structure from Experimental Evolution

scientific article published on 11 December 2019

Protein design and variant prediction using autoregressive generative models

scientific article published on 23 April 2021

Protein structure determination by combining sparse NMR data with evolutionary couplings

scientific article (publication date: August 2015)

Protein structure prediction from sequence variation ⬇️

scientific article (publication date: November 2012)

Rapid generation of potent antibodies by autonomous hypermutation in yeast

scientific article published on 11 November 2020

Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans

scientific article

Remote viewing exposed

scientific article

Scientific discovery in the age of artificial intelligence

scientific article published on 2 August 2023

Sequence co-evolution gives 3D contacts and structures of protein complexes

scientific article published on 25 September 2014

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

scientific article (publication date: August 2010)

Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex

scientific article published on 09 March 2020

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

scientific article (publication date: 3 November 2015)

Structure and mutagenic analysis of the lipid II flippase MurJ from

article published in the Proceedings of the National Academy of Sciences of the United States of America

Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.

scientific article

Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel

scientific article (publication date: December 2014)

Structured States of Disordered Proteins from Genomic Sequences

scientific article published on September 2016

Target mRNA abundance dilutes microRNA and siRNA activity

scientific article (publication date: 20 April 2010)

The EVcouplings Python framework for coevolutionary sequence analysis

scientific article published on 01 May 2019

The developmental miRNA profiles of zebrafish as determined by small RNA cloning

scientific article

The microRNA.org resource: targets and expression

scientific article

The small RNA profile during Drosophila melanogaster development

scientific article (publication date: August 2003)

Three-dimensional structures of membrane proteins from genomic sequencing

scientific article

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

scientific article (publication date: June 2009)

mRNA turnover rate limits siRNA and microRNA efficacy

scientific article (publication date: 16 November 2010)

mRNA turnover rate limits siRNA and microRNA efficacy

scientific article (publication date: 21 December 2010)

miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1.

scientific article

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome ⬇️

scientific article (publication date: August 2012)

List of works by Debora Marks

3D RNA and Functional Interactions from Evolutionary Couplings

A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

Antiparallel protocadherin homodimers use distinct affinity- and specificity mediating regions in cadherin repeats 1-4

Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development

CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy

Combining Evolutionary Covariance and NMR Data for Protein Structure Determination

Computational analysis of mouse piRNA sequence and biogenesis ⬇️

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

Correction: Human MicroRNA Targets

Cryo-electron microscopy structure of the lipid droplet-formation protein seipin

Deep generative models of genetic variation capture the effects of mutations

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis

FreeContact: fast and free software for protein contact prediction from residue co-evolution

Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Gene expression. MicroRNA control of protein expression noise

Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013

Granulocyte transfusions for preventing infections in patients with neutropenia or neutrophil dysfunction

Human MicroRNA targets

Identification of virus-encoded microRNAs

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

Inferring protein 3D structure from deep mutation scans

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

MicroRNA profiling of the murine hematopoietic system

MicroRNA targets in Drosophila

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

Mutation effects predicted from sequence co-variation

Noise control is a primary function of microRNAs and post-transcriptional regulation

Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2

Pathway and network analysis of cancer genomes

PconsFold: improved contact predictions improve protein models

Population-specific design of de-immunized protein biotherapeutics.

Prediction of human microRNA targets

Protein 3D structure computed from evolutionary sequence variation

Protein Structure from Experimental Evolution

Protein design and variant prediction using autoregressive generative models

Protein structure determination by combining sparse NMR data with evolutionary couplings

Protein structure prediction from sequence variation ⬇️

Rapid generation of potent antibodies by autonomous hypermutation in yeast

Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans

Remote viewing exposed

Scientific discovery in the age of artificial intelligence

Sequence co-evolution gives 3D contacts and structures of protein complexes

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

Structure and mutagenic analysis of the lipid II flippase MurJ from

Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.

Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel

Structured States of Disordered Proteins from Genomic Sequences

Target mRNA abundance dilutes microRNA and siRNA activity

The EVcouplings Python framework for coevolutionary sequence analysis

The developmental miRNA profiles of zebrafish as determined by small RNA cloning

The microRNA.org resource: targets and expression

The small RNA profile during Drosophila melanogaster development

Three-dimensional structures of membrane proteins from genomic sequencing

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

mRNA turnover rate limits siRNA and microRNA efficacy

mRNA turnover rate limits siRNA and microRNA efficacy

miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1.

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome ⬇️