Monthly Archives: January 2018

Conference on Cancer by YLS and Smilow

Panels of interest below + Siddhartha Mukherjee and NCI Director are keynote speakers.

The Solomon Center for Health Law and Policy at Yale Law School, in collaboration with Smilow Cancer Hospital and Yale Cancer Center, will host a major interdisciplinary conference addressing topics at the cutting edge of cancer policy. This event will bring together leading figures in the worlds of cancer care, research, regulation, and policymaking to assess the current state of cancer policy and discuss ways in which law can influence its development.

Panel 3: Cancer, Health Justice, and Disparities

Cary Gross, MD—Professor of Medicine (General Medicine) and of Epidemiology (Chronic Diseases), Yale School of Medicine
Eugene Rusyn, JD—Yale Law School


  • Dayna Bowen Matthew, JD—William J. Matheson and Robert M. Morgenthau Distinguished Professor of Law, University of Virginia School of Law
  • Otis Brawley, MD—Chief Medical Officer, American Cancer Society
  • Blase Polite, MD—Associate Professor of Medicine, University of Chicago Medical Center
  • Deborah Schrag, MD, MPH—Chief, Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute; Professor of Medicine, Harvard Medical School
  • Lindsay Wiley, JD, MPH—Professor of Law and Director, Health Law and Policy, Program, American University Washington College of Law

Panel 4: Drug Development and the Cost of Researching and Treating Cancer

Charles Fuchs, MD, MPH—Director of Yale Cancer Center and Physician-in-Chief of Smilow Cancer Hospital
Aaron Kesselheim, MD, JD, MPH—Associate Professor of Medicine, Harvard Medical School


  • Peter Bach, MD, MAPP—Director of the Center for Health Policy and Outcomes, Memorial Sloan Kettering Cancer Center
  • Gideon Blumenthal, MD—Deputy Director (acting), Office of Hematology Oncology Products, U.S. Food and Drug Administration
  • Levi Garraway, JD, PhD—Senior Vice President, Global Development & Medical Affairs, Eli Lilly; Director, Joint Center for Cancer Precision Medicine
  • Amy Kapczynski, JD—Professor of Law and Faculty Director, Global Health Justice Partnership, Yale Law School
  • Jeffrey Schwartz, MBA—Managing Director, Bain Capital Life Sciences
  • Ellen Sigal, PhD—Chairperson and Founder, Friends of Cancer Research

farnam disk usage

total 4.78405E+11 of 500 TB
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dw396 0

Journal Club by GG on selected papers and notes from PSB18

[tags scilit,jclub,GG,fromjclub,conferences,psb18]

Cell-specific prediction and application of drug-induced gene expression Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencodersFunctional network community detection can disaggregate and filter multiple underlying pathways in enrichment analysesA heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methodsCoalitional game theory as a promising approach to identify candidate autism genesNetwork analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentialsAn ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data

*Minutes* Jan 9 2018


Quantum Computing


QC call minutes 1/11/18:

· Somatic Mosaicism in Brain project: consequences for SCZ (others in Consortium for ASD, Tourette’s and Epilepsy); specifically, CNVs in single cells; 300 cells per individual, 5 SCZ, 5 CTRLs, 4000 data points per cell, seeking SVM for data classification, or significant features such as genes relevant to SCZ; reduce the resolution and coarse-grain to meet current size limitations of IBM Qubit system – 50 qubits.

· Kanix Wang, U of Chicago (Andrey Rezesky’s lab) Classification of common human determinants: separate genotypic influence from environment and combine to produce phenotypes; define “Disease Liability” that accounts for the genotypic influence (Gaussian distributed); correlation between disease pairs; issues with large sample size (data on 129K families), reduced through filtering, as well as large numbers of disease, reduced as well; model involves decomposition of variance using genetic + several environmental factors, variance among couples, siblings and families; determine heritability; lower size to meet limitations

· Mike Gandal (UCLA) integrative models of psychiatric disease genomic regulation: integration of genotypes, RNA-seq, QTLs into single network and connect this with phenotype; current approach WGCNA; QC could help with non-linearity aspect, small-size + high complexity is sort of problem to deal with;

· Dimension of available space 4^(N-1), N = number of qubits, so lots of problem space, but there are other bottlenecks to large-scale tasks: T1 energy leak (weaker) < quantum coherence < measurement fidelity (environmental noise, precision of acquisition) < gate fidelity (bad control over phase) are issues, need better control; max 100-200 gates, this limits complexity of feature space; cannot debug as this causes wavefunction collapse

· Gerstein lab to come up with proposal presentation for next call