Publications

\(^\dagger\), * denote equal contributions

Preprints

  1. Arunabha Majumdar, Kathryn Burch, Sriram Sankararaman, Bogdan Pasaniuc, W. James Gauderman, and John S. Witte
    A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes
    bioRxiv (2020)

  2. Nadav Rakocz, Boyang Fu, Eran Halperin\(^\dagger\), Sriram Sankararaman\(^\dagger\)
    A Statistical Model for Quantifying the Needed Duration of Social Distancing for the COVID-19 Pandemic
    medRxiv (2020)

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

Publications

  1. Sriram Sankararaman
    Methods for detecting introgressed archaic sequences
    Current Opinions in Genetics and Development, (2020) [PDF]

  2. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Aaron Zhou, Bogdan Pasaniuc, and Sriram Sankararaman
    Efficient variance components analysis across millions of genomes
    Nature Communications (2020) [PDF]
    Preliminary version presented at RECOMB 2019 and NeurIPS Machine Learning in Computational Biology Workshop 2019.

  3. Ruth Johnson, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, and Sriram Sankararaman
    A scalable method for estimating the regional polygenicity for complex traits
    RECOMB (2020) [bioRxiv]

  4. Gregory Plumb, Jonathan Terhorst, Sriram Sankararaman, and Ameet Talwalkar
    Explaining Groups of Points in Low-Dimensional Representations
    ICML (2020) [PDF]

  5. Yue Wu, Eleazar Eskin\(^\dagger\), Sriram Sankararaman\(^\dagger\)
    A unifying framework for imputing summary statistics in Genome-wide Association Studies
    Journal of Computational Biology (2020) [PDF]
    Preliminary version presented at RECOMB 2018

  6. Aman Agrawal*, Alec M. Chiu*, Minh Le, Eran Halperin, and Sriram Sankararaman
    Scalable probabilistic PCA for large-scale genetic variation data
    PLoS Genetics (2020) [PDF, Supporting Information]

  7. Arun Durvasula, Sriram Sankararaman
    Recovering signals of ghost archaic introgression in African populations
    Science Advances (2020) [PDF, Supporting Information]

  8. Brian Hill*, Robert Brown*, Eilon Gabel, Christine Lee, Maxime Cannesson, Loes Olde Loohuis, Ruth Johnson, Brandon Jew, Uri Maoz, Aman Mahajan, Sriram Sankararaman\(^\dagger\), Ira Hofer\(^\dagger\), Eran Halperin\(^\dagger\)
    Preoperative predictions of in-hospital mortality using electronic medical record data
    British Journal of Anaesthesia (2019) [PDF, Supporting Information]

  9. Kangcheng Hou*, Kathryn Burch*, Arunabha Majumdar, Huwenbo Shi, Nicholas Mancuso, Yue Wu, Sriram Sankararaman, and Bogdan Pasaniuc
    Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture
    Nature Genetics (2019) [PDF, Supporting Information]

  10. Yue Wu, Anna Yaschenko, Mohammadreza Heydary, Sriram Sankararaman
    Fast estimation of genetic correlation for Biobank-scale data
    RECOMB (2019) [bioRxiv]

  11. Elior Rahmani, Regev Schweiger, Brooke Rhead, Lindsey Criswell, Lisa Barcellos, Eleazar Eskin, Saharon Rosset, Sriram Sankararaman, and Eran Halperin
    Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology
    Nature Communications (2019) [PDF, Supporting Information]
    Preliminary version presented at RECOMB 2018

  12. Arun Durvasula and Sriram Sankararaman
    A statistical model for reference-free inference of archaic local ancestry
    PLoS Genetics (2019) [PDF, Supporting Information]

  13. Yue Wu and Sriram Sankararaman
    A scalable estimator of SNP heritability for biobank-scale data
    Bioinformatics (special issue of ISMB) (2018) [PDF]

  14. Ruth Johnson, Huwenbo Shi, Bogdan Pasaniuc\(^\dagger\) and Sriram Sankararaman\(^\dagger\)
    A unifying framework for joint trait analysis under a non-infinitesimal model
    Bioinformatics (special issue of ISMB) (2018) [PDF]

  15. Molly Schumer, Chenling Xu, Daniel Powell, Arun Durvasula, Laurits Skov, Chris Holland, John Blazier, Sriram Sankararaman, et al.
    Natural selection interacts with recombination to shape the evolution of hybrid genomes
    Science (2018) [PDF, Supporting Information]

  16. Charleston Chiang, Serghei, Mangul, Christopher Robles, and Sriram Sankararaman
    A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese
    Molecular Biology and Evolution (2018) [PDF]

  17. Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea Ju, Ayellet Segre, Jong Wha Joo, Hyejung Won, Sriram Sankararaman, et al.
    Widespread allelic heterogeneity in complex traits
    The American Journal of Human Genetics (2017) [PDF]

  18. Bernard Jegou, Sriram Sankararaman, Antoine Rolland, David Reich, and Frederic Chalmel
    Meiotic genes are enriched in regions of reduced archaic ancestry
    Molecular Biology and Evolution (2017) [PDF]

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

  20. Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, and David Reich
    A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years
    Proceedings of the National Academy of Sciences (2016) [PDF]

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

  22. James Zou, Danny Park, Esteban Burchard, Dara Torgerson, Maria Pino-Yanes, Yun Song, Sriram Sankararaman\(^\dagger\), Eran Halperin\(^\dagger\), and Noah Zaitlen\(^\dagger\)
    Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns
    Proceedings of the National Academy of Sciences (2016) [PDF]

  23. Swapan Mallick, Heng Li, Mark Lipson, et al.
    The Simons genome diversity project: 300 genomes from 142 diverse populations
    Nature (2016) [PDF]

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

  25. Fernando Racimo,Sriram Sankararaman, Rasmus Nielsen and Emilia Huerta-Sanchez
    Evidence for archaic adaptive introgression in humans
    Nature Reviews Genetics (2015) [PDF]

  26. James Zou, Eran Halperin, Esteban Burchard and Sriram Sankararaman
    Inferring parental genomic ancestries using pooled semi-Markov processes
    Bioinformatics (special issue of ISMB) (2015) [PDF]

  27. Pier Francesco Palamara, Laurent Francioli, et al.
    Leveraging distant relatedness to quantify human mutation and gene-conversion rates
    The American Journal of Human Genetics (2015)

  28. Kay Prufer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, et al.
    The complete genome sequence of a Neanderthal from the Altai Mountains
    Nature (2014) [PDF]

  29. Sriram Sankararaman, Swapan Mallick, Michael Dannemann, Kay Prufer, Janet Kelso, Svante Paabo, Nick Patterson and David Reich
    The genomic landscape of Neanderthal ancestry in present-day humans
    Nature (2014) [PDF]

  30. The SIGMA Type 2 Diabetes Consortium
    Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico
    Nature (2014) [PDF]

  31. Noah Zaitlen, Bogdan Pasaniuc, Sriram Sankararaman, Gaurav Bhatia, et al.
    Leveraging population admixture to characterize the heritability of complex traits
    Nature genetics (2014) [PDF]

  32. Bogdan Pasaniuc*, Sriram Sankararaman*, Dara Torgerson, et al.
    Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation
    Bioinformatics (2013) [PDF]

  33. Gaurav Bhatia, Nick Patterson, Sriram Sankararaman and Alkes Price
    Estimating and interpreting \(F_{ST}\): the impact of rare variants
    Genome research (2013) [PDF]

  34. Alexandre Bouchard-Cote, Sriram Sankararaman and Michael Jordan
    Phylogenetic inference via sequential Monte Carlo
    Systematic biology (2012) [PDF]

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

  36. Yael Baran*, Bogdan Pasaniuc*, Sriram Sankararaman*, et al.
    Fast and accurate inference of local ancestry in Latino populations
    Bioinformatics (2012) [PDF]

  37. Sriram Sankararaman, Nick Patterson, Heng Li, Svante Paabo and David Reich
    The date of interbreeding between Neandertals and modern humans
    PLoS genetics (2012) [PDF]

  38. Michael Turchin, Charleston Chiang, Cameron Palmer, Sriram Sankararaman, David Reich, Joel Hirschhorn, Genetic Investigation of ANthropometric Traits (GIANT) Consortium et al.
    Evidence of widespread selection on standing variation in Europe at height-associated SNPs
    Nature genetics (2012) [PDF]

  39. Sriram Sankararaman, Fei Sha, Jack F Kirsch, Michael I Jordan and Kimmen Sjolander
    Active site prediction using evolutionary and structural information
    Bioinformatics (2010) [PDF]

  40. Colin Hodgkinson, Mary-Anne Enoch, Vibhuti Srivastava, et al.
    Genome-wide association identifies candidate genes that influence the human electroencephalogram
    Proceedings of the National Academy of Sciences (2010) [PDF]

  41. Sriram Sankararaman*, Guillaume Obozinski*, Michael Jordan and Eran Halperin
    Genomic privacy and limits of individual detection in a pool
    Nature genetics (2009) [PDF]

  42. Bogdan Pasaniuc*, Sriram Sankararaman*, Gad Kimmel and Eran Halperin
    Inference of locus-specific ancestry in closely related populations
    Bioinformatics (special issue of ISMB) (2009) [PDF]

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

  44. Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund and Kimmen Sjolander
    ResBoost: characterizing and predicting catalytic residues in enzymes
    BMC bioinformatics (2009) [PDF]

  45. Sriram Sankararaman*, Gad Kimmel*, Eran Halperin, Michael Jordan
    On the inference of ancestries in admixed populations
    Genome research (2008) [PDF]

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

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

  48. Christine F Skibola, et al.
    Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma
    PloS one (2008)

  49. S Sriram, Tamma Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    The influence of QoS routing on the achievable capacity in TDMA-based ad hoc wireless networks
    Wireless Networks (2008) [PDF]

  50. Tyson Condie Varun, Varun Kacholia, Sriram Sankararaman, Joseph M Hellerstein and Petros Maniatis
    Induced churn as shelter from routing-table poisoning
    Network and Distributed System Security Symposium (NDSS) (2006) [PDF]

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

  52. S Sriram, T Bheemarjuna Reddy, BS Manoj and C Siva Ram Murthy
    On the end-to-end call acceptance and the possibility of deterministic QoS guarantees in ad hoc wireless networks
    ACM International Symposium on Mobile ad hoc Networking and Computing (MobiHoc) (2005) [PDF]

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

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

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