satijalab.org

Satija Lab

Welcome to the Satija Lab. Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually - a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors. We’re located at the New York Genome Center. Christoph designed our " How many cells.

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Satija Lab | satijalab.org Reviews

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Welcome to the Satija Lab. Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually - a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors. We’re located at the New York Genome Center. Christoph designed our How many cells.

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Satija Lab | satijalab.org Reviews

https://satijalab.org

Welcome to the Satija Lab. Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually - a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors. We’re located at the New York Genome Center. Christoph designed our " How many cells.

INTERNAL PAGES

satijalab.org

1

How Many Cells

http://satijalab.org/howmanycells

How many cells do we need to sample so that we see at least n cells of each type? This depends on the number of cell type present and the diversity, i.e. the entropy. When entropy is very low, few or one cell type dominates the population and all other types are present at low fractions. We assume the worst case scenario - one cell type dominates the population. For every type the number of cells in the population is much larger than the minimum number of cells desired in the sample. This website was cre...

2

People

http://satijalab.org/people

D Phil, Statistics. Joint w/Gord Fishell, NYUMC. University of Hamburg, Germany. Diplom, University of Konstanz, Germany. Joint w/Dan Littman, NYUMC. Hong Kong University of Science and Technology. PhD, Biomedical Sciences. KU Leuven - University of Leuven, Belgium. Flemish Institute for Biotechnology (VIB). University of Texas at Austin. BA, Biological Sciences. BS, Cell Biology. The College of New Jersey.

3

Publications

http://satijalab.org/publications

Breton G, Zheng S, Valieris R, da Silva IT, Satija R, Nussenzweig MC. Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c or CD141 DCs. Journal of Experimental Medicine. Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin, B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO. A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells. Avraham R, Hasele...

4

News

http://satijalab.org/news

Christoph designed our " How many cells. Tool, to help think about experimental design. The lab has been selected for the 2016 NIH New Innovator Award. We’re looking forward to growing and are recruiting postdocs! Check out our webinar with Nature and 10X genomics: " Defining the immune system at single cell resolution with Seurat. Lana Harshman and Jan Slabbaert join the lab! Interested in single cell genomics but need help getting started?

5

Seurat

http://satijalab.org/seurat

Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction (PCA, ICA, t-SNE), standard unsupervised clustering algorithms (density clustering, hierarchical clustering, k-means), and the discovery of differentially expressed genes and markers. Seurat also features two recently developed computational methods for single cell analysis:.

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cgsb.as.nyu.edu

Faculty | Center for Genomics and Systems Biology | NYU

http://cgsb.as.nyu.edu/page/faculty

COLLEGE OF ARTS AND SCIENCE. GRADUATE SCHOOL OF ARTS AND SCIENCE. Campaign for the Center. NYU Department of Biology. Kenneth D. Birnbaum. Associate Professor of Biology. Faculty Director of the Cellular Analysis Core. PhD 2000 (Biology), New York University; M.S. 1993 (Environmental Science), University of Wisconsin; B.A. 1984 (Biology/English), University of Pennsylvania. Email: ken.birnbaum@nyu.edu. List of Publications from Pubmed. Richard A. Bonneau. Faculty Director of Bioinformatics. Director, Cen...

biology.fas.nyu.edu

Faculty | Department of Biology | New York University

http://www.biology.fas.nyu.edu/page/people

COLLEGE OF ARTS AND SCIENCE. GRADUATE SCHOOL OF ARTS AND SCIENCE. Faculty in New York. Efrain C. Azmitia. Professor of Biology and Neural Science. Neuroplasticity of the brain regulated by neuronal serotonin and glial S-100 protein. Kenneth D. Birnbaum. Associate Professor of Biology. Faculty Director of the Cellular Analysis Core. Director, PhD Program. Developmental and evolutionary genomics of plants. The origin and genetic programming of cell types. Professor of Biology and Neural Science. Chromatin,...

biology.as.nyu.edu

Faculty | Department of Biology | New York University

http://biology.as.nyu.edu/page/people

COLLEGE OF ARTS AND SCIENCE. GRADUATE SCHOOL OF ARTS AND SCIENCE. Faculty in New York. Efrain C. Azmitia. Professor of Biology and Neural Science. Neuroplasticity of the brain regulated by neuronal serotonin and glial S-100 protein. Kenneth D. Birnbaum. Associate Professor of Biology. Faculty Director of the Cellular Analysis Core. Developmental and evolutionary genomics of plants. The origin and genetic programming of cell types. Professor of Biology and Neural Science. Director, PhD Program. Transcript...

radiant-project.eu

C1omics2015

http://radiant-project.eu/C1omics2015.html

Located in a new state of the art research facility housing the Manchester Cancer Research Centre. This workshop aims to bring together biomedical researchers, technological innovators and data scientists working on single-cell omics methodologies and applications. Workshop speakers include:. ETH Swiss Federal Institute of Technology, Zurich. Babraham Institute, Cambridge. Cancer Research UK Manchester Institute. European Molecular Biology Laboratory, Heidelberg. Best Western Willow Bank. A number of bus...

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Welcome to the Satija Lab. Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually - a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors. We’re located at the New York Genome Center. Christoph designed our " How many cells.

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