Research Publications

Preprints

  1. Scalable multi-component linear mixed models with application to SNP heritability estimation
    Ali Pazokitoroudi, Yue Wu, Kathryn S Burch, Kangcheng Hou, Bogdan Pasaniuc and Sriram Sankararaman
    bioRxiv (2019)

  2. Fast estimation of genetic correlation for Biobank-scale data
    Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary and Sriram Sankararaman
    bioRxiv (2019)

  3. 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 and Bogdan Pasaniuc
    bioRxiv (2019)

  4. Recovering signals of ghost archaic admixture in the genomes of present-day Africans
    Arun Durvasula and Sriram Sankararaman
    bioRxiv (2018)

  5. 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 and Eran Halperin
    bioRxiv (2018)

  6. Haplotype-based eQTL mapping finds evidence for complex gene regulatory regions poorly tagged by marginal SNPs
    Robert Brown, Sriram Sankararaman and Bogdan Pasaniuc
    bioRxiv (2018)

  7. Preoperative predictions of in-hospital mortality using electronic medical record data
    Brian Hill, Robert Brown, Eilon Gabel, Christine Lee, Maxime Cannesson, Loes Olde Loohuis, Ruth Johnson, Brandon Jew, Uri Maoz, Aman Mahajan, Sriram Sankararaman, Ira Hofer and Eran Halperin
    bioRxiv (2018)

Journals

  1. A scalable estimator of SNP heritability for biobank-scale data
    Yue Wu and Sriram Sankararaman
    Bioinformatics (2018)

  2. A unifying framework for joint trait analysis under a non-infinitesimal model
    Ruth Johnson, Huwenbo Shi, Bogdan Pasaniuc and Sriram Sankararaman
    Bioinformatics (2018)

  3. Natural selection interacts with recombination to shape the evolution of hybrid genomes
    Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal et al.
    Science (2018)

  4. A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese
    Charleston Chiang, Serghei, Mangul, Christopher Robles and Sriram Sankararaman
    Mol. Biol. Evol. (2018)

  5. Widespread allelic heterogeneity in complex traits
    Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea J-T Ju, Ayellet V Segre, Jong Wha J Joo, Hyejung Won, Sriram Sankararaman, Bogdan Pasaniuc, Sagiv Shifman et al.
    The American Journal of Human Genetics (2017)

  6. Meiotic genes are enriched in regions of reduced archaic ancestry
    B Jégou, S Sankararaman, AD Rolland, D Reich and F Chalmel
    Molecular biology and evolution (2017)

  7. The combined landscape of Denisovan and Neanderthal ancestry in present-day humans
    Sriram Sankararaman, Swapan Mallick, Nick Patterson and David Reich
    Current Biology (2016)

  8. 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 and David Reich
    Proceedings of the National Academy of Sciences (2016)

  9. Colocalization of GWAS and eQTL signals detects target genes
    Farhad Hormozdiari, Martijn Van De Bunt, Ayellet V Segre, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Sriram Sankararaman, Bogdan Pasaniuc and Eleazar Eskin
    The American Journal of Human Genetics (2016)

  10. Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns
    James Y Zou, Danny S Park, Esteban G Burchard, Dara G Torgerson, Maria Pino-Yanes, Yun S Song, Sriram Sankararaman, Eran Halperin and Noah Zaitlen
    Proceedings of the National Academy of Sciences (2016)

  11. 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 et al.
    Nature (2016)

  12. Calibrating the human mutation rate via ancestral recombination density in diploid genomes
    Mark Lipson, Po-Ru Loh, Sriram Sankararaman, Nick Patterson, Bonnie Berger and David Reich
    PLoS genetics (2015)

  13. Evidence for archaic adaptive introgression in humans
    Fernando Racimo, Sriram Sankararaman, Rasmus Nielsen and Emilia Huerta-Sánchez
    Nature Reviews Genetics (2015)

  14. Inferring parental genomic ancestries using pooled semi-Markov processes
    James Zou, Eran Halperin, Esteban Burchard and Sriram Sankararaman
    Bioinformatics (2015)

  15. Leveraging distant relatedness to quantify human mutation and gene-conversion rates
    Pier Francesco Palamara, Laurent C Francioli, Peter R Wilton, Giulio Genovese, Alexander Gusev, Hilary K Finucane, Sriram Sankararaman, Shamil R Sunyaev, Paul IW de Bakker, John Wakeley et al.
    The American Journal of Human Genetics (2015)

  16. 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 and Noah Zaitlen
    Proceedings of the National Academy of Sciences (2015)

  17. 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 et al.
    Nature (2014)

  18. The genomic landscape of Neanderthal ancestry in present-day humans
    Sriram Sankararaman, Swapan Mallick, Michael Dannemann, Kay Prüfer, Janet Kelso, Svante Pääbo, Nick Patterson and David Reich
    Nature (2014)

  19. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico
    SIGMA Type 2 Diabetes Consortium et al.
    Nature (2014)

  20. 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 et al.
    Nature genetics (2014)

  21. Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation
    Bogdan Pasaniuc, Sriram Sankararaman, Dara G Torgerson, Christopher Gignoux, Noah Zaitlen, Celeste Eng, William Rodriguez-Cintron, Rocio Chapela, Jean G Ford, Pedro C Avila et al.
    Bioinformatics (2013)

  22. Estimating and interpreting FST: the impact of rare variants
    Gaurav Bhatia, Nick Patterson, Sriram Sankararaman and Alkes L Price
    Genome research (2013)

  23. Phylogenetic inference via sequential Monte Carlo
    Alexandre Bouchard-Côté, Sriram Sankararaman and Michael I Jordan
    Systematic biology (2012)

  24. 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 et al.
    Bioinformatics (2012)

  25. The date of interbreeding between Neandertals and modern humans
    Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo and David Reich
    PLoS genetics (2012)

  26. 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, Joel N Hirschhorn, Genetic Investigation of ANthropometric Traits (GIANT) Consortium et al.
    Nature genetics (2012)

  27. Active site prediction using evolutionary and structural information
    Sriram Sankararaman, Fei Sha, Jack F Kirsch, Michael I Jordan and Kimmen Sjölander
    Bioinformatics (2010)

  28. 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 et al.
    Proceedings of the National Academy of Sciences (2010)

  29. Genomic privacy and limits of individual detection in a pool
    Sriram Sankararaman, Guillaume Obozinski, Michael I Jordan and Eran Halperin
    Nature genetics (2009)

  30. Inference of locus-specific ancestry in closely related populations
    Bogdan Pa{ş}aniuc, Sriram Sankararaman, Gad Kimmel and Eran Halperin
    Bioinformatics (2009)

  31. INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
    Sriram Sankararaman, Bryan Kolaczkowski and Kimmen Sjölander
    Nucleic acids research (2009)

  32. ResBoost: characterizing and predicting catalytic residues in enzymes
    Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund and Kimmen Sjölander
    BMC bioinformatics (2009)

  33. Estimating local ancestry in admixed populations
    Sriram Sankararaman, Srinath Sridhar, Gad Kimmel and Eran Halperin
    The American Journal of Human Genetics (2008)

  34. INTREPID:INformation-theoretic TREe traversal for Protein functional site IDentification
    Sriram Sankararaman and Kimmen Sjolander
    Bioinformatics (2008)

  35. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma
    Christine F Skibola, Paige M Bracci, Eran Halperin, Alexandra Nieters, Alan Hubbard, Randi A Paynter, Danica R Skibola, Luz Agana, Nikolaus Becker, Patrick Tressler et al.
    PloS one (2008)

  36. On the inference of ancestries in admixed populations
    Sriram Sankararaman, Gad Kimmel, Eran Halperin and Michael I Jordan
    Genome research (2008)

  37. TrickleDNS: A Safety Net for the Domain Name System
    Sriram Sankararaman, Venugopalan Ramasubramanian, Lakshminarayanan Subramanian and Ion Stoica
    (2007)

  38. MuSeQoR: Multi-path failure-tolerant security-aware QoS routing in Ad hoc wireless networks
    T Bheemarjuna Reddy, S Sriram, BS Manoj and C Siva Ram Murthy
    Computer Networks (2006)

  39. Enhancing a biomedical information extraction system with dictionary mining and context disambiguation
    Sougata Mukherjea, L Venkata Subramaniam, Gaurav Chanda, Sriram Sankararaman, Ravi Kothari, Vishal Batra, Deo Bhardwaj and Biplav Srivastava
    IBM Journal of Research and Development (2004)

Conferences

  1. A unifying framework for summary statistic imputation
    Yue Wu, Eleazar Eskin and Sriram Sankararaman
    Research in Computational Molecular Biology: 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings(2018)

  2. Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies
    Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman and Eran Halperin
    Research in Computational Molecular Biology: 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings(2018)

  3. TrickleDNS: Bootstrapping DNS security using social trust
    Sriram Sankararaman, Jay Chen, Lakshminarayanan Subramanian and Venugopalan Ramasubramanian
    2012 Fourth International Conference on Communication Systems and Networks (COMSNETS 2012)(2012)

  4. Induced churn as shelter from routing-table poisoning
    Tyson Condie Varun, Varun Kacholia, Sriram Sankararaman, Joseph M Hellerstein and Petros Maniatis
    In Proc. 13th Annual Network and Distributed System Security Symposium (NDSS(2006)

  5. On the end-to-end call acceptance and the possibility of deterministic QoS guarantees in ad hoc wireless networks
    S Sriram, T Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    Proceedings of the 6th ACM international symposium on Mobile ad hoc networking and computing(2005)

  6. The influence of QoS routing on the achievable capacity in TDMA-based ad hoc wireless networks
    S Sriram, Tamma Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    IEEE Global Telecommunications Conference, 2004. GLOBECOM’04.(2004)

  7. MuSeQoR: multi-path failure-tolerant security-aware qos routing in ad hoc wireless networks
    S Sriram, T Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    International Conference on High-Performance Computing(2004)

  8. The influence of QoS routing on the achievable capacity in TDMA-based ad hoc wireless networks
    S Sriram, Tamma Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    IEEE Global Telecommunications Conference, 2004. GLOBECOM’04.(2004)