Author Archives: user

JClub by BW on “3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets”, Genome Medicine

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3D clusters of somatic mutations…reveal numerous rare mutations as functional targets
https://GenomeMedicine.BiomedCentral.com/articles/10.1186/s13073-016-0393-x Introduces 3DHotSpots, which is one of a number of recent approaches (incl. CLUMPS, Hotspot3D, Mutation3D & HotMAPS) for finding groupings of somatic SNVs via structure

farnam disk usage

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gerstein 4.7584E+11
gg487 67696389760
sl857 40017335680
fn64 37157733248
mg888 31877796224
jx98 28996563456
tg397 26743508608
jz435 26325017344
sk972 21813506432
pse5 20578109440
sl2373 15409180928
dl598 15304594048
cs784 13730144512
ll426 13685552640
mr724 11768326784
sl847 8821790592
pmm49 8177639424
wum2 8016643840
jad248 7989755008
yy222 6347266176
rrk24 6182451584
yf9 5816445952
hm444 5719131264
mihali 5459016704
lc848 4090249984
meg98 3995189120
ah633 3367398912
bp272 2906803456
xk4 2371836544
jjl86 1774867968
rdb9 1763952640
msp48 1748680320
as2665 1596345472
ky26 1583088768
ml724 1557992448
jl56 1480538368
ha275 1467031936
jw2394 1423358336
sb238 1275168128
gf3 1189340928
jrb97 1012897664
cy288 876655616
pdm32 750578816
slw67 717032064
lh372 671649152
jsr59 592016256
as898 506352512
dc547 424609664
mpw6 385383040
hz244 374372096
km735 337744640
nb23 324053504
ls926 314810880
keckadmins 265108480
aa544 249558400
xl348 237337088
simen 163574272
xz374 162198144
lr579 159751424
yf95 150772480
nmb38 115795456
jjl83 109213440
mas343 96425216
yk336 95688832
williams 95688832
xc279 85381888
zl222 68034176
wb244 63682432
rka24 59127808
yy448 46536704
aa65 44632832
gene760 33406080
zhao 25241600
amg89 21919360
co254 21889920
an377 19965312
xm24 19335680
jc2296 17970560
jw72 17455616
njc2 16694016
mx55 11160960
root 9156608
jk935 6167936
cc59 4636672
shuch 2935168
yz464 1122176
gene760_2016 475520
bab99 387584
tl444 326144
dr395 185472
mj332 60160
rm658 4096
jjp76 3968
lc664 3200

Bass 405 Audio Video Instruction Sheet

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the Audio/Visual Department, has left new instructions in Bass 405 for using the audio/visual equipment in that room. I have been asked to send a copy of those instructions (attached) on to you in case you may need them.

…

Attached is the instruction sheet for the Bass 405 AV system. I will place a copy of it on the podium in 405. If you have any further questions feel free to contact me.

Classroom Technology & Media Specialist
ITS – Media Technology Services
Yale University

Bass 405 Audio Video Instructions

Touch the podium monitor screen to wake it up.

Select from the 4 sources on the left of the screen. Look for the projector to light up at this point. The volume for all sources is controlled with the “Source” buttons on the right of the screen.

TO USE LAPTOP:

Connect your laptop with either VGA, HDMI, or the Mini Display Port cables. Once connected the system will ask you to confirm your choice. If correct, select “yes”.
If your source doesn’t display right away you may need to select it again.

TO USE LOCAL PC:

Wake the PC with the mouse or keyboard.
Log in with your Net ID, and password and continue as you would with any other Yale PC.

TO USE WIRELESS DISPLAY:

With a laptop, tablet, or phone go to your web browser and enter the web address that shows on the screen. (xxx.xxx.xxx.xxx)
If you already have the app, open it and select the “Enter IP’ tab and enter the listed IP address.
If you don’t already have it, press the button to “Get the app and connect”. Follow the instructions to download the app and connect.

TO USE BLU-RAY (OR DVD):

Insert your disc into the OPPO player in the rack below.
Use the buttons on the monitor to select menu options and transport control.

Do not forget to shut down the system!

Press the power button in the upper right corner of the screen. Select “Yes” on the next page and make sure the projector goes off. Do not turn off the monitor power.
Bass 405 Audio Video Instructions.docx

Invited Guest: Dr. Nancy Smider, Director of Research Informatics at Epic

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We have invited Dr. Nancy Smider, Director of Research Informatics, at Epic Corporation in Madison, Wisconsin to visit and speak to our faculty about the EHR’s research roadmap and future EHR functionality. The meeting will be held on February 1, 2018 @ Noon in Hope 216. Lunch will be provided. All are welcome to attend.

Epic Enabling Research

Guest speaker:

Nancy Smider, PhD

Director, Research Informatics

Epic Corporation in Madison, Wisconsin

Hope 216

February 1, 2018

12 Noon

Nancy Smider, PhD

Director, Research Informatics

Epic

Nancy Smider, PhD, is the Director of Research Informatics at Epic. She focuses on Epic’s electronic health record system as an enabling and accelerating technology in support of the clinical research mission of organizations. Nancy also leads Epic’s annual Research Advisory Council conference which draws over 400 attendees from more than 150 of Epic’s customers, providing a broad perspective on the research-related efforts of leading healthcare organizations across the country, and globally. Nancy earned her PhD in 1993 from the University of Wisconsin, Madison. She did her Post-Doctoral fellowship in health services research, after which she accepted a position as a Research Scientist at the University of Wisconsin, School of Medicine, where she continued her work as part of a multi-disciplinary team examining biopsychosocial models of health and disease. She joined Epic in 2001

Google Sells A.I. for Building A.I. (Novices Welcome) – The New York Times

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$GOOG Sells AI for Building #AI
https://www.NYTimes.com/2018/01/17/technology/google-sells-ai.html QT: “Humans must label the data before the system can
learn…once images…labeled…[it] operates w/o human
involvement…It can build a model from scratch.” How can one preview this? Will it be integrated into gphotos?

QT:{{”
Initially, Google will open this service only to a small group of businesses.
…
But sometimes, there is no substitute for good old human labor. With Google’s new service, humans must label the data before the system can learn from it. …

Google says that once images are labeled, its new service operates without human involvement….Given more time, it
can build a model from scratch, specifically for the problem at hand.

If you are a zoologist who wants an algorithm that identifies jaguars and giraffes, said Fei-Fei Li, chief scientist inside the Google cloud group, all you have to do is supply the right images. “You upload jaguars and giraffes,” she said. “And you are done.”
“}}

Highlights of 2017

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*** UPDATED on 1/22/2018 ***

Mark’s 2017 Faculty Activity Report (FAR),
summarizing key lab "activities" of the past year.

* Here are dump directories with some excerpts:

http://files.gersteinlab.org/public-docs/2018/01.10/

These include:

* A full updated CV describing my lab’s activities (in too much detail):

http://files.gersteinlab.org/public-docs/2018/01.10/Full-CV-M-Gerstein–for-FAR-bld8Jan18-cv57.pdf

The CV is based on :

– Compiling the people in the lab, viz:

http://files.gersteinlab.org/public-docs/2018/01.10/cv57-22-bld8Jan18–AdaptedFrom–gerstein_lab_people_12_7_17.pdf

http://files.gersteinlab.org/public-docs/2018/01.10/cv57-23-bld27dec17–EditOn–Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf

– A dump up to the end of ’17 of all of our scientific papers and our
"other writings" too.

http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18–papers-simple-refmt.pdf

http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18–addendum-Rest.JustOtherPubs.pdf

* There’s also an update on lectures in ’17:
http://lectures.gersteinlab.org/summary/

* Private "meetings" link, with authentication only for reference:
http://meetings.gersteinlab.org/2018/01.08/FAR-PDFs-to-post/
http://meetings.gersteinlab.org/2018/01.08/FAR-docs-to-post/

* For reference, this involved updating a variety of places on the wiki, viz:

http://info.gersteinlab.org/MBG-Profile
http://info.gersteinlab.org/Current_M_Gerstein_CV
http://info.gersteinlab.org/Additional_Information_about_Personnel
http://info.gersteinlab.org/Pubmed_query#Misc

* Finally, I’ve done little write up of some highlights, viz:
http://files.gersteinlab.org/public-docs/2018/01.22/GersteinLab-Research-Highlights-in-2017.pdf

farnam disk usage

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total 4.79668E+11 of 500TB
gg487 71410486528
sl857 40375044992
fn64 37876835328
mg888 31877607936
jx98 29259842176
tg397 26743508608
jz435 26324399488
sk972 21899746944
pse5 20579710464
sl2373 15404329344
dl598 15304594048
cs784 13730144512
ll426 12401832960
mr724 11768326784
sl847 8821790592
pmm49 8177639424
wum2 8016643712
jad248 7989755008
yy222 6347266176
rrk24 6182451584
yf9 5816445952
hm444 5719131264
mihali 5456919552
lc848 4090249984
meg98 3995189504
ah633 3367398912
bp272 2906803456
xk4 2368624256
rdb9 1763952640
jjl86 1755126656
msp48 1748680320
as2665 1596345472
ky26 1583088768
ml724 1557992448
jw2394 1537979776
jl56 1480538368
ha275 1467031936
sb238 1275168128
gf3 1189340928
jrb97 1012897664
cy288 876654080
slw67 717022208
lh372 671649152
pdm32 636279936
jsr59 592016256
as898 506352512
dc547 424609664
mpw6 385383040
hz244 374372096
km735 337744640
nb23 324053504
ls926 314810880
keckadmins 265108480
aa544 249558400
xl348 237337088
simen 163574272
xz374 162198144
lr579 159751424
yf95 150761344
nmb38 115795456
jjl83 109213440
mas343 96425216
yk336 95688832
williams 95688832
xc279 85381888
zl222 68034176
wb244 63682432
rka24 59127808
yy448 46536704
aa65 44632832
gene760 33406080
zhao 25241600
amg89 21919360
co254 21889920
an377 19965312
xm24 19335680
jc2296 17970560
jw72 17455616
njc2 16694016
mx55 11160960
root 9156608
jk935 6167936
cc59 4636672
shuch 2935040
yz464 1122176
gene760_2016 475520
bab99 387584
tl444 326144
dr395 185472
mj332 60160
rm658 4096
jjp76 3968
lc664 3200

REGISTER NOW: Yale Policy, Politics & Law of Cancer Conference, Feb. 8-9, 2018

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Colleagues:

Yale Law School and Yale Cancer Center are hosting an all-star conference on the Policy, Politics and Law of Cancer on Thursday, February 8th and Friday, February 9th at Yale Law School.

Speakers include Harold Varmus, Siddhartha Mukherjee, Ned Sharpless, Levi Garraway and many others. We thought this gathering would be of special interest to members of the Combined Program in the Biological and Biomedical Sciences and we would be delighted if you wished to join us.

The agenda and registration button is below.

Please save the date for a Conference Co-Sponsored by Yale Cancer Center and Smilow Cancer Hospital on

February 8-9, 2018 at Yale Law School
A major interdisciplinary conference addressing topics at the cutting edge of cancer policy, including the role that Washington, D.C. plays in cancer research and treatment; the business of cancer; disparities in cancer; legal and ethical issues associated with cutting edge therapies; and the cost of cancer treatment
Register Now

Keynote Speakers
Siddhartha Mukherjee, MD, DPhil: Author of The Emperor of All Maladies and Assistant Professor of Medicine, Columbia University Medical Center

Norman Sharpless, MD: Director, National Cancer Institute

Conference Speakers

More in Progress
  • Peter Bach, MD, MAPP: Director of the Center for Health Policy and Outcomes, Memorial Sloan Kettering Cancer Center
  • Robert Bazell, PhD: Professor (Adjunct) of Molecular, Cellular, and Developmental Biology, Yale University
  • Edward Benz, MD: President and CEO Emeritus, Dana-Farber Cancer Institute
  • Gideon Blumenthal, MD: Deputy Director (Acting), Office of Hematology Oncology Products, U.S. Food and Drug Administration
  • Otis Brawley, MD: Chief Medical Officer, American Cancer Society
  • Erik Fatemi: Senior Vice President, Cornerstone Government Affairs
  • Howard Forman, MD, MBA: Professor of Radiology and Biomedical Imaging, Public Health (Health Policy) and Professor of Epidemiology (Chronic Diseases), Yale School of Medicine
  • Charles Fuchs, MD, MPH: Director of Yale Cancer Center and Physician-in-Chief of Smilow Cancer Hospital
  • Levi Garraway, MD, PhD: Senior Vice President, Global Development & Medical Affairs, Eli Lilly; Director, Joint Center for Cancer Precision Medicine
  • Abbe Gluck, JD: Professor of Law and Faculty Director, Solomon Center for Health Law and Policy, Yale Law School
  • Nancy Goodman, JD, MPP: Executive Director, Kids Against Cancer
  • Cary Gross, MD: Professor of Medicine (General Medicine) and Epidemiology (Chronic Diseases), Yale School of Medicine
  • Peggy Hamburg, MD: Former Commissioner of the FDA (2009-2015)
  • Roy Herbst, MD, PhD: Ensign Professor of Medicine (Medical Oncology) and Professor of Pharmacology, Yale School of Medicine; Chief of Medical Oncology, Yale Cancer Center and Smilow Cancer Hospital
  • Amy Kapczynski, JD: Professor of Law and Faculty Director, Global Health Justice Partnership, Yale Law School
  • Aaron Kesselheim, MD, JD, MPH: Associate Professor of Medicine, Harvard Medical School; Director of the Program on Regulation, Therapeutics and Law at Brigham and Women’s Hospital
  • Jorge Lopez, Jr., JD: Executive Vice President and General Counsel, Memorial Sloan Kettering Cancer Center
  • Abe Lopman, MBA: Senior Vice President, Operations; Executive Director, Smilow Cancer Hospital at Yale New Haven
  • Dayna Bowen Matthew, JD: William L. Matheson and Robert M. Morgenthau Distinguished Professor of Law, University of Virginia School of Law
  • Barbara McAneny, MD: Co-Founder and CEO, New Mexico Oncology Hematology Consultants
  • Lee Newcomer, MD, MHA: Senior Vice President, Oncology, Genetics and Women’s Health, UnitedHealthcare
  • Randall Oyer, MD: Medical Director, Oncology Program, Lancaster General Hospital
  • Blase Polite, MD: Associate Professor of Medicine, University of Chicago Medical Center
  • Katerina Politi, PhD: Associate Professor, Yale School of Medicine
  • Nicholson Price, JD, PhD: Assistant Professor of Law, University of Michigan Law School
  • Gregory Raskin, MD: Vice President, Technology Development, Memorial Sloan Kettering Cancer Center
  • Jessica Roberts, JD: Associate Professor and Director, Health Law & Policy Institute, University of Houston Law Center
  • Joseph Ross, MD, MHS: Associate Professor of Medicine (General Medicine) and Associate Professor of Public Health (Health Policy), Yale School of Medicine
  • Eugene Rusyn, JD: Lecturer in Law and Senior Fellow, Solomon Center for Health Law and Policy, Yale Law School
  • Charles Sawyers, MD: Chair, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
  • Richard Schilsky, MD: Chief Medical Officer, American Society of Clinical Oncology
  • Deborah Schrag, MD, MPH: Chief, Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute; Professor of Medicine, Harvard Medical School
  • Jeffrey Schwartz, MBA: Managing Director, Bain Capital Life Sciences
  • Ellen Sigal, PhD: Chairperson and Founder, Friends of Cancer Research
  • Harold Varmus, MD: Lewis Thomas University Professor of Medicine, Weill Cornell Medical College; Former Director of National Cancer Institute & the National Institutes of Health; and former President & CEO of Memorial Sloan Kettering Cancer Center
  • Lindsay Wiley, JD, MPH: Professor of Law and Director, Health Law and Policy Program, American University Washington College of Law

Additional participants from the Yale community expected.

Agenda

For the agenda and conference updates, please check the conference website.
Thursday, February 8, 2018
4:00 p.m. – 6:45 p.m.

Friday, February 9, 2018
8:30 a.m. – 5:00 p.m.
Sterling Law Building, Yale Law School
127 Wall Street, New Haven

Free & Open to the Public
All are Welcome


Shuttles to and from the Sterling Law Building and the Yale School of Medicine will be provided throughout the day timed for arrival and departure for each panel presentation.

This event is supported by the Oscar M. Ruebhausen Fund at Yale Law School.
Email the Solomon Center for more information