A. Laederach

发表

Computational functional genomics

Mike P. Liang, O. Troyanskaya, R. Altman, 2004, IEEE Signal Process. Mag..

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

Magdalena A. Jonikas, D. Baker, R. Altman, 2008, Proceedings of the National Academy of Sciences.

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

D. Herschlag, Rhiju Das, A. Laederach, 2006, Journal of molecular biology.

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

A. Laederach, Scott O. Quarrier, Joshua S. Martin, 2010, RNA.

A pipeline for computational design of novel RNA-like topologies

T. Schlick, Swati Jain, A. Laederach, 2018, Nucleic acids research.

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

R. Altman, A. Laederach, M. Brenowitz, 2008, Nucleic acids research.

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

Mike P. Liang, R. Altman, A. Laederach, 2006, Journal of molecular biology.

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

R. Altman, D. Herschlag, Rhiju Das, 2005, RNA.

Toward interoperable bioscience data

Anne E. Trefethen, Catherine A. Shang, Gully A. Burns, 2012, Nature Genetics.

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

Alain Laederach, Silvia Giliani, Luigi D Notarangelo, 2014, Human molecular genetics.

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

Magdalena A. Jonikas, R. Altman, D. Herschlag, 2009, RNA.

Sharing and archiving nucleic acid structure mapping data.

Craig L. Zirbel, R. Knight, D. Mathews, 2011, RNA.

Towards an understanding of RNA structural modalities: a riboswitch case study

Christine E. Heitsch, Hee Rhang Yoon, A. Laederach, 2019, Computational and mathematical biophysics.

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

Magdalena A. Jonikas, A. Laederach, Joshua S. Martin, 2013, Biophysical journal.

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

A. Laederach, M. Brenowitz, Somdeb Mitra, 2008, Current opinion in chemical biology.

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

Magdalena A. Jonikas, R. Altman, A. Laederach, 2007, Proceedings of the National Academy of Sciences.

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

A. Laederach, Katrina M. Kutchko, 2016, Wiley interdisciplinary reviews. RNA.

Disease-Associated Mutations That Alter the RNA Structural Ensemble

Alain Laederach, A. Laederach, Joshua S. Martin, 2010, PLoS genetics.

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

A. Laederach, Ruipeng Lu, E. Mucaki, 2015, bioRxiv.

Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential

A. Laederach, S. Ramos, S. Montgomery, 2022, Nucleic acids research.

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

Alain Laederach, A. Laederach, Joshua S. Martin, 2012, BMC Genomics.

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

Russ B Altman, Alain Laederach, R. Altman, 2011, RNA.

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

K. Weeks, A. Laederach, Nathaniel J. Moorman, 2015, RNA.

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

Nikolay V. Dokholyan, David Gotz, Alain Laederach, 2017, Biophysical journal.

Ieee Signal Processing Magazine Computational Functional Genomics

Mike P. Liang, O. Troyanskaya, R. Altman, 2001 .

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper.

K. Weeks, A. Laederach, Thomas W Christy, 2021, PLoS computational biology.

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

Eliseos J. Mucaki, A. Laederach, Ruipeng Lu, 2015, BMC Medical Genomics.

Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

D. Mathews, K. Weeks, Lela Lackey, 2022, eLife.

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

K. Weeks, Lela Lackey, A. Laederach, 2017, Proceedings of the National Academy of Sciences.

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

Howard Y. Chang, Alain Laederach, Kun Qu, 2015, Nucleic acids research.

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

Eric P. Nawrocki, Craig L. Zirbel, J. Clemente, 2011, Standards in genomic sciences.

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. Laederach, Julie A. Johnson, L. Pelleymounter, 2011, Molecular genetics and metabolism.

Membrane RNAs in bacteria

A. Laederach, Wes A. Sanders, 2011, Molecular microbiology.

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

D. Mathews, A. Laederach, Stanislav Bellaousov, 2017, Viruses.

Structural conservation of MALAT1 long non-coding RNA in cells and in evolution

C. Burch, A. Laederach, Anaïs Monroy-Eklund, 2022, bioRxiv.

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

A. Laederach, Joshua S. Martin, N. Walter, 2015, Nature Methods.

Global 5′-UTR RNA structure regulates translation of a SERPINA1 mRNA

K. Weeks, Lela Lackey, A. Laederach, 2022, Nucleic acids research.

Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

A. Laederach, Joshua S. Martin, N. Walter, 2016 .

On the characterization of carbon blacks by various techniques

A. Laederach, H. Stoeckli, D. Huguenin, 1994 .

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

A. Laederach, T. Centeno, F. Stoeckli, 1994 .

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

Peter J. Reilly, Alain Laederach, A. Laederach, 2003, J. Comput. Chem..

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

Kendall W. Cradic, A. Laederach, A. Andreotti, 2003, Journal of molecular biology.

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

Kendall W. Cradic, A. Laederach, A. Andreotti, 2002, Protein science : a publication of the Protein Society.

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

A. Laederach, E. Pletneva, N. Kostić, 2001, Journal of the American Chemical Society.

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

T. Schlick, Swati Jain, A. Laederach, 2021, Journal of the American Chemical Society.

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

T. Schlick, Swati Jain, A. Laederach, 2021, bioRxiv.

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

J. Parker, Lela Lackey, A. Laederach, 2018, The Journal of Neuroscience.

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

J. Nutt, W. Scott, K. Doheny, 2010, Nature Genetics.

Characterization of a Disease-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing

Gloria M. Sheynkman, E. Silverman, A. Laederach, 2020, medRxiv.

Distinct responses to rare codons in select Drosophila tissues

A. Laederach, C. Counter, D. Fox, 2022, bioRxiv.

Disease-associated human genetic variation through the lens of precursor and mature RNA structure

A. Laederach, Justin M. Waldern, Jayashree Kumar, 2021, Human Genetics.

Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility

A. Laederach, Aaztli Coria, A. Borodavka, 2022, bioRxiv.

Structural divergence creates new functional features in alphavirus genomes

Alain Laederach, M. Heise, A. Laederach, 2018, Nucleic acids research.

The potential of the riboSNitch in personalized medicine

Alain Laederach, A. Laederach, S. Ramos, 2015, Wiley interdisciplinary reviews. RNA.

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

Daniel Herschlag, Russ B Altman, Rhiju Das, 2008, Nature Protocols.

Regulatory RNA: Session Introduction

Vasant Honavar, Robert L. Jernigan, Drena Dobbs, 2016 .

The structure of the influenza A virus genome

Alain Laederach, Ervin Fodor, A. Laederach, 2017, Nature Microbiology.

Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing

D. Mathews, Lela Lackey, A. Laederach, 2021 .

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

Lela Lackey, A. Laederach, Aaztli Coria, 2018, RNA.

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease

Lela Lackey, A. Laederach, Evonne McArthur, 2015, PloS one.

Classification of RNA structure change by ‘gazing’ at experimental data

Alain Laederach, Chanin Tolson Woods, A. Laederach, 2017, Bioinform..

Structural effects of linkage disequilibrium on the transcriptome.

Alain Laederach, A. Laederach, Joshua S. Martin, 2012, RNA.

Automated docking of maltose, 2‐deoxymaltose, and maltotetraose into the soybean β‐amylase active site

A. Laederach, P. Coutinho, M. Dowd, 1999, Proteins.

Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans.

K. Weeks, A. Laederach, A. M. Mustoe, 2018, Biochemistry.

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

E. Silverman, Lela Lackey, A. Laederach, 2021, PLoS genetics.

Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.

K. Weeks, A. Laederach, N. Dokholyan, 2021, Biochemistry.

Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking

A. Laederach, P. Reilly, C. Aikens, 2004, Proteins.

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

Joshua S. Martin, Alain Laederach, Justin Ritz, 2013, PLoS Comput. Biol..

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

A. Laederach, A. Andreotti, P. Breheny, 2003, Journal of the American Chemical Society.

Submitted 2-28-04 Arg 343 in Human Surfactant Protein D Governs Discrimination between Glucose and N-Acetylglucosamine Ligands

A. Laederach, D. Voelker, M. Allen, 2017 .

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

A. Laederach, D. Voelker, M. Allen, 2004, Glycobiology.

Protein-carbohydrate and protein-protein interactions: using models to better understand and predict specific molecular recognition

A. Laederach, 2003 .

Cigarette smoking-associated isoform switching and 3′ UTR lengthening via alternative polyadenylation

R. Bowler, A. Laederach, C. Hersh, 2021, medRxiv.

Automated docking of α‐(1→4)‐ and α‐(1→6)‐linked glucosyl trisaccharides and maltopentaose into the soybean β‐amylase active site

W. M. Rockey, A. Laederach, P. Reilly, 2000 .

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

A. Laederach, S. Ramos, Rita M. Meganck, 2017, RNA.

Local RNA structural changes induced by crystallization are revealed by SHAPE.

Quentin Vicens, Alain Laederach, T. Cech, 2007, RNA.

Modeling protein recognition of carbohydrates

Alain Laederach, A. Laederach, P. Reilly, 2005, Proteins.

The Effects of Rare SERPINA1 Variants on Lung Function and Emphysema in SPIROMICS.

E. Hoffman, F. Martinez, E. Bleecker, 2020, American journal of respiratory and critical care medicine.

RNA folding: A clear path to RNA catalysis.

A. Laederach, Amanda C Solem, 2015, Nature chemical biology.

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

A. Laederach, M. Wolfgang, T. Yahr, 2016, Journal of bacteriology.

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

A. Laederach, H. Stoeckli, J. Affolter, 1996 .

Mapping the Kinetic Barriers of a Large RNA Molecule's Folding Landscape

A. Laederach, Joshua S. Martin, M. Brenowitz, 2014, PloS one.

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

Mohammad Poursina, Kishor D Bhalerao, Samuel C Flores, 2011, Methods in enzymology.

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

A. Laederach, M. Allen, P. Reilly, 2001, Biochemistry.

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

J. Nutt, W. Scott, K. Doheny, 2017 .

Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3′UTR Variation in Chikungunya Virus

M. Heise, A. Laederach, Katrina M. Kutchko, 2020, Journal of Virology.

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

A. Laederach, A. Andreotti, D. Fulton, 2002, Biochemistry.

Informatics challenges in structured RNA

Alain Laederach, A. Laederach, 2007, Briefings Bioinform..

Coplanar and coaxial orientations of RNA bases and helices.

R. Altman, A. Schwartzman, A. Laederach, 2007, RNA.

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

Joshua S. Martin, Alain Laederach, Katrina Simmons, 2009, Algorithms.

Docking carbohydrates to proteins: Empirical free energy functions

A. Laederach, 2006 .

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

K. Weeks, A. Laederach, Catherine A Giannetti, 2021, bioRxiv.

Molecular biology: A second layer of information in RNA

A. Laederach, S. Ramos, 2014, Nature.

Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation

A. Laederach, D. Fox, Jessica K. Sawyer, 2023, bioRxiv.

The structure of the influenza A virus genome

A. Laederach, S. Rockman, L. Brown, 2019, Nature Microbiology.

A Functional riboSNitch in the 3' Untranslated Region of

Lela Lackey, A. Laederach, M. Kurz, 2019 .

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

Magdalena A. Jonikas, A. Laederach, D. Herschlag, 2009 .