Author: rbaltman

AMIA Translational Bioinformatics Year in Review 2018 has been delivered.

I am happy to share the slides from my AMIA TBI year-in-review talk for 2018 (26 MB).  I delivered it at the conference yesterday.  I also have a supplementary file with “shout out” papers that I couldn’t cover but were great contributions as well.  I also have a bibliography of the papers presented here.  Congrats to all authors (and many others not highlighted in either file) who did great work this year.   I want to once again thank the AMIA student work group members who helped me gather and score the papers (they are highlighted in the talk), and the AMIA leadership for inviting me.

This is likely the last annual review I will do at the conference, and it has been a great 11 year run.   The complete set of slides for all 11 talks are available here.

For those who are interested, I have a radio show entitled “The Future of Everything” on SiriusXM 121 Insight Channel (Saturday mornings).  After the episodes air, they are freely available at (which links to Soundcloud) and on iTunes here.

I am mild-moderately active on twitter @rbaltman.


Annual call for AMIA Year-in-Review Talk!

Friends in Translational Bioinformatics (most in BCC to avoid long list),

Once again, I am preparing an annual review of progress in translational bioinformatics, and am seeking nominations for exciting papers published between January 2017 and the present.  The talk will be on March 14 in San Francisco as part of

The previous talks are available at:

This talk will be the 11th and I hope is a useful way to highlight great work in our field.

To remind you, I am looking for papers that relate clinical entities (patients, diseases, drugs, symptoms, signs, populations) to molecular entities (genes, molecules, RNA, proteins) using informatics technologies.  Self-nominations are welcome, and nominations of the papers of others are even better.  You can send me papers and I will worry about whether they are eligible.  I have a team of students working with me to sift through articles.

You can send me the paper, the citation, PMID, or whatever.  If you want to tell me why you nominate a paper, great, but you don’t have to–I will read the papers and try to form an opinion.

Thanks so much for your help.  I try to acknowledge all contributors in the the talk (let me know if you prefer to be anonymous).  Please forward this message to colleagues who may have thoughts.

Nominate great papers by junior scientists who may not get the recognition they deserve!


Thanks very much, your efforts help make this a useful exercise.

Russ Altman
Stanford University
Biomedical Informatics Program

Dropbox links broken. Here’s new ones.


Many of the links below have been broken because of changes in Dropbox that I probably didn’t pay attention to.  Here are links to the talks from previous years.

Thanks, Russ Altman












If there are other files you would like that have broken links, send me a message and I’ll get those posted as well.



My 2017 AMIA TBI Year-in-Review

This was the 10th AMIA translational bioinformatics year in review!  Thanks to Atul Butte for inviting me 10 years ago to do this (and to the subsequent 9 program chairs who re-upped the invitation), and it has become an annual ritual for me.   Here is the PDF as presented on Wednesday 3/29/17.  Thanks to all that helped, especially the members of the trainee group (see below) who helped with paper discovery and scoring.  For interest, I have zip files of the quarterfinalists, semifinalists and the presented papers (plus/minus a few last minute changes that are not reflected in these zip files, but are reflected in the final talk)  in html and xml form.




My AMIA TBI Year in Review 2016

Thanks to everyone who attended the talk.  The slides are here, and I have Endnote XML files for final papers and shout outs (slightly inaccurate because of last minute changes, sorry).  I would particularly like to thank the AMIA Student Working group, who under the leadership of Julie Doberne Chen and Kate Fultz Hollis did a fabulous job ranking nearly 250 papers.  In addition to Julie and Kate, they are:  Michelle Dow, Margaret Donovan, Jingran Wen, Lincoln Sheets, Juandalyn Burke, Joseph RomanoHyunggu Jung, Kun-Hsing Yu, Tim Herr, and Garima Gupta.

Slides from TBI Year in Review 2015

Thanks to all for your patience with my remote presentation today.  I could feel the energy, even though I wasn’t there.  I hope the presentation made sense and was ok.  In any case, here are the slides from the talk (warning: ~45MB), and this year I have also created a zip’ed archive with *.bib, *.xml and *.pdf versions of the final 215, final 101, and final 52.   Thanks for your support!

Materials from Translational Bioinformatics Year in Review 2013

Thanks to all who contributed and showed interest in my talk today at the AMIA Joint Summits on Translational Science.  Thanks also to the amazing tweet army that did real time updates during the talk.   I am pleased to post this  year’s slides.  As usual, I take responsibility for any mistakes, mischaracterizations, or misjudgments.  The goal here is just to show the excitement of translational bioinformatics and some of the cool stuff that is happening. 

The slides from the 2013 annual review of TBI are available here.  

XML files (compatible with ENDNOTE and others) and a PDF bibliography are also available for the final list of papers (40 papers, xml, pdf), finalists (97, xml, pdf), semifinalists (240, xml, pdf), and quarterfinalists (348, xml, pdf).  

Previous slides are available for my talks in 2008, 200920102011 and 2012.  Enjoy!

Post suggestions for articles here any time, I have a place to keep them for when I turn my attention to this early each year.