Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

(2021) Cesar L. Cuevas-Velazquez et al.   Nature Communications

Transcribed microsatellite allele lengths are often correlated with gene expression in natural sunflower populations

(2020) Chathurani Ranathunge et al.   MOLECULAR ECOLOGY

A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis

(2020) Jae-Hoon Jung et al.   NATURE

Early Light-Inducible Protein (ELIP) Can Enhance Resistance to Cold-Induced Photooxidative Stress in Chlamydomonas reinhardtii

(2020) Ji Woong Lee et al.   Frontiers in Physiology

Phenotypic and genome-wide association with the local environment of Arabidopsis

(2019) Ángel Ferrero-Serrano et al.   Nature Ecology & Evolution

Patterns of microsatellite distribution across eukaryotic genomes

(2019) Surabhi Srivastava et al.   BMC GENOMICS

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

(2019) Ole K Tørresen et al.   NUCLEIC ACIDS RESEARCH

ORANGE Represses Chloroplast Biogenesis in Etiolated Arabidopsis Cotyledons via Interaction with TCP14

(2019) Tianhu Sun et al.   PLANT CELL

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

(2018) Ole K. Tørresen et al.   BMC GENOMICS

Massive variation of short tandem repeats with functional consequences across strains ofArabidopsis thaliana

(2018) Maximilian O. Press et al.   GENOME RESEARCH

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Phasome analysis of pathogenic and commensal Neisseria species expands the known repertoire of phase variable genes, and highlights common adaptive strategies

(2018) Joseph J. Wanford et al.   PLoS One

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genome-wide profiling of heritable and de novo STR variations

(2017) Thomas Willems et al.   NATURE METHODS

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Molecular recognition features (MoRFs) in three domains of life

(2016) Jing Yan et al.   Molecular BioSystems

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

(2016) Aleena Francis et al.   Scientific Reports

Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

(2015) Rita Gemayel et al.   MOLECULAR CELL

High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

(2015) Zhenling Peng et al.   NUCLEIC ACIDS RESEARCH

Circadian regulation of abiotic stress tolerance in plants

(2015) Jack Grundy et al.   Frontiers in Plant Science

Tools and Strategies to Match Peptide-Ligand Receptor Pairs

(2014) M. A. Butenko et al.   PLANT CELL

Development of Gateway Binary Vectors R4L1pGWB Possessing the Bialaphos Resistance Gene (bar) and the Tunicamycin Resistance Gene as Markers for Promoter Analysis in Plants

(2013) Yuji TANAKA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

(2012) Fatemeh Miri Disfani et al.   BIOINFORMATICS

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

ESpritz: accurate and fast prediction of protein disorder

(2011) Ian Walsh et al.   BIOINFORMATICS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Uncertainty analysis in protein disorder prediction

(2011) Mohamed F. Ghalwash et al.   Molecular BioSystems

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Development of Gateway Binary Vectors, R4L1pGWBs, for Promoter Analysis in Higher Plants

(2009) Shinya NAKAMURA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Stem Cell Signaling in Arabidopsis Requires CRN to Localize CLV2 to the Plasma Membrane

(2009) A. Bleckmann et al.   PLANT PHYSIOLOGY

Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins

(2009) Michelle Simon et al.   GENOME BIOLOGY