Spatiotemporal, optogenetic control of gene expression in organoids

Tumor organoids: applications in cancer modeling and potentials in precision medicine

(2022) Hanxiao Xu et al.   Journal of Hematology & Oncology

Museum of spatial transcriptomics

(2022) Lambda Moses et al.   NATURE METHODS

Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

(2021) Xitiz Chamling et al.   Nature Communications

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

(2021) Emanuel Wyler et al.   iScience

Single-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific features

(2021) Teresa Rayon et al.   DEVELOPMENT

Human brain organogenesis: Toward a cellular understanding of development and disease

(2021) Kevin W. Kelley et al.   CELL

Self-organization of human dorsal-ventral forebrain structures by light induced SHH

(2021) Riccardo De Santis et al.   Nature Communications

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

(2019) Julien Delile et al.   DEVELOPMENT

Specification of positional identity in forebrain organoids

(2019) Gustav Y. Cederquist et al.   NATURE BIOTECHNOLOGY

Commissural axon guidance in the developing spinal cord: from Cajal to the present day

(2019) J. D. Comer et al.   Neural Development

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Dorsal-ventral patterned neural cyst from human pluripotent stem cells in a neurogenic niche

(2019) Y. Zheng et al.   Science Advances

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Morphogen gradient reconstitution reveals Hedgehog pathway design principles

(2018) Pulin Li et al.   SCIENCE

Genome-wide analysis of PDX1 target genes in human pancreatic progenitors

(2018) Xianming Wang et al.   Molecular Metabolism

Three-dimensional induction of dorsal, intermediate and ventral spinal cord tissues from human pluripotent stem cells

(2018) Takenori Ogura et al.   DEVELOPMENT

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development

(2018) Sueli Marques et al.   DEVELOPMENTAL CELL

Light Control of the Tet Gene Expression System in Mammalian Cells

(2018) Mayumi Yamada et al.   Cell Reports

PiGx: reproducible genomics analysis pipelines with GNU Guix

(2018) Ricardo Wurmus et al.   GigaScience

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

CRISPR–Cas9-based photoactivatable transcription systems to induce neuronal differentiation

(2017) Yuta Nihongaki et al.   NATURE METHODS

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs

(2016) Eva Kutejova et al.   DEVELOPMENTAL CELL

CRISPR-Cas9-based Photoactivatable Transcription System

(2015) Yuta Nihongaki et al.   CHEMISTRY & BIOLOGY

Proteomics Quality Control: Quality Control Software for MaxQuant Results

(2015) Chris Bielow et al.   JOURNAL OF PROTEOME RESEARCH

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

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

(2013) Polyxeni Philippidou et al.   NEURON

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Improved Tet-responsive promoters with minimized background expression

(2010) Rainer Loew et al.   BMC BIOTECHNOLOGY

Establishing and Interpreting Graded Sonic Hedgehog Signaling during Vertebrate Neural Tube Patterning: The Role of Negative Feedback

(2009) V. Ribes et al.   Cold Spring Harbor Perspectives in Biology