cole-trapnell-lab.github.io cole-trapnell-lab.github.io

cole-trapnell-lab.github.io

trapnell lab

The Trapnell Lab at the University of Washington's Department of Genome Sciences. Studies cell differentiation, reprogramming, and other transitions between stable or metastable cellular states. We also study the role of cell-cell communication in governing these processes. We aim to identify genes that control cellular transitions, primarily using single-cell genomics. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Posted 16 Jul 2015. Posted 07 May 2015.

http://cole-trapnell-lab.github.io/

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The Trapnell Lab at the University of Washington's Department of Genome Sciences. Studies cell differentiation, reprogramming, and other transitions between stable or metastable cellular states. We also study the role of cell-cell communication in governing these processes. We aim to identify genes that control cellular transitions, primarily using single-cell genomics. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Posted 16 Jul 2015. Posted 07 May 2015.
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trapnell lab | cole-trapnell-lab.github.io Reviews

https://cole-trapnell-lab.github.io

The Trapnell Lab at the University of Washington's Department of Genome Sciences. Studies cell differentiation, reprogramming, and other transitions between stable or metastable cellular states. We also study the role of cell-cell communication in governing these processes. We aim to identify genes that control cellular transitions, primarily using single-cell genomics. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Posted 16 Jul 2015. Posted 07 May 2015.

INTERNAL PAGES

cole-trapnell-lab.github.io cole-trapnell-lab.github.io
1

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

http://cole-trapnell-lab.github.io/papers/cusanovich

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Darren A. Cusanovich, Riza Daza, Andrew Adey, Hannah Pliner, Lena Christiansen, Kevin L. Gunderson, Frank J. Steemers, Cole Trapnell, Jay Shendure 2015.

2

Join

http://cole-trapnell-lab.github.io/misc/join

The lab has open positions for graduate students and postdocs. If you’d like to join the Trapnell lab, please get in touch. Graduate students from the Genome Sciences. Programs of the University of Washington. Can join the group. Students from other departments are welcome as well, although co-mentorship with a department faculty member may be required. Rotation students are welcome.

3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

http://cole-trapnell-lab.github.io/papers/silverman-rnase-footprinting

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Ian M Silverman, Fan Li, Anissa Alexander, Loyal Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory. 2014.

4

trapnell lab / papers

http://cole-trapnell-lab.github.io/papers

Single-cell transcriptome sequencing recent advances and remaining challenges. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Hanchate et al. 2015. Defining cell types and states with single-cell genomics. Genome Research 25: 1491-1498. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cacciarelli, Trapnell, and Ziller et al. 2015. Cell 162:2 412 424. Cusanovich et al. 2015. Pulmonary macrophage transplantation therapy.

5

Cufflinks

http://cole-trapnell-lab.github.io/cufflinks

Transcriptome assembly and differential expression analysis for RNA-Seq. Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. December 10, 2014. December...

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LINKS TO THIS WEBSITE

salzberg-lab.org salzberg-lab.org

Older Lab News | Salzberg Lab

https://salzberg-lab.org/about/older-lab-news

Computational biology and genomics @JHU. Opinion pieces and editorials. December 2015. Steven Salzberg is named a Highly Cited Researcher. By Thomson Reuters, in the areas of both computer science and microbiology. October 2015. Postdocs Daehwan Kim and Florian Breitwieser each give plenary talks at the 2015 Genome Informatics Conference at Cold Spring Harbor Laboratory. June 1, 2015. NSF awards a new 3-year research grant to Mihaela Pertea for her work on transcriptome reconstruction. Sept 2014. Pos...

cmb.washington.edu cmb.washington.edu

Computational Molecular Biology program

http://cmb.washington.edu/faculty.htm

UW Computational Molecular Biology. Akeyj [ a t ] u.washington.edu. UW Biochemistry; Adjunct UW Genome Sciences, Bioengineering, Computer Science and Engineering, Chemical Engineering, and Physics. Dabaker [ a t ] u.washington.edu. UW Bioengineering; Adjunct UW Radiology. Jbb2 [ a t ] uw.edu. FHCRC; Affiliate UW Epidemiology. Trevor [ a t ] bedford.io. Cbergst [ a t ] uw.edu. FHCRC Basic Sciences; Affiliate UW Genome Sciences. Jbloom [ a t ] fhcrc.org. Hbolouri [ a t ] fhcrc.org. Rogerb [ a t ] uw.edu.

bioconductor.org bioconductor.org

Bioconductor - BioC 2015: Where Software and Biology Connect

http://bioconductor.org/BioC2015

BioC 2015: Where Software and Biology Connect. BioC 2015: Where Software and Biology Connect. July 21-22, 2015 (Developer Day: July 20). Fred Hutchinson Cancer Research Center, Seattle, WA. To launch an Amazon Machine Image (AMI) for this conference:. Create an Amazon Web Services (AWS) Account. If you don’t already have one. Start the instance ami-b1f221da. See the documentation for this. Make sure your security group. Has port 80 accessible. Paste the Public DNS name of your instance into a web browser.

pedsfellowship.fhcrc.org pedsfellowship.fhcrc.org

Mentors — The Children's/UW/Hutchinson Center Pediatric Hematology-Oncology Fellowship Program

http://pedsfellowship.fhcrc.org/people/mentors

The Children's/UW/Hutchinson Center Pediatric Hematology-Oncology Fellowship Program. A World-Class Pediatric Hematology-Oncology Research and Training Collaboration between Seattle Children's Hospital, the University of Washington, and Fred Hutchinson Cancer Research Center. Maya Hughes, MD. Christopher Lux, MD PhD. Agne Taraseviciute, MD PhD. Raghav Chawla, MD PhD. Wayne Liang, MD. Julie Rivers, MD. Allie Kaeding, MD. Tyler Ketterl, MD. Jamie Stokke, MD. Living in the NW. August 31, 2016. Colleen Delan...

gs.washington.edu gs.washington.edu

UW Genome Sciences: Faculty

http://www.gs.washington.edu/faculty/index.htm

Population genetics and molecular evolution. Akeyj [ a t ] uw.edu. Caberg [ a t ] uw.edu. Computational systems biology; metagenomics; human microbiome; complex networks. Elbo [ a t ] uw.edu. A t ] uw.edu. Proteomics, mass spectrometry and advanced technology development. T ] uw.edu. Yeast genetics and evolution. Maitreya [ a t ] uw.edu. Human genomics and molecular evolution. A t ] gs.washington.edu. Evolution; no longer taking graduate students. A t ] gs.washington.edu. A t ] uw.edu. A t ] uw.edu.

salzberg-lab.org salzberg-lab.org

Lab Members | Salzberg Lab

https://salzberg-lab.org/lab-members

Computational biology and genomics @JHU. Opinion pieces and editorials. Steven Salzberg, Ph.D. Bloomberg Distinguished Professor of Biomedical Engineering. Mihaela Pertea, Ph.D. Associate Professor of Medicine and Computer Science. Art Delcher, Ph.D. Adjunct Professor (retired as of July 1, 2016). Aleksey Zimin, Ph.D. Adjunct Associate Research Scientist. Geo Pertea, M.S., M.D. Bioinformatics Engineer and Senior Software Engineer. Daniela Puiu, M.S. Bioinformatics Engineer and Senior Software Engineer.

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trapnell lab

The Trapnell Lab at the University of Washington's Department of Genome Sciences. Studies cell differentiation, reprogramming, and other transitions between stable or metastable cellular states. We also study the role of cell-cell communication in governing these processes. We aim to identify genes that control cellular transitions, primarily using single-cell genomics. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Posted 16 Jul 2015. Posted 07 May 2015.

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