Pollard Group -- Gladstone Institutes, UC San Francisco








docpollard.com WWW

We develop and apply
statistical methods for
the comparative analysis
of genomic data.
Current projects include
detecting fast evolving
regions of the primate
genome and studying
microbial diversity
using metagenomic data.

Lab News...

Ocotber 2016:We published MIDAS, open source software and a genomic database for quantifying strain-level genetic variation in microbiome samples using shotgun metagenomics data. Our analyses of mother-infant microbiome transmission and global ocean population structure revealed striking patterns missed at the species level. Read the paper and press release.

August 2016: We published a perspective on comparative metagenomics, focused on the challenges associated with accurate quantification of taxa and genes. Read the paper.

August 2016: Our review of research about Human Accelerated Regions was published in The Scientist.

July 2016: Alex Pico, Anders Riutta, and collaborators modernized WikiPathways and linked it to other biological knowledge bases using semantic web and ontology approaches. Read the press release.

May 2016: Our work on Human Accelerated Regions was featured in a Live Science article about "Prehistoric X-Men".

May 2016: The White House Office of Science and Technology Policy announces the National Microbiome Initiative that Katie Pollard helped to plan.

April 2016: Katie Pollard, Nevan Krogan, Peter DiLaura, and Leah Makley speak about network biology at a Gladstone symposium on the Future of Precision Medicine.

April 2016: Our machine-learning analysis of the 3D structure of the human genome revealed proteins bound to looping chromatin that predict the genes targeted by long-range enhancers. The study was published in Nature Genetics, highlighted in a News and Views by John Stam, and featured in a story in Nature Reviews Genetics. It was also recommended by F1000. More details are available in a press release.

March 2016: We published a pair of studies with the Ahituv lab and Illing lab on limb development enhancers that distinguish bats from other mammals, one in PLoS Genetics and one in Nature Genetics. This work was covered by the Washington Post and other media. The study was featured on the Nature Genetics cover.

February 2016: Katie Pollard is featured in a Carry the One Radio Podcast about microbiome science.

January 2016: The White House solicits input on the Unified Microbiome Initiative, which we helped plan.

January 2016: Google hosted Katie Pollard for a Gladstone Open Classroom about big data and the microbiome. Watch the talk.

November 2015: The Leakey Foundation hosts Katie Pollard for a high school outreach event and a public lecture at the Houston Museum of Natural History.

October 2015: Katie Pollard contributed to a policy manuscript on a Unified Microbiome Initiative, which was covered in the New York Times and other media.

August 2015: Katie Pollard spoke about cryptic functional variation in the human microbiome at the 2015 Joint Statistical Meetings. Her talk was highlighted in the media, including on the NPR Blog Shots.

July 2015: Members of the Pollard lab were featured on LabTV, a project that helps the scientistis of tomrrow meet diverse faces in the field to learn about their biomedical research and career paths.

July 2015: A feature story about Human Accelerated Regions (HARs) appeared in Science. Liz Pennisi covered the discovery and analysis of HARs by the Pollard lab, as well as recent follow up work by several other groups to show that HARs function as developmental enhancers.

June 2015: Bioinformatics PhD student Stephen Nayfach received the UCSF Fletcher Jones Fellowship.

March 2015: Katie Pollard and Shannon Bennett are discussing the human microbiome for a City Arts and Lectures organized by the California Academy of Sciences. The event took place on March 4 at the Nourse Theater and was broadcast on NPR.

February 2015: We participated in a session on obesity and the human microbiome at the AAAS Meeting in San Jose, CA. Our results about statistical inconsistencies received attention from a variety of media (see press release and news story). This research started with Mariel Finucane's paper about variability across studies and continued this year with Stephen Nayfach's observations about average genome size counfounding. Stephen's paper was accepted at Genome Biology on the day before the talk!

October 2014: We contributed to an opinion paper in Cell on the importance of developing standards and policies in the emerging field of microbiome research.

July 2014:We received an NIH grant to study the longitudinal and functional dynamics of the autoimmune microbiome with Shomi Sanjabi and Tom Sharpton.

July 2014: Katie Pollard was a guest speaker on City Visions Radio: Exploring the Human Microbiome. The show aired on KALW 91.7 and is available online.

July 2014: Katie Pollard contributed to a white paper on the American Statistical Association's Big Data R&D Initiative, which responded to calls from the NSF and White House. Details here.

June 2014: Graduate student Stephen Nayfach received a Genentech Fellowship for his work on genomic variation in the human microbiome.

February 2014: Postdoc Josh Ladau received a poster award at the Gordon and Betty Moore Foundation's Marine Microbiology Initiative RA and Postdoctoral Scholar Summit.

December 2013: Postdoc Josh Ladau's figure of predicted microbial diversity in the American tallgrass prairie before agriculture was selected by Wired Magazine as one of the best scientific visualizations of 2013.

November 2013: Using a combination of bioinformatics and experimental approaches, we showed that many Human Accelerated Regions (HARs) function as developmental enhancers, some with differences in activity between humans and chimps. The paper was published in a special theme issue of Phil Trans Royal Society B on enhancer evolution. Images of HAR enhancers can be viewed through our EnhancerBrowser website. More info here.

November 2013: Postdoc Josh Ladau and Katie Pollard used niche modeling to predict microbial community diversity in the tallgrass prarie of the United States before agriculture dramatically changed this ecosystem. This project was a collaboration with Noah Fierer and others at University of Colorado. The paper was published in Science and appeared in Nature News. More info here.

October 2013: Katie Pollard and Gladstone President Sandy Williams were confirmed as Fellows of the California Academy of Sciences. (News story here.)

September 2013: Katie participated in The New Diagnosis, a panel discussion of technology in health care and research at TechCrunch Disprut 2013.

September 2013: The Pollard lab's work on the human gut microbiome was featured on ABC News. We are collaborating with Shomi Sanjabi's lab to study changes in the gut microbiome during the onset of autoimmune disease.

August 2013: Katie Pollard was featured in an Amstat News story about the benefits of postdoctoral fellowships. Amstat News is the magazine of the American Statistical Association.

May 2013: The Pollard lab's investigations into the human microbiome and its role in autoimmune diseases was covered in a news story on KQED radio. The lab is collaborating with Carlos Bustamante and colleagues to study the microbiomes of Khoisan people in South Africa (more info here).

October 2012: Our collaborative work with Benoit Bruneau's lab on the epigenetics of heart development was published in Cell and featured on ABC News.

July 2012: The Gordon and Betty Moore Foundation awarded the Pollard lab $1.3 million for research into the global mapping of microbial functions using metagenomic data. This project is a collaboration with the laboratory of Jonathan Eisen at UC Davis that builds upon our iSEEM Project.

June 2012: The Pollard lab and colleagues published the initial results of the Human Microbiome Project in Nature and PLoS ONE. We analyzed microbial community DNA from 18 body sites of 242 healthy adults living in St. Louis and Houston. The Pollard lab's main contribution was establishment of a rigorous procedure for identifying novel types of microbes, which we used to characterize new gut bacteria, including several members of the recently discovered genus Barnesiella. Our work was featured on ABC News and was selected as the NHGRI Genomic Advance of the Month. (Press Release)

June 2012: Several of our discoveries about Human Accelerated Regions were featured in a story about human evolution in the New Scientist.

September 2011: Postdoc Samantha Riesenfeld was awarded an NRSA Fellowship from the National Institute of Child Health and Human Development to study vertebrate gene regulatory elements in collaboration with Nadav Ahituv.

August 2011: The Pollard lab received a 4-year $1.5 million grant from the National Science Foundation's Mathematical Biology Program to explore the human microbiome through development of novel convex geometry and comparative genomics approaches.

January 2011: Postdocs Tony Capra and Samantha Riesenfeld were both awarded Informatics Fellowships from the PhRMA Foundation.

June 2010: Katie Pollard appeared on Episode 2 of The Age of the Genome, a BBC Radio special hosted by Richard Dawkins. The lab was also featured on the UCSF Science Cafe.

April 2010: Our approach to studying human-chimp differences in non-coding DNA was featured in Ursula Goodenough's NPR Blog.

January 2010: The Pollard Lab and Gladstone Bioinformatics Core were awarded NHLBI funds to study the epigenetics of heart development in a collaborative project with Benoit Bruneau and others. The Gladstone team is part of a nation-wide consortium called Bench to Bassinet.

December 2009: Katie Pollard was featured in a John Rubin documentary entitled What Darwin Never Knew, that aired December 29 on NOVA. She is featured in an accompanying on-line interivew about The DNA of Human Evolution. Watch the episode.

October 2009: The Gladstone Institutes Science for Life lecture featured Katie Pollard talking about human evolution and Erin Wang playing cello pieces from different periods in the evolution of the instrument.

October 2009: Katie Pollard appeared on the German science TV program Quarks & Co.

July 2009: Katie Pollard and Nadav Ahituv received a UCSF Program for Breakthrough Biomedical Research (PBBR) Integrative Research Award. The one-year grant supports collaborative, interdisciplinary research on a high-risk topic.

June 2009: Katie Pollard appeared on Are We Alone?, a SETI Radio program that aired on Public Radio station KALW.

May 2009: Our research about human-chimp genetic differences was featured in the National Institutue of General Medical Sciences (NIGMS) Magazine Computing Life and the NIH Biomedical Beat news digest.

Katie Pollard's article entitled What Makes Us Human? was the Scientific American cover story in May 2009. Our comparative genomics research was featured on ABC News (click on second photo to play video).