Works by Sankararaman, Sriram

Results: 43

Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students.

Published in:

PLoS ONE, 2022, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0268861

By:

Coller, Hilary A.;
Beggs, Stacey;
Andrews, Samantha;
Maloy, Jeff;
Chiu, Alec;
Sankararaman, Sriram;
Pellegrini, Matteo;
Freimer, Nelson;
Johnson, Tracy;
Papp, Jeanette;
Eskin, Eleazar;
Hoffmann, Alexander

Publication type:

Article

A statistical model for reference-free inference of archaic local ancestry.

Published in:

PLoS Genetics, 2019, v. 15, n. 5, p. 1, doi. 10.1371/journal.pgen.1008175

By:

Durvasula, Arun;
Sankararaman, Sriram

Publication type:

Article

Advancing admixture graph estimation via maximum likelihood network orientation.

Published in:

Bioinformatics, 2021, v. 37, p. i142, doi. 10.1093/bioinformatics/btab267

By:

Molloy, Erin K;
Durvasula, Arun;
Sankararaman, Sriram

Publication type:

Article

A two-step approach to testing overall effect of gene–environment interaction for multiple phenotypes.

Published in:

Bioinformatics, 2020, v. 36, n. 24, p. 5640, doi. 10.1093/bioinformatics/btaa1083

By:

Majumdar, Arunabha;
Burch, Kathryn S;
Haldar, Tanushree;
Sankararaman, Sriram;
Pasaniuc, Bogdan;
Gauderman, W James;
Witte, John S

Publication type:

Article

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W390, doi. 10.1093/nar/gkp339

By:

Sankararaman, Sriram;
Kolaczkowski, Bryan;
Sjölander, Kimmen

Publication type:

Article

Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28553-9

By:

Cinelli, Carlos;
LaPierre, Nathan;
Hill, Brian L.;
Sankararaman, Sriram;
Eskin, Eleazar

Publication type:

Article

Evidence of widespread selection on standing variation in Europe at height-associated SNPs.

Published in:

Nature Genetics, 2012, v. 44, n. 9, p. 1015, doi. 10.1038/ng.2368

By:

Turchin, Michael C;
Chiang, Charleston WK;
Palmer, Cameron D;
Sankararaman, Sriram;
Reich, David;
Hirschhorn, Joel N

Publication type:

Article

Genomic privacy and limits of individual detection in a pool.

Published in:

Nature Genetics, 2009, v. 41, n. 9, p. 965, doi. 10.1038/ng.436

By:

Sankararaman, Sriram;
Obozinski, Guillaume;
Jordan, Michael I;
Halperin, Eran

Publication type:

Article

The Date of Interbreeding between Neandertals and Modern Humans.

Published in:

PLoS Genetics, 2012, v. 8, n. 10, p. 1, doi. 10.1371/journal.pgen.1002947

By:

Sankararaman, Sriram;
Patterson, Nick;
Heng Li;
Pääbo, Svante;
Reich, David

Publication type:

Article

Accurate modeling of replication rates in genome-wide association studies by accounting for Winner's Curse and study-specific heterogeneity.

Published in:

G3: Genes | Genomes | Genetics, 2022, v. 12, n. 12, p. 1, doi. 10.1093/g3journal/jkac261

By:

Zou, Jennifer;
Jinjing Zhou;
Faller, Sarah;
Brown, Robert P.;
Sankararaman, Sriram S.;
Eskin, Eleazar

Publication type:

Article

Evaluating supervised and unsupervised background noise correction in human gut microbiome data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009838

By:

Briscoe, Leah;
Balliu, Brunilda;
Sankararaman, Sriram;
Halperin, Eran;
Garud, Nandita R.

Publication type:

Article

Evidence for archaic adaptive introgression in humans.

Published in:

Nature Reviews Genetics, 2015, v. 16, n. 6, p. 359, doi. 10.1038/nrg3936

By:

Racimo, Fernando;
Sankararaman, Sriram;
Nielsen, Rasmus;
Huerta-Sánchez, Emilia

Publication type:

Article

VISTA: an integrated framework for structural variant discovery.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae462

By:

Sarwal, Varuni;
Lee, Seungmo;
Yang, Jianzhi;
Sankararaman, Sriram;
Chaisson, Mark;
Eskin, Eleazar;
Mangul, Serghei

Publication type:

Article

MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae272

By:

Boetto, Christophe;
Frouin, Arthur;
Henches, Léo;
Auvergne, Antoine;
Suzuki, Yuka;
Patin, Etienne;
Bredon, Marius;
Chiu, Alec;
Consortium, Milieu Interieur;
Sankararaman, Sriram;
Zaitlen, Noah;
Kennedy, Sean P;
Quintana-Murci, Lluis;
Duffy, Darragh;
Sokol, Harry;
Aschard, Hugues

Publication type:

Article

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.67077

By:

Findley, Anthony S.;
Monziani, Alan;
Richards, Allison L.;
Rhodes, Katherine;
Ward, Michelle C.;
Kalita, Cynthia A.;
Alazizi, Adnan;
Pazokitoroudi, Ali;
Sankararaman, Sriram;
Xiaoquan Wen;
Lanfear, David E.;
Pique-Regi, Roger;
Gilad, Yoav;
Luca, Francesca

Publication type:

Article

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes.

Published in:

PLoS Genetics, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pgen.1005550

By:

Lipson, Mark;
Loh, Po-Ru;
Sankararaman, Sriram;
Patterson, Nick;
Berger, Bonnie;
Reich, David

Publication type:

Article

MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations.

Published in:

Molecular Biology & Evolution, 2023, v. 40, n. 1, p. 1, doi. 10.1093/molbev/msad001

By:

Zhang, Xinjun;
Kim, Bernard;
Singh, Armaan;
Sankararaman, Sriram;
Durvasula, Arun;
Lohmueller, Kirk E

Publication type:

Article

Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells.

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 1, p. 1, doi. 10.1093/molbev/msab304

By:

Jagoda, Evelyn;
Xue, James R;
Reilly, Steven K;
Dannemann, Michael;
Racimo, Fernando;
Huerta-Sanchez, Emilia;
Sankararaman, Sriram;
Kelso, Janet;
Pagani, Luca;
Sabeti, Pardis C;
Capellini, Terence D

Publication type:

Article

A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group—Han Chinese.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 11, p. 2736, doi. 10.1093/molbev/msy170

By:

Chiang, Charleston W K;
Mangul, Serghei;
Robles, Christopher;
Sankararaman, Sriram

Publication type:

Article

A unifying framework for joint trait analysis under a non-infinitesimal model.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. i195, doi. 10.1093/bioinformatics/bty254

By:

Johnson, Ruth;
Shi, Huwenbo;
Pasaniuc, Bogdan;
Sankararaman, Sriram

Publication type:

Article

A scalable estimator of SNP heritability for biobank-scale data.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. i187, doi. 10.1093/bioinformatics/bty253

By:

Wu, Yue;
Sankararaman, Sriram

Publication type:

Article

Inferring parental genomic ancestries using pooled semi-Markov processes.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i190, doi. 10.1093/bioinformatics/btv239

By:

Zou, James Y.;
Halperin, Eran;
Burchard, Esteban;
Sankararaman, Sriram

Publication type:

Article

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation.

Published in:

Bioinformatics, 2013, v. 29, n. 11, p. 1407, doi. 10.1093/bioinformatics/btt166

By:

Pasaniuc, Bogdan;
Sankararaman, Sriram;
Torgerson, Dara G.;
Gignoux, Christopher;
Zaitlen, Noah;
Eng, Celeste;
Rodriguez-Cintron, William;
Chapela, Rocio;
Ford, Jean G.;
Avila, Pedro C.;
Rodriguez-Santana, Jose;
Chen, Gary K.;
Le Marchand, Loic;
Henderson, Brian;
Reich, David;
Haiman, Christopher A.;
Gonzàlez Burchard, Esteban;
Halperin, Eran

Publication type:

Article

Fast and accurate inference of local ancestry in Latino populations.

Published in:

Bioinformatics, 2012, v. 28, n. 10, p. 1359, doi. 10.1093/bioinformatics/bts144

By:

Baran, Yael;
Pasaniuc, Bogdan;
Sankararaman, Sriram;
Torgerson, Dara G.;
Gignoux, Christopher;
Eng, Celeste;
Rodriguez-Cintron, William;
Chapela, Rocio;
Ford, Jean G.;
Avila, Pedro C.;
Rodriguez-Santana, Jose;
Burchard, Esteban Gonzàlez;
Halperin, Eran

Publication type:

Article

Active site prediction using evolutionary and structural information.

Published in:

Bioinformatics, 2010, v. 26, n. 5, p. 617, doi. 10.1093/bioinformatics/btq008

By:

Sankararaman, Sriram;
Fei Sha;
Kirsch, Jack F.;
Jordan, Michael I.;
Sjölander, Kimmen

Publication type:

Article

Inference of locus-specific ancestry in closely related populations.

Published in:

Bioinformatics, 2009, v. 25, n. 12, p. i213, doi. 10.1093/bioinformatics/btp197

By:

Bogdan Pasaniuc;
Sriram Sankararaman;
Gad Kimmel;
Eran Halperin

Publication type:

Article

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.

Published in:

Bioinformatics, 2008, v. 24, n. 21, p. 2445, doi. 10.1093/bioinformatics/btn474

By:

Sriram Sankararaman;
Kimmen SjÃ¶lander

Publication type:

Article

Fast kernel-based association testing of non-linear genetic effects for biobank-scale data.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-40346-2

By:

Fu, Boyang;
Pazokitoroudi, Ali;
Sudarshan, Mukund;
Liu, Zhengtong;
Subramanian, Lakshminarayanan;
Sankararaman, Sriram

Publication type:

Article

Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 10, p. 1, doi. 10.1371/journal.pcbi.1009483

By:

Johnson, Ruth;
Burch, Kathryn S.;
Hou, Kangcheng;
Paciuc, Mario;
Pasaniuc, Bogdan;
Sankararaman, Sriram

Publication type:

Article

Methylation risk scores are associated with a collection of phenotypes within electronic health record systems.

Published in:

NPJ Genomic Medicine, 2022, v. 7, n. 1, p. 1, doi. 10.1038/s41525-022-00320-1

By:

Thompson, Mike;
Hill, Brian L.;
Rakocz, Nadav;
Chiang, Jeffrey N.;
Geschwind, Daniel;
Sankararaman, Sriram;
Hofer, Ira;
Cannesson, Maxime;
Zaitlen, Noah;
Halperin, Eran

Publication type:

Article

Scalable probabilistic PCA for large-scale genetic variation data.

Published in:

PLoS Genetics, 2020, v. 16, n. 5, p. 1, doi. 10.1371/journal.pgen.1008773

By:

Agrawal, Aman;
Chiu, Alec M.;
Le, Minh;
Halperin, Eran;
Sankararaman, Sriram

Publication type:

Article

Personalized mood prediction from patterns of behavior collected with smartphones.

Published in:

NPJ Digital Medicine, 2024, p. 1, doi. 10.1038/s41746-024-01035-6

By:

Balliu, Brunilda;
Douglas, Chris;
Seok, Darsol;
Shenhav, Liat;
Wu, Yue;
Chatzopoulou, Doxa;
Kaiser, William;
Chen, Victor;
Kim, Jennifer;
Deverasetty, Sandeep;
Arnaudova, Inna;
Gibbons, Robert;
Congdon, Eliza;
Craske, Michelle G.;
Freimer, Nelson;
Halperin, Eran;
Sankararaman, Sriram;
Flint, Jonathan

Publication type:

Article

Non‐Invasive Touch‐Based Lithium Monitoring Using an Organohydrogel‐Based Sensing Interface (Adv. Mater. Technol. 14/2023).

Published in:

Advanced Materials Technologies, 2023, v. 8, n. 14, p. 1, doi. 10.1002/admt.202370063

By:

Lin, Shuyu;
Zhu, Jialun;
Yeung, Justin;
Wu, Tsung‐Yu;
Cheng, Xuanbing;
Zhao, Yichao;
Wang, Bo;
Tan, Jiawei;
Peeters, Sophie;
Seroussi, Ariel;
Sankararaman, Sriram;
Milla, Carlos;
Emaminejad, Sam

Publication type:

Article

Non‐Invasive Touch‐Based Lithium Monitoring Using an Organohydrogel‐Based Sensing Interface.

Published in:

Advanced Materials Technologies, 2023, v. 8, n. 14, p. 1, doi. 10.1002/admt.202202141

By:

Lin, Shuyu;
Zhu, Jialun;
Yeung, Justin;
Wu, Tsung‐Yu;
Cheng, Xuanbing;
Zhao, Yichao;
Wang, Bo;
Tan, Jiawei;
Peeters, Sophie;
Seroussi, Ariel;
Sankararaman, Sriram;
Milla, Carlos;
Emaminejad, Sam

Publication type:

Article

The lingering effects of Neanderthal introgression on human complex traits.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.80757

By:

Xinzhu Wei;
Robles, Christopher R.;
Pazokitoroudi, Ali;
Ganna, Andrea;
Gusev, Alexander;
Durvasula, Arun;
Gazal, Steven;
Po-Ru Loh;
Reich, David;
Sankararaman, Sriram

Publication type:

Article

Efficient variance components analysis across millions of genomes.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17576-9

By:

Pazokitoroudi, Ali;
Wu, Yue;
Burch, Kathryn S.;
Hou, Kangcheng;
Zhou, Aaron;
Pasaniuc, Bogdan;
Sankararaman, Sriram

Publication type:

Article

Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma.

Published in:

PLoS ONE, 2008, v. 3, n. 7, p. 1, doi. 10.1371/journal.pone.0002816

By:

Skibola, Christine F.;
Bracci, Paige M.;
Halperin, Eran;
Nieters, Alexandra;
Hubbard, Alan;
Paynter, Randi A.;
Skibola, Danica R.;
Agana, Luz;
Becker, Nikolaus;
Tressler, Patrick;
Forrest, Matthew S.;
Sankararaman, Sriram;
Conde, Lucia;
Holly, Elizabeth A.;
Smith, Martyn T.

Publication type:

Article

Phylogenetic Inference via Sequential Monte Carlo.

Published in:

Systematic Biology, 2012, v. 61, n. 4, p. 579, doi. 10.1093/sysbio/syr131

By:

Bouchard-Côté, Alexandre;
Sankararaman, Sriram;
Jordan, Michael I.

Publication type:

Article

The genomic landscape of Neanderthal ancestry in present-day humans.

Published in:

Nature, 2014, v. 507, n. 7492, p. 354, doi. 10.1038/nature12961

By:

Sankararaman, Sriram;
Mallick, Swapan;
Dannemann, Michael;
Prüfer, Kay;
Kelso, Janet;
Pääbo, Svante;
Patterson, Nick;
Reich, David

Publication type:

Article

The complete genome sequence of a Neanderthal from the Altai Mountains.

Published in:

Nature, 2014, v. 505, n. 7481, p. 43, doi. 10.1038/nature12886

By:

Prüfer, Kay;
Racimo, Fernando;
Patterson, Nick;
Jay, Flora;
Sankararaman, Sriram;
Sawyer, Susanna;
Heinze, Anja;
Renaud, Gabriel;
Sudmant, Peter H.;
de Filippo, Cesare;
Li, Heng;
Mallick, Swapan;
Dannemann, Michael;
Fu, Qiaomei;
Kircher, Martin;
Kuhlwilm, Martin;
Lachmann, Michael;
Meyer, Matthias;
Ongyerth, Matthias;
Siebauer, Michael

Publication type:

Article

Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60339-7

By:

Wei, Angela;
Border, Richard;
Fu, Boyang;
Cullina, Sinéad;
Brandes, Nadav;
Jang, Seon-Kyeong;
Sankararaman, Sriram;
Kenny, Eimear E.;
Udler, Miriam S.;
Ntranos, Vasilis;
Zaitlen, Noah;
Arboleda, Valerie A.

Publication type:

Article

Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging.

Published in:

NPJ Digital Medicine, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s41746-021-00411-w

By:

Rakocz, Nadav;
Chiang, Jeffrey N.;
Nittala, Muneeswar G.;
Corradetti, Giulia;
Tiosano, Liran;
Velaga, Swetha;
Thompson, Michael;
Hill, Brian L.;
Sankararaman, Sriram;
Haines, Jonathan L.;
Pericak-Vance, Margaret A.;
Stambolian, Dwight;
Sadda, Srinivas R.;
Halperin, Eran

Publication type:

Article

Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11052-9

By:

Rahmani, Elior;
Eskin, Eleazar;
Sankararaman, Sriram;
Halperin, Eran;
Schweiger, Regev;
Rhead, Brooke;
Criswell, Lindsey A.;
Barcellos, Lisa F.;
Rosset, Saharon

Publication type:

Article