Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions

[1]  Yīmíng Bào,et al.  Molecular evolutionary analysis of human primary microcephaly genes , 2021, BMC ecology and evolution.

[2]  Syed Shujait Ali,et al.  Phylogenetic Analysis and Structural Perspectives of RNA-Dependent RNA-Polymerase Inhibition from SARs-CoV-2 with Natural Products , 2020, Interdisciplinary Sciences: Computational Life Sciences.

[3]  V. Pande,et al.  Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase , 2020, Journal of biomolecular structure & dynamics.

[4]  Rabail Zehra,et al.  Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population , 2018, Genome biology and evolution.

[5]  R. Gainetdinov,et al.  Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development , 2017, Genome biology and evolution.

[6]  S. Bissière,et al.  Long-Lived Binding of Sox2 to DNA Predicts Cell Fate in the Four-Cell Mouse Embryo , 2017, Mechanisms of Development.

[7]  Helen M. Berman,et al.  DNAproDB: an interactive tool for structural analysis of DNA–protein complexes , 2017, Nucleic Acids Res..

[8]  W. Huttner,et al.  Human-specific genomic signatures of neocortical expansion , 2017, Current Opinion in Neurobiology.

[9]  J. Wysocka,et al.  Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution , 2016, Cell.

[10]  Axel Visel,et al.  Progressive Loss of Function in a Limb Enhancer during Snake Evolution , 2016, Cell.

[11]  Soher Balkhy,et al.  Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior , 2016, Cell.

[12]  N. Shubin,et al.  Regulatory evolution of Tbx5 and the origin of paired appendages , 2016, Proceedings of the National Academy of Sciences.

[13]  Valeria Levi,et al.  Long-Lived Binding of Sox2 to DNA Predicts Cell Fate in the Four-Cell Mouse Embryo , 2016, Cell.

[14]  G C P van Zundert,et al.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. , 2016, Journal of molecular biology.

[15]  R. Myers,et al.  Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins , 2016, Cell.

[16]  J. Capra,et al.  The evolution of the human genome. , 2015, Current opinion in genetics & development.

[17]  Y. Kawakami,et al.  Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development , 2015, Development, growth & differentiation.

[18]  F. Gage,et al.  Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest , 2015, Cell.

[19]  R. Gordân,et al.  Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex , 2015, Current Biology.

[20]  J. Akey,et al.  Complex history of admixture between modern humans and Neandertals. , 2015, American journal of human genetics.

[21]  Katherine S Pollard,et al.  Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. , 2014, Current opinion in genetics & development.

[22]  Philip L. F. Johnson,et al.  The complete genome sequence of a Neandertal from the Altai Mountains , 2013, Nature.

[23]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[24]  H. Burbano,et al.  A recent evolutionary change affects a regulatory element in the human FOXP2 gene. , 2013, Molecular biology and evolution.

[25]  G. Bejerano,et al.  Enhancers: five essential questions , 2013, Nature Reviews Genetics.

[26]  Ross C. Walker,et al.  An overview of the Amber biomolecular simulation package , 2013 .

[27]  Hani Z. Girgis,et al.  A High-Resolution Enhancer Atlas of the Developing Telencephalon , 2013, Cell.

[28]  Nadav Ahituv,et al.  Function and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution , 2013, PLoS genetics.

[29]  A. Masood,et al.  Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers , 2013, BMC Genomics.

[30]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[31]  Dmitri I. Svergun,et al.  WeNMR: Structural Biology on the Grid , 2011, Journal of Grid Computing.

[32]  Giorgio Manzi,et al.  Evolution of the base of the brain in highly encephalized human species. , 2011, Nature communications.

[33]  Alexandre M. J. J. Bonvin,et al.  CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK , 2011, PloS one.

[34]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[35]  Alex A. Pollen,et al.  Human-specific loss of regulatory DNA and the evolution of human-specific traits , 2011, Nature.

[36]  M. Levine.  Transcriptional Enhancers in Animal Development and Evolution , 2010, Current Biology.

[37]  Inanç Birol,et al.  The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. , 2010, Genome research.

[38]  Evgeny B. Krissinel,et al.  Crystal contacts as nature's docking solutions , 2010, J. Comput. Chem..

[39]  Bert L. de Groot,et al.  Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations , 2010, PLoS Comput. Biol..

[40]  Alexandre M. J. J. Bonvin,et al.  3D-DART: a DNA structure modelling server , 2009, Nucleic Acids Res..

[41]  O. V. Galzitskaya,et al.  Radius of gyration as an indicator of protein structure compactness , 2008, Molecular Biology.

[42]  Sean B. Carroll,et al.  The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species , 2008, Cell.

[43]  A. Visel,et al.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers , 2008, Nature Genetics.

[44]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[45]  L. Hellman,et al.  Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions , 2007, Nature Protocols.

[46]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[47]  Gregory A Voth,et al.  Modeling real dynamics in the coarse-grained representation of condensed phase systems. , 2006, The Journal of chemical physics.

[48]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[49]  D. Kleinjan,et al.  Long-range control of gene expression: emerging mechanisms and disruption in disease. , 2005, American journal of human genetics.

[50]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[51]  G. Marius Clore,et al.  Molecular Basis for Synergistic Transcriptional Activation by Oct1 and Sox2 Revealed from the Solution Structure of the 42-kDa Oct1·Sox2·Hoxb1-DNA Ternary Transcription Factor Complex* , 2004, Journal of Biological Chemistry.

[52]  Matthias Wilmanns,et al.  Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. , 2003, Genes & development.

[53]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[54]  M. Bianchi,et al.  Spatially Precise DNA Bending Is an Essential Activity of the Sox2 Transcription Factor* , 2001, The Journal of Biological Chemistry.

[55]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[56]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[57]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[58]  A. Cooper,et al.  Thermodynamic fluctuations in protein molecules. , 1976, Proceedings of the National Academy of Sciences of the United States of America.