Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals

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Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals

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Expanding evolutionary neuroscience: insights from comparing variation in behavior

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A non-invasive method to generate induced pluripotent stem cells from primate urine

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Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

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(2021) J. B. Smaers et al.   Science Advances

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

(2021) Alexandro E. Trevino et al.   CELL

H3 acetylation selectively promotes basal progenitor proliferation and neocortex expansion

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Folding brains: from development to disease modeling

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Phylogenetics is the New Genetics (for Most of Biodiversity)

(2020) Stacey D. Smith et al.   TRENDS IN ECOLOGY & EVOLUTION

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

(2020) Christian D. Huber et al.   PLoS Genetics

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Trnp1 organizes diverse nuclear membrane‐less compartments in neural stem cells

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Human-specific ARHGAP11B increases size and folding of primate neocortex in the fetal marmoset

(2020) Michael Heide et al.   SCIENCE

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

(2018) Ikuo K. Suzuki et al.   CELL

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Developing in 3D: the role of CTCF in cell differentiation

(2018) Rodrigo G. Arzate-Mejía et al.   DEVELOPMENT

Insm1 Induces Neural Progenitor Delamination in Developing Neocortex via Downregulation of the Adherens Junction Belt-Specific Protein Plekha7

(2018) Stefania Tavano et al.   NEURON

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

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(2018) Risako Nakai et al.   Scientific Reports

UniProt: a worldwide hub of protein knowledge

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Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex

(2018) Nereo Kalebic et al.   eLife

Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates

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Beyond editing to writing large genomes

(2017) Raj Chari et al.   NATURE REVIEWS GENETICS

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

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Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

Primate brain size is predicted by diet but not sociality

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A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes

(2016) Emeric Figuet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Brain evolution and development: adaptation, allometry and constraint

(2016) Stephen H. Montgomery et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A restricted period for formation of outer subventricular zone defined by Cdh1 and Trnp1 levels

(2016) Maria Ángeles Martínez-Martínez et al.   Nature Communications

The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice

(2016) Xiang-Chun Ju et al.   eLife

Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex

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Evolutionary changes in promoter and enhancer activity during human corticogenesis

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Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

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Dual Effect of CTCF Loss on Neuroprogenitor Differentiation and Survival

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

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Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral Cortex by Control of Radial Glial Fate

(2013) Ronny Stahl et al.   CELL

Conical expansion of the outer subventricular zone and the role of neocortical folding in evolution and development

(2013) Eric Lewitus et al.   Frontiers in Human Neuroscience

Amplification of progenitors in the mammalian telencephalon includes a new radial glial cell type

(2013) Gregor-Alexander Pilz et al.   Nature Communications

The secondary loss of gyrencephaly as an example of evolutionary phenotypical reversal

(2013) Iva Kelava et al.   Frontiers in Neuroanatomy

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling

(2012) A. M. BODDY et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Functional primate genomics—leveraging the medical potential

(2012) Wolfgang Enard   JOURNAL OF MOLECULAR MEDICINE-JMM

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

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CTCF Promotes Muscle Differentiation by Modulating the Activity of Myogenic Regulatory Factors

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

The evolution of primate general and cultural intelligence

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A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

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The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL