List of works - Alain Laederach

A Functional riboSNitch in the 3' Untranslated Region of FKBP5 Alters MicroRNA-320a Binding Efficiency and Mediates Vulnerability to Chronic Post-Traumatic Pain

scientific article published on 27 August 2018

A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population

scientific article

A pipeline for computational design of novel RNA-like topologies.

scientific article published in August 2018

A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure

scientific article published on 9 January 2018

Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

scientific article published on 16 November 2021

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression

scientific article published on 6 November 2017

Arg343 in human surfactant protein D governs discrimination between glucose and N-acetylglucosamine ligands

scientific article published on 28 April 2004

Automated docking of alpha-(1-->4)- and alpha-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site.

scientific article published on August 2000

Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean beta-amylase active site

scientific article

Classification of RNA structure change by 'gazing' at experimental data

scientific article

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

scientific article

Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease

scientific article

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

scientific article

Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: Intramolecular contact versus asymmetric homodimerization

scholarly article by Alain Laederach published in January 2002

Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization

scientific article

Computational functional genomics

Coplanar and coaxial orientations of RNA bases and helices

scientific article published on 5 March 2007

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

scientific article

Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk.

scientific article

Disease-associated mutations that alter the RNA structural ensemble

scientific article

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

scholarly article

Distinct responses to rare codons in select <i>Drosophila</i> tissues

scientific article published on 06 May 2022

Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs

scientific article published on 14 October 2008

Evaluating our ability to predict the structural disruption of RNA by SNPs ⬇️

scientific article published on June 18, 2012

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

scientific article

Evolutionary evidence for alternative structure in RNA sequence co-variation

scientific article (publication date: 2013)

Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding

scientific article published on March 2009

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

scientific article published on 13 May 2008

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

scientific article published on 14 December 2021

Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA.

scientific article published on 28 April 2017

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease

scientific article published on 19 October 2015

Informatics challenges in structured RNA.

scientific article published on 4 July 2007

Ligand specificity modulated by prolyl imide bond Cis/Trans isomerization in the Itk SH2 domain: a quantitative NMR study

scientific article

Local RNA structural changes induced by crystallization are revealed by SHAPE

scientific article

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule

scientific article published on 30 March 2006

Mapping the kinetic barriers of a Large RNA molecule's folding landscape

scientific article

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

scientific article

Membrane RNAs in bacteria

scientific article published on January 2011

Modeling protein recognition of carbohydrates

scientific article

Molecular biology: A second layer of information in RNA.

scientific article

Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR

scientific article

On Adaptivity in Coarse Grain Molecular Dynamics

article

On the characterization of carbon blacks by various techniques

On the characterization of industrial carbon blacks by physico-chemical and by empirical parameters

Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues

scientific article published on July 2001

Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF.

scientific article

RNA folding: A clear path to RNA catalysis

scientific article published on November 2015

RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways

scientific article

Rapid Quantification and Analysis of Kinetic •OH Radical Footprinting Data Using SAFA ⬇️

scientific article published on November 17, 2009

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

scientific article

Selecting against accidental RNA interactions

scientific article

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments

scientific article published on January 2008

Sharing and archiving nucleic acid structure mapping data

scientific article (publication date: July 2011)

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

scientific article published on 28 September 2015

Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia

scientific article published on 05 September 2013

Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives

scientific article

Specific empirical free energy function for automated docking of carbohydrates to proteins

scientific article published in November 2003

Strategies for articulated multibody-based adaptive coarse grain simulation of RNA.

scientific article

Structural effects of linkage disequilibrium on the transcriptome

scientific article published on 22 November 2011

Structural inference of native and partially folded RNA by high-throughput contact mapping

scholarly article

Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

scientific article published on 26 April 2017

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding

scientific article published on 15 August 2006

The potential of the riboSNitch in personalized medicine

scientific article

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains

scientific article

The structure of the influenza A virus genome

scientific article published on 22 July 2019

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution

scientific article

Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns

scientific article published on 19 March 2013

Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking

scientific article

Water adsorption in carbons described by the dubinin–astakhov and dubinin–serpinski equations

article by Fritz Stoeckli et al published 1994 in Journal of the Chemical Society, Faraday Transactions

List of works by Alain Laederach

A Functional riboSNitch in the 3' Untranslated Region of FKBP5 Alters MicroRNA-320a Binding Efficiency and Mediates Vulnerability to Chronic Post-Traumatic Pain

A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population

A pipeline for computational design of novel RNA-like topologies.

A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure

Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression

Arg343 in human surfactant protein D governs discrimination between glucose and N-acetylglucosamine ligands

Automated docking of alpha-(1-->4)- and alpha-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site.

Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean beta-amylase active site

Classification of RNA structure change by 'gazing' at experimental data

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: Intramolecular contact versus asymmetric homodimerization

Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization

Computational functional genomics

Coplanar and coaxial orientations of RNA bases and helices

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk.

Disease-associated mutations that alter the RNA structural ensemble

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

Distinct responses to rare codons in select <i>Drosophila</i> tissues

Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs

Evaluating our ability to predict the structural disruption of RNA by SNPs ⬇️

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

Evolutionary evidence for alternative structure in RNA sequence co-variation

Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA.

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease

Informatics challenges in structured RNA.

Ligand specificity modulated by prolyl imide bond Cis/Trans isomerization in the Itk SH2 domain: a quantitative NMR study

Local RNA structural changes induced by crystallization are revealed by SHAPE

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule

Mapping the kinetic barriers of a Large RNA molecule's folding landscape

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Membrane RNAs in bacteria

Modeling protein recognition of carbohydrates

Molecular biology: A second layer of information in RNA.

Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR

On Adaptivity in Coarse Grain Molecular Dynamics

On the characterization of carbon blacks by various techniques

On the characterization of industrial carbon blacks by physico-chemical and by empirical parameters

Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues

Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF.

RNA folding: A clear path to RNA catalysis

RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways

Rapid Quantification and Analysis of Kinetic •OH Radical Footprinting Data Using SAFA ⬇️

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

Selecting against accidental RNA interactions

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments

Sharing and archiving nucleic acid structure mapping data

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia

Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives

Specific empirical free energy function for automated docking of carbohydrates to proteins

Strategies for articulated multibody-based adaptive coarse grain simulation of RNA.

Structural effects of linkage disequilibrium on the transcriptome

Structural inference of native and partially folded RNA by high-throughput contact mapping

Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding

The potential of the riboSNitch in personalized medicine

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains

The structure of the influenza A virus genome

Toward interoperable bioscience data

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution

Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns

Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking

Water adsorption in carbons described by the dubinin–astakhov and dubinin–serpinski equations