Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

Towards sequence-based prediction of mutation-induced stability changes in unseen non-homologous proteins

(2014) Lukas Folkman et al.   BMC GENOMICS

Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches

(2014) C. C. H. Chang et al.   BRIEFINGS IN BIOINFORMATICS

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

(2014) Minghui Li et al.   Journal of Chemical Theory and Computation

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Microarrays for high-throughput genotyping of MICA alleles using allele-specific primer extension

(2014) I. C. Baek et al.   TISSUE ANTIGENS

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

(2014) J. X. Binder et al.   Database-The Journal of Biological Databases and Curation

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing

(2013) Ning Sun et al.   BIOTECHNOLOGY AND BIOENGINEERING

Identification of properties important to protein aggregation using feature selection

(2013) Yaping Fang et al.   BMC BIOINFORMATICS

A novel approach for protein subcellular location prediction using amino acid exposure

(2013) Arvind Mer et al.   BMC BIOINFORMATICS

Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants

(2013) Lukas Folkman et al.   BMC BIOINFORMATICS

An AT-Hook Domain in MeCP2 Determines the Clinical Course of Rett Syndrome and Related Disorders

(2013) Steven Andrew Baker et al.   CELL

An inducible transgene expression system for zebrafish and chick

(2013) S. S. Gerety et al.   DEVELOPMENT

Design, evaluation, and screening methods for efficient targeted mutagenesis with transcription activator-like effector nucleases in medaka

(2013) Satoshi Ansai et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

The emerging use of zebrafish to model metabolic disease

(2013) A. Seth et al.   Disease Models & Mechanisms

Swimming into prominence: the zebrafish as a valuable tool for studying human myopathies and muscular dystrophies

(2013) Elizabeth M. Gibbs et al.   FEBS Journal

Targeted chromosomal deletions and inversions in zebrafish

(2013) A. Gupta et al.   GENOME RESEARCH

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Mechanisms of Disease-Causing Missense Mutations

(2013) Shannon Stefl et al.   JOURNAL OF MOLECULAR BIOLOGY

GOASVM: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition

(2013) Shibiao Wan et al.   JOURNAL OF THEORETICAL BIOLOGY

Activity-dependent phosphorylation of MeCP2 threonine 308 regulates interaction with NCoR

(2013) Daniel H. Ebert et al.   NATURE

Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor

(2013) Matthew J Lyst et al.   NATURE NEUROSCIENCE

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP

(2013) Morten Bo Johansen et al.   PLoS One

Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System

(2013) Woong Y. Hwang et al.   PLoS One

Molecular Dynamic Simulation Reveals Damaging Impact of RAC1 F28L Mutation in the Switch I Region

(2013) Ambuj Kumar et al.   PLoS One

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Spontaneous Reactivation of Clusters of X-Linked Genes Is Associated with the Plasticity of X-Inactivation in Mouse Trophoblast Stem Cells

(2013) Agnès Dubois et al.   STEM CELLS

The CRISPR System—Keeping Zebrafish Gene Targeting Fresh

(2013) Patrick R. Blackburn et al.   Zebrafish

The first mecp2-null zebrafish model shows altered motor behaviors

(2013) Thomas Pietri et al.   Frontiers in Neural Circuits

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

(2013) Maria José Truco et al.   G3-Genes Genomes Genetics

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization

(2013) Rudi Agius et al.   PLoS Computational Biology

SNPdbe: constructing an nsSNP functional impacts database

(2012) C. Schaefer et al.   BIOINFORMATICS

Predicting folding free energy changes upon single point mutations

(2012) Zhe Zhang et al.   BIOINFORMATICS

WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms

(2012) S.-M. Chi et al.   BIOINFORMATICS

LocTree2 predicts localization for all domains of life

(2012) Tatyana Goldberg et al.   BIOINFORMATICS

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

Analyzing Effects of Naturally Occurring Missense Mutations

(2012) Zhe Zhang et al.   Computational and Mathematical Methods in Medicine

Response to: Statistical Analysis of Missense Mutation Classifiers

(2012) Vishal Acharya et al.   HUMAN MUTATION

Reverse Genetic Approaches in Zebrafish

(2012) Peng Huang et al.   Journal of Genetics and Genomics

Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

(2012) Dipali G. Sashital et al.   MOLECULAR CELL

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates

(2012) Khanh Dao Duc et al.   BMC Biophysics

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Functional studies of single-nucleotide polymorphic variants of human glutathione transferase T1-1 involving residues in the dimer interface

(2011) P. David Josephy et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

Functional Non-Synonymous Polymorphisms Prediction Methods: Current Approaches and Future Developments

(2011) M. Gonzalez-Castejon et al.   CURRENT MEDICINAL CHEMISTRY

Hansa: An automated method for discriminating disease and neutral human nsSNPs

(2011) Vishal Acharya et al.   HUMAN MUTATION

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function

(2011) Sonia Cohen et al.   NEURON

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

(2011) G. De Baets et al.   NUCLEIC ACIDS RESEARCH

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

The linear interaction energy method for the prediction of protein stability changes upon mutation

(2011) Lauren Wickstrom et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated Prediction of Protein Association Rate Constants

(2011) Sanbo Qin et al.   STRUCTURE

Zebrafish: An in vivo model for the study of neurological diseases

(2011) Jonathan Best   Neuropsychiatric Disease and Treatment

Monoclonal Antibodies Bind A SNP-Sensitive Epitope that is Present Uniquely in Mycobacterium avium Subspecies Paratuberculosis

(2011) John P. Bannantine et al.   Frontiers in Microbiology

Going from where to why—interpretable prediction of protein subcellular localization

(2010) Sebastian Briesemeister et al.   BIOINFORMATICS

Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

(2010) Vladimir Potapov et al.   BMC BIOINFORMATICS

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

(2010) Hanka Venselaar et al.   BMC BIOINFORMATICS

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

(2010) Shaolei Teng et al.   BMC GENOMICS

Transgenic zebrafish models of neurodegenerative diseases

(2010) Jonathan J. Sager et al.   Brain Structure & Function

Single-Nucleotide Polymorphisms Inside MicroRNA Target Sites Influence Tumor Susceptibility

(2010) Milena S. Nicoloso et al.   CANCER RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Waltz, an exciting new move in amyloid prediction

(2010) Mikael Oliveberg   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

YLoc—an interpretable web server for predicting subcellular localization

(2010) Sebastian Briesemeister et al.   NUCLEIC ACIDS RESEARCH

Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases

(2010) Ankit Gupta et al.   NUCLEIC ACIDS RESEARCH

AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

(2010) M. Masso et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Predicting kinetic constants of protein-protein interactions based on structural properties

(2010) Hongjun Bai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of subcellular locations of proteins: Where to proceed?

(2010) Kenichiro Imai et al.   PROTEOMICS

Microsphere-Based Rolling Circle Amplification Microarray for the Detection of DNA and Proteins in a Single Assay

(2009) Tania Konry et al.   ANALYTICAL CHEMISTRY

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

(2009) Michael Ryan et al.   BIOINFORMATICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence

(2009) S. O. Garbuzynskiy et al.   BIOINFORMATICS

svmPRAT: SVM-based Protein Residue Annotation Toolkit

(2009) Huzefa Rangwala et al.   BMC BIOINFORMATICS

Simple and efficient site-directed mutagenesis using two single-primer reactions in parallel to generate mutants for protein structure-function studies

(2009) Oded Edelheit et al.   BMC BIOTECHNOLOGY

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods

(2009) Janita Thusberg et al.   HUMAN MUTATION

SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins

(2009) Sebastian Briesemeister et al.   JOURNAL OF PROTEOME RESEARCH

Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression

(2009) Jinkuk Kim et al.   NATURE BIOTECHNOLOGY

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

(2009) Ayşegül Özen et al.   BMC STRUCTURAL BIOLOGY

Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction

(2009) Mati Cohen et al.   PLoS Computational Biology

The zinc-binding motif of human RECQ5β suppresses the intrinsic strand-annealing activity of its DExH helicase domain and is essential for the helicase activity of the enzyme

(2008) Hua Ren et al.   BIOCHEMICAL JOURNAL

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis

(2008) M. Masso et al.   BIOINFORMATICS

OnD-CRF: predicting order and disorder in proteins conditional random fields

(2008) L. Wang et al.   BIOINFORMATICS

Diagnostic criteria for the Zappella variant of Rett syndrome (the preserved speech variant)

(2008) A. Renieri et al.   BRAIN & DEVELOPMENT

The Zyggregator method for predicting protein aggregation propensities

(2008) Gian Gaetano Tartaglia et al.   CHEMICAL SOCIETY REVIEWS

Rett Syndrome-causing Mutations in Human MeCP2 Result in Diverse Structural Changes That Impact Folding and DNA Interactions

(2008) Rajarshi P. Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Predicting protein fold pattern with functional domain and sequential evolution information

(2008) Hong-Bin Shen et al.   JOURNAL OF THEORETICAL BIOLOGY

MicroRNA-10a Binds the 5′UTR of Ribosomal Protein mRNAs and Enhances Their Translation

(2008) Ulf Andersson Ørom et al.   MOLECULAR CELL

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Investigating genotype-phenotype relationships in Rett syndrome using an international data set

(2008) A. Bebbington et al.   NEUROLOGY

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays

(2008) S. Macgregor et al.   NUCLEIC ACIDS RESEARCH

Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding

(2008) Ye Yang et al.   NUCLEIC ACIDS RESEARCH

The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity

(2008) S. Gentile et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust prediction of mutation-induced protein stability change by property encoding of amino acids

(2008) S. Kang et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms

(2008) Tammy M. K. Cheng et al.   PLoS Computational Biology

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols

Electrostatic rate enhancement and transient complex of protein–protein association

(2007) Ramzi Alsallaq et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE