Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures

Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility

(2020) Viola Volpato et al.   Disease Models & Mechanisms

ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair

(2019) Joseph R. Klim et al.   NATURE NEUROSCIENCE

Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

(2019) Ze’ev Melamed et al.   NATURE NEUROSCIENCE

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

(2019) Julien Delile et al.   DEVELOPMENT

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

(2019) Jellert T. Gaublomme et al.   Nature Communications

Motor Neuron Susceptibility in ALS/FTD

(2019) Audrey M. G. Ragagnin et al.   Frontiers in Neuroscience

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods

(2019) Monika Krzak et al.   Frontiers in Genetics

Transcriptome–pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS

(2018) Florian Krach et al.   ACTA NEUROPATHOLOGICA

TDP-43 regulates the alternative splicing of hnRNP A1 to yield an aggregation-prone variant in amyotrophic lateral sclerosis

(2018) Jade-Emmanuelle Deshaies et al.   BRAIN

Amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease (AD) are characterised by differential activation of ER stress pathways: focus on UPR target genes

(2018) L. Montibeller et al.   CELL STRESS & CHAPERONES

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons

(2018) Yingxiao Shi et al.   NATURE MEDICINE

Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior

(2018) Anupama Sathyamurthy et al.   Cell Reports

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

Modeling sporadic ALS in iPSC-derived motor neurons identifies a potential therapeutic agent

(2018) Koki Fujimori et al.   NATURE MEDICINE

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

14-3-3 eta isoform colocalizes TDP-43 on the coarse granules in the anterior horn cells of patients with sporadic amyotrophic lateral sclerosis

(2016) Takahiko Umahara et al.   BRAIN RESEARCH

Decoding ALS: from genes to mechanism

(2016) J. Paul Taylor et al.   NATURE

ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks

(2016) Ritchie Ho et al.   NATURE NEUROSCIENCE

Cerebellar c9RAN proteins associate with clinical and neuropathological characteristics of C9ORF72 repeat expansion carriers

(2015) Tania F. Gendron et al.   ACTA NEUROPATHOLOGICA

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Molecular and cellular development of spinal cord locomotor circuitry

(2015) Daniel C. Lu et al.   Frontiers in Molecular Neuroscience

Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm

(2015) Ethan S. Lippmann et al.   Stem Cell Reports

Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1

(2014) Evangelos Kiskinis et al.   Cell Stem Cell

Combinatorial analysis of developmental cues efficiently converts human pluripotent stem cells into multiple neuronal subtypes

(2014) Yves Maury et al.   NATURE BIOTECHNOLOGY

The phenotypic variability of amyotrophic lateral sclerosis

(2014) Bart Swinnen et al.   Nature Reviews Neurology

Discovery of a Biomarker and Lead Small Molecules to Target r(GGGGCC)-Associated Defects in c9FTD/ALS

(2014) Zhaoming Su et al.   NEURON

A Quantitative Framework to Evaluate Modeling of Cortical Development by Neural Stem Cells

(2014) Jason L. Stein et al.   NEURON

Loss of nuclear TDP-43 in amyotrophic lateral sclerosis (ALS) causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurones

(2014) J. Robin Highley et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis

(2013) Giovanni Nardo et al.   BRAIN

A Small Molecule Screen in Stem-Cell-Derived Motor Neurons Identifies a Kinase Inhibitor as a Candidate Therapeutic for ALS

(2013) Yin M. Yang et al.   Cell Stem Cell

Hoxgenes and region-specific sensorimotor circuit formation in the hindbrain and spinal cord

(2013) Maria Di Bonito et al.   DEVELOPMENTAL DYNAMICS

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Neuronatin gene: Imprinted and misfolded

(2013) Rajiv Madathiparambil Joseph   GENOMICS

Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS

(2013) Hong Joo Kim et al.   NATURE

Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization

(2013) Polyxeni Philippidou et al.   NEURON

Targeting RNA Foci in iPSC-Derived Motor Neurons from ALS Patients with a C9ORF72 Repeat Expansion

(2013) D. Sareen et al.   Science Translational Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis

(2011) Janine Kirby et al.   BRAIN

SnapShot: Spinal Cord Development

(2011) William A. Alaynick et al.   CELL

Isl1 Is required for multiple aspects of motor neuron development

(2011) Xingqun Liang et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Mutations in CHMP2B in Lower Motor Neuron Predominant Amyotrophic Lateral Sclerosis (ALS)

(2010) Laura E. Cox et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Pattern of spread and prognosis in lower limb-onset ALS

(2009) Martin R. Turner et al.   Amyotrophic Lateral Sclerosis

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients

(2009) Christiaan GJ Saris et al.   BMC GENOMICS

Sporadic ALS has compartment-specific aberrant exon splicing and altered cell–matrix adhesion biology

(2009) Stuart J. Rabin et al.   HUMAN MOLECULAR GENETICS

Herp enhances ER-associated protein degradation by recruiting ubiquilins

(2008) Tae-Yeon Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Identification of Phox2b-regulated genes by expression profiling of cranial motoneuron precursors

(2008) Patrick Pla et al.   Neural Development