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Nir Yosef | Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley

I am an Assistant professor at the Department of EECS and a member of the Center for Computational Biology at UC Berkeley. I started my research group in January of 2014 after spending some time as a postdoc at the Broad Institute and Harvard medical school. The overarching goal of my research is to utilize high-throughput genomic data…

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Nir Yosef | Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley | niryosef.wordpress.com Reviews

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I am an Assistant professor at the Department of EECS and a member of the Center for Computational Biology at UC Berkeley. I started my research group in January of 2014 after spending some time as a postdoc at the Broad Institute and Harvard medical school. The overarching goal of my research is to utilize high-throughput genomic data…

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Nir Yosef | Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley | niryosef.wordpress.com Reviews

https://niryosef.wordpress.com

I am an Assistant professor at the Department of EECS and a member of the Center for Computational Biology at UC Berkeley. I started my research group in January of 2014 after spending some time as a postdoc at the Broad Institute and Harvard medical school. The overarching goal of my research is to utilize high-throughput genomic data…

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CMPBIO290 | Nir Yosef

https://niryosef.wordpress.com/teaching/cmpbio290

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. DE with an impulse model. Special topics course in computational molecular biology (CS294-108, CMPBIO290). A graduate seminar class that covers recent computational methods for modeling various mechanisms related to the regulation of gene expression, primarily based on high throughput sequencing data. 177 Stanley. Tues and Thurs from 5:00-6:30pm. This year’s Syllabus. Inference of transcriptional reg...

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Group | Nir Yosef

https://niryosef.wordpress.com/group

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. DE with an impulse model. Graduate Student (CB); joint with Rasmus Nielsen. Graduate Student (EECS); joint with Ras Bodik. Carlos Buen Abad Najar. Graduate Student (CB); joint with Liana Lareau. Graduate Student (EECS); joint with Anthony Joseph. Blog at WordPress.com.

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Software | Nir Yosef

https://niryosef.wordpress.com/tools

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. DE with an impulse model. FastProject uses gene sets to analyze low-dimensional projections of single-cell RNAseq expression data. Learn More. ImpulseDE2 and ImpulseDE use a single-impulse functional model to identify genes that are differentially expressed in a single time course (across time) or between two time courses. Find out more. Create a free website or blog at WordPress.com.

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FastProject | Nir Yosef

https://niryosef.wordpress.com/tools/fastproject

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. DE with an impulse model. DeTomaso D., Yosef, N., “FastProject: A Tool for Low-Dimensional Analysis of. Single-Cell RNA-Seq Data”, 2016. Detailed installation instructions for Windows, OSX, and Linux are documented Here. For more instructions on how to run/configure the software see the FastProject Wiki. The latest copy of the FastProject source can be found at the project’s Official Repository.

5

SCONE | Nir Yosef

https://niryosef.wordpress.com/tools/scone

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. DE with an impulse model. SCONE (Single-Cell Overview of Normalized Expression) is an R Biodconductor package. That supports a rational, data-driven framework for assessing the efficacy of various normalization workflows, encouraging users to explore trade-offs inherent to their data set prior to finalizing a data normalization strategy. We provide an interface for running multiple normalization ...

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Education | MIEP

http://www.modelingimmunity.org/education/summer-school-symposium

Computational Immunology: Models and Tools. 2014 Summer School and Symposium on Computational Immunity. COMPUTATIONAL IMMUNOLOGY: Models and Tools. 1st Ed. This book provides an applied approach to generating and refining hypotheses using computational modeling and simulation studies, and is an ideal resource for immunologists, computational biologists, bioinformaticians, biotechnologists, and computer scientists. The book is based on the notes and presentations stemming from MIEP, a program that int...

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Nir Yosef | Department of Electrical Engineering & Computer Science, Center for Computational Biology, UC Berkeley

Department of Electrical Engineering and Computer Science, Center for Computational Biology, UC Berkeley. I am an Assistant professor at the Department of EECS and a member of the Center for Computational Biology at UC Berkeley. I started my research group in January of 2014 after spending some time as a postdoc at the Broad Institute. And Harvard medical school. Plasticity, and response to acute stimulation. Check out the publications. Page for a more complete survey of our research.

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