Monthly Archives: September 2017
Here is the STAR Methods format (Structured, Transparent, Accessible Reporting) introduced last year by Cell, marketed as a structure that “promotes transparent reporting of experimental design and
methodological details.” Details are in the links below.
Editorial: http://www.cell.com/cell/fulltext/S0092-8674(16)31072-8 Instructions: http://www.cell.com/star-authors-guide
Two CBB events: Rafael Irizarry, Computational Biology and Bioinformatics speaker on 10-4-17
Dr. Rafael Irizarry from Harvard University will be the guest speaker.
Title: “Overcoming Bias and Batch Effects in single cell and bulk RNAseq Data”
Date: Wednesday, October 4, 2017
Time: 4:00 seminar 5:00 refreshments
Place: BML Auditorium, 310 Cedar Street
Hosted by: Steven Kleinstein, PhD
Flyer is attached for your review.
farnam pi_gerstein diskusage
total usage: 368 TB of 446 TB
Breaking Into The Brain | Chemical & Engineering News
Breaking Into the #Brain
http://CEN.ACS.org/articles/92/i2/Breaking-Brain.html Contrasts potential for drug discovery in neuro-diseases v #cancer (which is “easier”)
interesting brain v cancer contrast
Biostatistics Seminar: 9/26/17 – 12:00 Noon – LEPH 115
Please join the Biostatistics Seminar scheduled for Tuesday, September 26, 2017 at 12:00 Noon in LEPH 115.
Yale calendar Link: YSPH Biostatistics Seminar: “Constructing Tumor-Specific Gene Regulatory Networks Based on Samples with Tumor Purity Heterogeneity”
Speaker: Pei Wang, PhD
Institution: Icahn School of Medicine at Mount Sinai
Time & Place: 12:00 Noon in LEPH 115, 60 College St.
11:45 AM Lunch in LEPH 108
Title: “Constructing Tumor-Specific Gene Regulatory Networks Based on Samples with Tumor Purity Heterogeneity”
Tumor tissue samples often contain an unknown fraction of normal cells. This problem well known as tumor purity heterogeneity (TPH) was recently recognized as a severe issue in omics studies. Specifically, if TPH is ignored when inferring co-expression networks, edges are likely to be estimated among genes with mean shift between normal and tumor cells rather than among gene pairs interacting with each other in tumor cells. To address this issue, we propose TSNet a new method which constructs tumor-cell specific gene/protein co-expression networks based on gene/protein expression profiles of tumor tissues. TSNet treats the observed expression profile as a mixture of expressions from different cell types and explicitly models tumor purity percentage in each tumor sample. The advantage of TSNet over existing methods ignoring TPH is illustrated through extensive simulation examples. We then apply TSNet to estimate tumor specific co-expression networks based on breast cancer expression profiles. We identify novel co-expression modules and hub structure specific to tumor cells.
BIS Seminar Notice Sept 26_2017.pdf
Math-applied Applied Math/Analysis Seminar
I have attached the Applied Math/Analysis Seminar notice for Elana Fertig, the talk will be held on Tuesday, September 26, 2017 in AKW 307 at 3:50pm
Please Note: Refreshments -AKW 3:30pm, 1st Floor before the talk.
Yale Systems Biology Institute – Seminar Series, Michael Miller, PhD Sept 26th @ 12:00pm West Campus
Please join us for the Yale Systems Biology Institute seminar on September 26th at 12:00 p.m., presented by Michael I. Miller, PhD of Johns Hopkins University.
MICHAEL I. MILLER, PhD
Director of Department of Biomedical Engineering and Director of the Center for Imaging Science in the Whiting School of Engineering
Johns Hopkins University
Talk Title: Computational Anatomy and Diffeomorphometry: A Dynamical Systems Model of Neuroanatomy in the Soft Condensed Matter Continuum
Tuesday, September 26
Yale West Campus Conference Center, Room 218
Lunch will be provided
26SEPT2017 – Michael Miller SBI Seminar.pdf V2.pdf