Savage, J. Doudna Link to Nature Link to MedRxiv. Jin, G. Fudenberg, K. Genome-wide variability in recombination activity is associated with meiotic chromatin organization , Genome Research, Roodgar, B. Good, N. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H.
Lee, A. Babveyh, S. Nesamoney, K. Snyder Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment , Genome Research, Bisanz, S.
Lyalina, P. Spanogiannopoulos, Q. Ang, J. Cai, S. Dickmann, M. Friedrich, S. Liu, S. Collins, D. Ingebrigtsen, S. Miller, J. Turnbaugh, A. Patterson, K. Pollard, K. Mai, J. Spranger, P. Caloric restriction disrupts the microbiota and colonization resistance , Nature, — Link to Nature. Alexanian, P. Przytycki, R. Micheletti, A.
Padmanabhan, L. Ye, J. Travers, B. Teran, Q. Duan, S. Ranade, F. Felix, R. Linares-Saldana, Y. Huang, G. Andreoletti, J. Yang, K. Ivey, R. Jain, T. McKinsey, M. Rosenfeld, C. Gifford, K. Haldar, D. A transcriptional switch governing fibroblast plasticity underlies reversibility of chronic heart disease , Nature, — Cooch, A.
Watson, A. Olarte, E. Crawford, J. DeRisi, B. Greenhouse, J. Hakim, K. Turcios, K. Pollard, L. Atkinson-McEvoy, R. Hirsch, R. Keller, T. Ruel, A. Cohen-Ross, A. Leon, N. Bardach Link to PPCH. Pittman, K. Ultraconservation of enhancers is not ultranecessary , Nature Genetics, 29— Lind, K. The gut microbiomes of species , Science, Link to Science. Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data , Microbiome, 9: Link to Microbiome Link to BioRxiv.
CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues , Genome Biology, Fozouni, S.
Son, M. Derby, G. Knott, C. Gray, M. Zhao, N. Switz, G. Kumar, S. Stephens, D. Boehm, C. Tsou, J. Shu, A. Bhuiya, M. Harris, P. Chen, J. Osterloh, A. Meyer-Franke, B. Joehnk, K. Walcott, A. Sil, C. Langelier, K. Pollard, E. Crawford, A. Puschnik, M. Phelps, A. Kistler, J. DeRisi, J. Doudna, D. Fletcher, M. Ott Link to Cell Link to MedRxiv. Bradley, K. Building a chemical blueprint for human blood , Nature, Zoonomia Consortium A comparative genomics multitool for scientific discovery and conservation , Nature, Link to Nature Press Release.
Nora, L. Caccianini, G. Fudenberg, V. Kameswaran, A. Nagle, A. Uebersohn, K. So, B. Hajj, A. Saux, A. Coulon, L. Mirny, K. Dahan, B. Gordon, J. Hiatt, …, K. Keough, A. Lind, … K. Pollard, … N. Krogan Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms , Science, eabe Fudenberg, D. Kelley, K. Damas, G. Hughes, K. Keough, C. Painter, N.
Persky, M. Corbo, M. Hiller, K. Koepfli, A. Pfenning, H. Zhao, D. Genereux, R. Swofford, K. Pollard, O. Ryder, M. Nweeia, K. Lindblad-Toh, E. Teeling, E. Karlsson, H. Lewin Gordon, F. Inoue, B. Martin, M. Schubach, V. Agarwal, S. Whalen, S. Feng, J. Zhao, T. Ashuach, R. Ziffra, A. Kreimer, I. Georgakopoulous-Soares, N. Yosef, C. Ye, K. Shendure, M. Kircher, N. Ahituv Markenscoff-Papadimitriou, S. Whalen, P. Thomas, F. Binyameen, T. Nowakowski, S. Sanders, M. State, K.
Rubenstein A chromatin accessibility atlas of the developing human telencephalon , Cell, 3 : Link to Cell Link to BioRxiv. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, Z. Shi, K. Parks, P. Hugenholtz, N. Segata, N. Kyrpides, R. Finn A unified sequence catalogue of over , reference genomes from the human gut microbiome , Nature Biotechnology, 3: — Kosti, S. Lyalina, K. Pollard, A. Butte, M. Sirota Meta-Analysis of vaginal microbiome data provides new insights into preterm birth , Frontiers in Microbiology, Link to Frontiers.
Phylogenize: a web tool to identify microbial genes underlying environment associations , Bioinformatics, 36 4 : Link to Bioinformatics Link to BioRxiv. Garud, K. Link to TIG. Schalbetter, G. Fudenberg, J. Baxter, K. Neale Principles of meiotic chromosome assembly revealed in S. Hoarfrost, S. Nayfach, J. Ladau, S. Yooseph, C. Arnosti, C. Dupont, K. Carmody, J. Bisanz, B. Bowen, C. Maurice, S. Louie, D. Treen, K. Chadaideh, V. Rekdal, E. Bess, P. Ang, K. Bauer, T. Balon, K. Pollard, T.
Northen, P. Cooking shapes the structure and function of the gut microbiome , Nature Microbiology, 4: — Lyalina, M. Olvera, S. Whalen, B. Conklin, K. Leveraging genetic variants for personalized and allele-specific sgRNA design , Genome Biology, article Lind, Y.
Lai, Y. Mostovoy, A. Holloway, A. Iannucci, A. Mak, M. Fondi, V. Orlandini, W. Eckalbar, M. Milan, M. Rovatsos, I. Kichigin, A. Makunin, V. Trifonov, E. Schijlen, L. Kratochvil, R. Fani, T. Jessop, T. Patarnello, J. Hicks, O. Ryder, J. Mendelson III, C. Ciofi, P. Kwok, K. Pollard, B. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards , Nature Evolution and Ecology, 3: — Stone, C.
Pratt, K. Samse-Knapp, T. Mohamed, E. Radzinsky, A. Schricker, P. Yu, K. Ivey, K. Unique transcription factor functions regulate epigenetic and transcriptional dynamics during cardiac reprogramming , Cell Stem Cell, 25 1 : Empowering statistical methods for cellular and molecular biologists , Molecular Biology of the Cell, 30 Link to MBoC. Engle, H. Tiriac, K. Rivera, A. Pommier, S. Whalen, T. Oni, B. Alagesan, E. Lee, M. Yao, M.
Lucito, B. Spielman, B. Da Silva, C. Schoepfer, K. Wright, B. Creighton, L. Afinowicz, K. Yu, R. Aust, P. Gimotty, K. Hruban, M. Goggins, C. Pilarsky, Y. Park, D. Pappin, M. Hollingsworth, D. Tuveson The glycan CA promotes pancreatitis and pancreatic cancer in mice , Science, : Armour, S. Sharpton A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome , mSystems, 4:e Link to mSystems Link to BioRxiv.
Ahmed, A. Avila-Herrera, K. Tun, G. Davis, K. Shah Evolution of mechanisms that control mating in Drosophila males , Cell Reports, 27 9 : P Link to Cell. Cristea, P. Dorrestein, J. Eisen, J. Gilbert, J. Huber, J. Jansson, R. Knight, K. Raes, P.
Silver, N. Webster, J. Xu Early-career scientists shaping the world , mSystems, 4:e Link to mSystems. The NIH-wide microbiome workshop writing team The human microbiome: Emerging themes at the horizon of the 21st century , Microbiome, Link to Microbiome. Nayfach, Z. Shi, R. Seshadri, K. Receive emails about upcoming NOVA programs and related content, as well as featured reporting about current events through a science lens.
Katie Pollard: I've had a long-standing interest in human origins and in anthropology, and I've been curious for a long time in this very broad question of what makes us human. Ever since our species began to walk around on the globe, we've probably been wondering about this. What we're trying to do in my lab is to bring a new type of data, genetic data, and a new tool, which is high-powered computing, to bear on this age-old and fundamental question.
When I was first studying human evolution, most of what we could use were things like bones and artifacts, things that we dug out of the ground, as well as what we observed looking around the Earth today—the behavior of humans and behavior of non-human primates. These were the tools of the trade. I also had an interest in math back then, but I saw very little connection between that and my interest in human origins.
Fortunately, in the next decade, we had a human genome project and then a chimp genome project, and there were major advances in computing. Suddenly this question of what makes us human had a whole new set of data and a whole new set of tools. And I was in a great position to jump into that field. Since chimps are our closest living relative on the tree of life, we can start to figure out what's special about us if we compare our DNA to their DNA.
If we can find the little pieces of our genome that are unique, somewhere hiding in there are messages about what makes humans human. When we finished the chimpanzee genome in and lined it up next to the human genome, we made the amazing discovery that our DNA is almost 99 percent identical. That seems like a bit of a paradox given all the differences we see between ourselves and chimps. But, in fact, it's not a paradox, because all it takes to make a new species, all it takes to make a human, is a few changes in just the right places.
Given that our DNA sequence has about three billion "letters" in it, one percent is still a pretty vast territory to search.
There are about 15 million human-specific letters that have changed in the last six million years, since humans and chimps had a common ancestor. No individual person is going to sit and look through that list.
So tackling this question of which of those 15 million made a difference required writing computer programs. After months of programming and debugging and running my computer code on a massive computer cluster, I finally had some results. The top hit was a sequence that was letters long. And, amazingly, 18 out of those letters were different between human and chimp. To put that in perspective, the same sequence is in the chicken genome and has only two differences between chimp and chicken.
There have been hundreds of millions of years of evolution separating chicken and chimp, and yet we only see two changes. After identifying those regions that were most significantly altered in the human lineage, we will use this functional information to develop testable hypotheses about the effects of the observed changes. Experimental investigations of these genomic regions will lead to new understanding of the evolution of human biology and health. Identification and characterization of the genetic changes leading to modern humans is of fundamental interest.
These investigations also promise to contribute to our understanding of the causal mechanisms behind human diseases, leading to directed treatment and prevention strategies.
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