Representative Publications
| Topic | Publication |
|---|---|
| Ancestry inference in admixed populations |
A statistical model for reference-free inference of archaic local ancestry
Fast and accurate inference of local ancestry in Latino populations.
Estimating local ancestry in admixed populations. |
| Scalable algorithms for large-scale genomics |
Efficient Variance Components Analysis Across Millions of Genomes
Scalable probabilistic PCA for large-scale genetic variation data |
| Genetic architecture of complex traits |
A unifying framework for joint trait analysis under a non-infinitesimal model. |
| Genomic privacy |
Genomic privacy and limits of individual detection in a pool. |
| Archaic admixture in human history |
Recovering signals of ghost archaic introgression in African populations
The landscape of Denisovan admixture in South Asians and Oceanians
The genomic landscape of Neanderthal ancestry in present-day humans
The date of interbreeding between Neandertals and modern humans |
Preprints
| Year | Title |
|---|---|
| 2020 |
A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes Arunabha Majumdar, Kathryn Burch, Sriram Sankararaman, Bogdan Pasaniuc, W. James Gauderman, John S. Witte |
| 2020 |
A Statistical Model for Quantifying the Needed Duration of Social Distancing for the COVID-19 Pandemic Nadav Rakocz, Boyang Fu, Eran Halperin+, Sriram Sankararaman+ |
| 2019 |
Fast estimation of genetic correlation for Biobank-scale data Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, Sriram Sankararaman |
| 2018 |
Haplotype-based eQTL mapping finds evidence for complex gene regulatory regions poorly tagged by marginal SNPs Robert Brown, Sriram Sankararaman, Bogdan Pasaniuc |
All Publications
Find us on Google, Pubmed or DBLP. * – denotes equal contribution; + - denotes equal contribution; members of the group are underlined
| Year | Publication |
|---|---|
| 2020 |
Methods for detecting introgressed archaic sequences Sriram Sankararaman Current Opinions in Genetics and Development |
| 2020 |
Explaining Groups of Points in Low-Dimensional Representations Gregory Plumb, Jonathan Terhorst, Sriram Sankararaman, Ameet Talwalkar Proceedings of the International Conference on Machine Learning (ICML) |
| 2020 |
Efficient Variance Components Analysis Across Millions of Genomes Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc, Sriram Sankararaman Nature Communications Earlier version presented at the Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2019 |
| 2020 |
A unifying framework for imputing summary statistics in Genome-wide Association Studies Yue Wu, Eleazar Eskin+ , Sriram Sankararaman+ Journal of Computational Biology Earlier version presented at the Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2018 |
| 2020 |
Scalable probabilistic PCA for large-scale genetic variation data Aman Agrawal*, Alec M. Chiu*, Minh Le, Eran Halperin, Sriram Sankararaman PLoS Genetics |
| 2020 |
Recovering signals of ghost archaic introgression in African populations Arun Durvasula, Sriram Sankararaman Science Advances |
| 2019 |
A statistical model for reference-free inference of archaic local ancestry Arun Durvasula, Sriram Sankararaman PLoS Genetics |
| 2019 |
Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture Kangcheng Hou*, Kathryn S Burch*, Arunabha Majumdar, Huwenbo Shi, Nicholas Mancuso, Yue Wu, Sriram Sankararaman, Bogdan Pasaniuc Nature Genetics |
| 2019 |
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology Elior Rahmani, Regev Schweiger, Brooke Rhead, Lindsey A. Criswell, Lisa F. Barcellos, Eleazar Eskin, Saharon Rosset, Sriram Sankararaman, Eran Halperin Nature Communications |
| 2019 |
Preoperative predictions of in-hospital mortality using electronic medical record data Brian Hill*, Robert P Brown*, Eilon Gabel, Christine Lee, Maxime Cannesson, Loes Olde Loohuis, Ruth Johnson, Brandon Jew, Uri Maoz, Aman Mahajan, Sriram Sankararaman+, Ira Hofer+, Eran Halperin+ British Journal of Anaesthesia |
| 2018 |
A Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese Charleston Chiang, Serghei Mangul, Christopher Robles, Sriram Sankararaman Molecular Biology and Evolution |
| 2018 |
A scalable estimator of SNP heritability for biobank-scale data Yue Wu, Sriram Sankararaman Bioinformatics (Proceedings of ISMB) |
| 2018 |
A unifying framework for joint trait analysis under a non-infinitesimal model. Ruth Johnson, Huwenbo Shi, Bogdan Pasaniuc+, Sriram Sankararaman+ Bioinformatics (Proceedings of ISMB) |
| 2018 |
Natural selection interacts with recombination to shape the evolution of hybrid genomes. Molly Schumer, Chenling Xu, Daniel Powell, Arun Durvasula, Laurits Skov, Chris Holland, John Blazier, Sriram Sankararaman, Peter Andolfatto, Gil Rosenthal, Molly Przeworski Science |
| 2017 |
Widespread Allelic Heterogeneity in Complex Traits. Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea Ju, Ayellet Segrè, Jong Wha J Joo, Hyejung Won, Sriram Sankararaman , Bogdan Pasaniuc, Sagiv Shifman, Eleazar Eskin American Journal of Human Genetics |
| 2017 |
Meiotic genes are enriched in genes of reduced archaic ancestry. Bernard Jegou, Sriram Sankararaman, Antoine D Rolland, David Reich, Frederic Chalmel Molecular Biology and Evolution |
| 2016 |
Colocalization of GWAS and eQTL Signals Detects Target Genes. Farhad Hormozdiari, Martijn van de Bunt, Ayellet Segrè, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Sriram Sankararaman, Bogdan Pasaniuc, Eleazar Eskin American Journal of Human Genetics |
| 2016 |
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon, Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin Rohland, Gabriel Renaud, Yaniv Erlich, Thomas Willems, Carla Gallo, Jeffrey P. Spence, Yun S. Song, Giovanni Poletti, Francois Balloux, George van Driem, Peter de Knijff, Irene Gallego Romero, Aashish R. Jha, Doron M. Behar, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Andres Moreno-Estrada, Olga L. Posukh, Elena Balanovska, Oleg Balanovsky, Sena Karachanak-Yankova, Hovhannes Sahakyan, Draga Toncheva, Levon Yepiskoposyan, Chris Tyler-Smith, Yali Xue, M. Syafiq Abdullah, Andres Ruiz-Linares, Cynthia M. Beall, Anna Di Rienzo, Choongwon Jeong, Elena B. Starikovskaya, Ene Metspalu, Jüri Parik, Richard Villems, Brenna M. Henn, Ugur Hodoglugil, Robert Mahley, Antti Sajantila, George Stamatoyannopoulos, Joseph T. S. Wee, Rita Khusainova, Elza Khusnutdinova, Sergey Litvinov, George Ayodo, David Comas, Michael F. Hammer, Toomas Kivisild, William Klitz, Cheryl A. Winkler, Damian Labuda, Michael Bamshad, Lynn B. Jorde, Sarah A. Tishkoff, W. Scott Watkins, Mait Metspalu, Stanislav Dryomov, Rem Sukernik, Lalji Singh, Kumarasamy Thangaraj, Svante Pääbo, Janet Kelso, Nick Patterson, David Reich. Nature |
| 2016 |
A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, David Reich Proceedings of the National Academy of Sciences |
| 2016 |
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans. Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich Current Biology |
| 2015 |
Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes. Mark Lipson, Po-Ru Loh, Sriram Sankararaman, Nick Patterson, Bonnie Berger, David Reich. PLoS Genetics |
| 2015 |
Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. Pier Francesco Palamara, Laurent Francioli, Peter Wilton, Giulio Genovese, Alexander Gusev, Hillary Finucane, Sriram Sankararaman; Genome of the Netherlands Consortium, Shamil Sunyaev, Paul de Bakker, John Wakeley, Itsik Pe'er, Alkes Price. American Journal of Human Genetics |
| 2015 |
Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns. James Zou, Danny Park, Esteban Burchard, Dara Torgerson, Maria Pino-Yanes, Yun Song, Sriram Sankararaman+, Eran Halperin+, Noah Zaitlen+. Proceedings of the National Academy of Sciences |
| 2015 |
Inferring parental genomic ancestries using pooled semi-Markov processes. James Zou, Eran Halperin, Esteban Burchard, Sriram Sankararaman. Bioinformatics (Proceedings of ISMB) |
| 2015 |
Evidence for archaic adaptive introgression in humans. Fernando Racimo, Sriram Sankararaman, Rasmus Nielsen, Emilia Huerta-Sánchez. Nature Reviews Genetics |
| 2014 |
Leveraging population admixture to characterize the heritability of complex traits. Noah Zaitlen, Bogdan Pasaniuc, Sriram Sankararaman, Gaurav Bhatia, Jianqi Zhang, Alexander Gusev, Taylor Young, Arti Tandon, Samuela Pollack, Bjarni J Vilhjálmsson, Themistocles L Assimes, Sonja I Berndt, William J Blot, Stephen Chanock, Nora Franceschini, Phyllis G Goodman, Jing He, Anselm J M Hennis, Ann Hsing, Sue A Ingles, William Isaacs, Rick A Kittles, Eric A Klein, Leslie A Lange, Barbara Nemesure, Nick Patterson, David Reich, Benjamin A Rybicki, Janet L Stanford, Victoria L Stevens, Sara S Strom, Eric A Whitsel, John S Witte, Jianfeng Xu, Christopher Haiman, James G Wilson, Charles Kooperberg, Daniel Stram, Alex P Reiner, Hua Tang, Alkes L Price. Nature Genetics |
| 2014 |
The genomic landscape of Neanderthal ancestry in present-day humans. Sriram Sankararaman, Swapan Mallick, Michael Dannemann, Kay Prüfer, Janet Kelso, Svante Pääbo, Nick Patterson, David Reich. Nature |
| 2014 |
The complete genome sequence of a Neanderthal from the Altai Mountains. Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H. Sudmant, Cesare de Filippo, Heng Li, Swapan Mallick, Michael Dannemann, Qiaomei Fu, Martin Kircher, Martin Kuhlwilm, Michael Lachmann, Matthias Meyer, Matthias Ongyerth, Michael Siebauer, Christoph Theunert, Arti Tandon, Priya Moorjani, Joseph Pickrell, James C. Mullikin, Samuel H. Vohr, Richard E. Green, Ines Hellmann, Philip L. F. Johnson, Hélène Blanche, Howard Cann, Jacob O. Kitzman, Jay Shendure, Evan E. Eichler, Ed S. Lein, Trygve E. Bakken, Liubov V. Golovanova, Vladimir B. Doronichev, Michael V. Shunkov, Anatoli P. Derevianko, Bence Viola, Montgomery Slatkin, David Reich, Janet Kelso, Svante Pääbo. Nature |
| 2013 |
Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. The SIGMA Type 2 Diabetes Consortium. Nature |
| 2013 |
Estimating and interpreting FST: the impact of rare variants. Gaurav Bhatia, Nick Patterson, Sriram Sankararaman, Alkes Price. Genome Research |
| 2013 |
Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. Bogdan Pasaniuc 1, Sriram Sankararaman, Dara G Torgerson, Christopher Gignoux, Noah Zaitlen, Celeste Eng, William Rodriguez-Cintron, Rocio Chapela, Jean G Ford, Pedro C Avila, Jose Rodriguez-Santana, Gary K Chen, Loic Le Marchand, Brian Henderson, David Reich, Christopher A Haiman, Esteban Gonzàlez Burchard, Eran Halperin. Bioinformatics |
| 2012 |
The date of interbreeding between Neandertals and modern humans. Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, David Reich. PLoS Genetics |
| 2012 |
Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Michael C Turchin, Charleston WK Chiang, Cameron D Palmer, Sriram Sankararaman, David Reich, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Joel N Hirschhorn. Nature Genetics |
| 2012 |
Fast and accurate inference of local ancestry in Latino populations. Yael Baran, Bogdan Pasaniuc, Sriram Sankararaman, Dara G Torgerson, Christopher Gignoux, Celeste Eng, William Rodriguez-Cintron, Rocio Chapela, Jean G Ford, Pedro C Avila, Jose Rodriguez-Santana, Esteban Gonzàlez Burchard, Eran Halperin. Bioinformatics |
| 2012 |
Phylogenetic inference via sequential Monte Carlo. Alexandre Bouchard-Côté, Sriram Sankararaman, Michael Jordan. Systems Biology |
| 2012 |
TrickleDNS: A High Integrity Domain Name System. Sriram Sankararaman, Venugopalan Ramasubramanian and Lakshminarayanan Subramanian. Fourth International Conference on Communication Systems and Networks (COMSNETS) |
| 2010 |
Genome-wide association identifies candidate genes that influence the human electroencephalogram. Colin A. Hodgkinson, Mary-Anne Enoch, Vibhuti Srivastava, Justine S. Cummins-Oman, Cherisse Ferrier, Polina Iarikova, Sriram Sankararaman, Goli Yamini, Qiaoping Yuan, Zhifeng Zhou, Bernard Albaugh, Kenneth V. White, Pei-Hong Shen, and David Goldman. Proceedings of the National Academy of Sciences |
| 2010 |
Active site prediction using evolutionary and structural information. Sriram Sankararaman, Fei Sha, Jack F Kirsch, Michael I Jordan, Kimmen Sjölander. Bioinformatics |
| 2009 |
Genomic privacy and limits of individual detection in a pool. Sriram Sankararaman, Guillaume Obozinski, Michael I Jordan, Eran Halperin. Nature Genetics |
| 2009 |
ResBoost: characterizing and predicting catalytic residues in enzymes. Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander. BMC Bioinformatics |
| 2009 |
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander. Nucleic Acids Research |
| 2009 |
Locus-specific Ancestry Inference in Closely-related populations Bogdan Pasaniuc* , Sriram Sankaraman * , Gad Kimmel, Eran Halperin. Bioinformatics (Proceedings of ISMB) |
| 2008 |
INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification. Sriram Sankararaman, Kimmen Sjölander. Bioinformatics |
| 2008 |
Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. Christine F Skibola 1, Paige M Bracci, Eran Halperin, Alexandra Nieters, Alan Hubbard, Randi A Paynter, Danica R Skibola, Luz Agana, Nikolaus Becker, Patrick Tressler, Matthew S Forrest, Sriram Sankararaman, Lucia Conde, Elizabeth A Holly, Martyn T Smith. PLoS One. |
| 2008 |
On the inference of ancestries in admixed populations. Sriram Sankararaman*, Gad Kimmel*, Eran Halperin, Michael I Jordan. Genome Research A previous version appeared in the Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB) |
| 2008 |
Estimating local ancestry in admixed populations. Sriram Sankararaman, Srinath Sridhar, Gad Kimmel, Eran Halperin. American Journal of Human Genetics |
| 2008 |
The Influence of QoS Routing on the Achievable Capacity in TDMA Based Adhoc Wireless Networks S. Sriram, T. Bheemarjuna Reddy, C. Siva Ram Murthy. Wireless Networks Journal |
| 2006 |
MuSeQoR: Multi-path Failure-tolerant Security-aware QoS Routing in Ad hoc Wireless Networks T. Bheemarjuna Reddy, S. Sriram, B. S. Manoj, C. Siva Ram Murthy. Computer Networks |
| 2006 |
Petros Maniatis, Induced Churn as Shelter from Routing-Table Poisoning Tyson Condie, Varun Kacholia, Sriram Sankararaman, Joseph M. Hellerstein. Proceedings of the 13th Annual Network and Distributed System Security Symposium (NDSS) |
| 2006 |
On the End-to-end Call Acceptance and the Possibility of Deterministic QoS Guarantees in Ad hoc Wireless Networks S. Sriram, T. Bheemarjuna Reddy, B. S. Manoj, and C. Siva Ram Murthy, Proceedings of the Sixth ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc) |
| 2004 |
MuSeQoR: Multi-path Failure-tolerant Security-aware QoS Routing in Ad hoc Wireless Networks S. Sriram, T. Bheemarjuna Reddy, B. S. Manoj, C. Siva Ram Murthy. Proceedings of the 11th IEEE International Conference on High Performance Computing (HiPC) |
| 2004 |
The Influence of QoS Routing on the Achievable Capacity in TDMA-based Ad hoc Wireless Networks S. Sriram, T. Bheemarjuna Reddy, B. S. Manoj, C. Siva Ram Murthy, Proceedings of the 47th annual IEEE Global Telecommunications Conference (GLOBECOM) |
| 2004 |
Enhancing a biomedical information extraction system with dictionary mining and context disambiguation. Sougata Mukherjea, L. Venkata Subramaniam, Gaurav Chanda, Sriram Sankararaman, Ravi Kothari, Vishal S. Batra, Deo N. Bhardwaj, Biplav Srivastava, IBM Journal of Research and Development |
Technical Reports
| Year | Publication |
|---|---|
| 2005 |
Key Consistency in DHTs Sriram Sankararaman, Byung-Gon Chun, Chawathe Yatin and Scott Shenker, EECS Department, University of California, Berkeley |
| 2005 |
Maelstrom: Churn as Shelter Tyson Condie, Varun Kacholia, Sriram Sankararaman, Joseph M. Hellerstein, Petros Maniatis, EECS Department, University of California, Berkeley |