Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Zinc chelation and Klf9 knockdown cooperatively promote axon regeneration after optic nerve injury

(2018) Ephraim F. Trakhtenberg et al.   EXPERIMENTAL NEUROLOGY

Intrinsic mechanisms of neuronal axon regeneration

(2018) Marcus Mahar et al.   NATURE REVIEWS NEUROSCIENCE

Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys

(2018) Paige E. Herman et al.   Scientific Reports

An Antagonistic Axon-Dendrite Interplay Enables Efficient Neuronal Repair in the Adult Zebrafish Central Nervous System

(2018) An Beckers et al.   MOLECULAR NEUROBIOLOGY

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

(2017) Aaron C. Daugherty et al.   GENOME RESEARCH

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Boosting Central Nervous System Axon Regeneration by Circumventing Limitations of Natural Cytokine Signaling

(2016) Marco Leibinger et al.   MOLECULAR THERAPY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program

(2016) Vijayendran Chandran et al.   NEURON

Matrix metalloproteinases as promising regulators of axonal regrowth in the injured adult zebrafish retinotectal system

(2015) Kim Lemmens et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Injury-Induced Decline of Intrinsic Regenerative Ability Revealed by Quantitative Proteomics

(2015) Stephane Belin et al.   NEURON

Subtype-Specific Regeneration of Retinal Ganglion Cells following Axotomy: Effects of Osteopontin and mTOR Signaling

(2015) Xin Duan et al.   NEURON

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Active mechanistic target of rapamycin plays an ancillary rather than essential role in zebrafish CNS axon regeneration

(2015) Heike Diekmann et al.   Frontiers in Cellular Neuroscience

Characterization of optic nerve regeneration using transgenic zebrafish

(2015) Heike Diekmann et al.   Frontiers in Cellular Neuroscience

Connecting the Retina to the Brain

(2014) Lynda Erskine et al.   ASN Neuro

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Jak/Stat Signaling Stimulates Zebrafish Optic Nerve Regeneration and Overcomes the Inhibitory Actions of Socs3 and Sfpq

(2014) F. Elsaeidi et al.   JOURNAL OF NEUROSCIENCE

Tcf3 promotes cell migration and wound repair through regulation of lipocalin 2

(2014) Qi Miao et al.   Nature Communications

Three-dimensional evaluation of retinal ganglion cell axon regeneration and pathfinding in whole mouse tissue after injury

(2013) Xueting Luo et al.   EXPERIMENTAL NEUROLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Neuronal c-Jun is required for successful axonal regeneration, but the effects of phosphorylation of its N-terminus are moderate

(2012) Crystal A. Ruff et al.   JOURNAL OF NEUROCHEMISTRY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Sustained axon regeneration induced by co-deletion of PTEN and SOCS3

(2011) Fang Sun et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transcriptional regulatory regions of gap43 needed in developing and regenerating retinal ganglion cells

(2009) Brandon W. Kusik et al.   DEVELOPMENTAL DYNAMICS

SOCS3 Deletion Promotes Optic Nerve Regeneration In Vivo

(2009) Patrice D. Smith et al.   NEURON

3.6kb Genomic sequence from Takifugu capable of promoting axon growth-associated gene expression in developing and regenerating zebrafish neurons

(2008) Ava J. Udvadia   GENE EXPRESSION PATTERNS

Changes of phospho-growth-associated protein 43 (phospho-GAP43) in the zebrafish retina after optic nerve injury: A long-term observation

(2008) Manabu Kaneda et al.   NEUROSCIENCE RESEARCH

Promoting Axon Regeneration in the Adult CNS by Modulation of the PTEN/mTOR Pathway

(2008) K. K. Park et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY