Publications

2023
  • Integrating sex-bias into studies of archaic introgression on chromosome X

    Chevy, ET, Huerta-Sanchez, E, Ramachandran, S

    PLoS Genetics 2023 Vol. 19:e1010399

  • Enabling interpretable machine learning for biological data with reliability scores

    Ahlquist, KD, Sugden, LA, Ramachandran, S

    PLoS Computational Biology 2023 Vol. 19:e1011175

2022
  • Counter the weaponization of genetics research by extremists

    Carlson, J, Henn, BM, Al-Hindi, DR, Ramachandran, S

    Nature 2022 Vol. 610:444-447

  • The drift of #MyBodyMyChoice discourse on Twitter

    Menghini, C, Uhr, J, Haddadan, S, Champagne, A, Sandstede, B, Ramachandran, S

    Proceedings of the 14th ACM Web Science Conference 2022 110-117

  • Uncertainty quantification in variable selection for genetic fine-mapping using bayesian neural networks

    Cheng, W, Ramachandran, S, Crawford, L

    iScience 2022 Vol. 25:104553

  • Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries

    Smith, SP, Shahamatdar, S, Cheng, W, Zhang, S, Paik, J, Graff, M, Haiman, C, Matise, TC, North, KE, Peters, U, Kenny, E, Gignoux, C, Wojcik, G, Crawford, L, Ramachandran, S

    American Journal of Human Genetics 2022 Vol. 109:871-884

  • Human genetic admixture through the lens of population genomics

    Gopalan, S, Smith, SP, Korunes, K, Hamid, I, Ramachandran, S, Goldberg, A

    Philosophical Transactions of the Royal Society B 2022 Vol. 377:20200410

  • Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

    Atkinson, EG, Dalvie, S, Pichkar, Y, Kalungi, A, Majara, L, Stevenson, A, Abebe, T, Akena, D, Alemayehu, M, Ashaba, FK, Atwoli, L, Baker, M, Chibnik, LB, Creanza, N, Daly, MJ, Fekadu, A, Gelaye, B, Gichuru, S, Injera, WE, James, R, Kariuki, SM, Kigen, G, Koen, N, Koenen, KC, Koenig, Z, Kwobah, E, Kyebuzibwa, J, Musinguzi, H, Mwema, RM, Neale, BM, Newman, CP, Newton, CRJC, Ongeri, L, Ramachandran, S, Ramesar, R, Shiferaw, W, Stein, DJ, Stroud, RE, Teferra, S, Yohannes, MT, Zingela, Z, Martin, AR, and NeuroGAP-Psychosis Study Team

    American Journal of Human Genetics 2022 Vol. 109:1667-1679

2021
  • Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila

    Spierer, AN, Mossman, JA, Smith, SP,, Crawford, L, Ramachandran, S, Rand, DM

    PLoS Genetics 2021 17:e1008887

  • Multi-scale inference of genetic trait architecture using biologically annotated neural networks

    Demetci, P, Cheng, W, Darnell, G, Zhou, X, Ramachandran, S, Crawford L

    PLoS Genetics 2021 Vol. 17:e1009754

2020
  • Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits

    Cheng, W, Ramachandran, S, Crawford L

    PLoS Genetics 2020 Vol. 16:e1008855

  • Germline features associated with immune infiltration in solid tumors

    Shahamatdar, S, He, MX, Reyna, MA, Gusev, A, AlDubayan, SH, Van Allen, EM, Ramachandran, S

    Cell Reports 2020 Vol. 30:2900-2908

  • Hierarchical clustering of gene-level association statistics reveals shared and differential genetic architecture among traits in the UK Biobank

    McGuirl, MR (joint first), Smith, SP (joint first), Sandstede, B, Ramachandran, S

    Genetics 2020 Vol. 215:511-529

2019
  • The inference of sex-biased human demography from whole-genome data

    Musharoff, S, Shringarpure, S, Bustamante, CD, Ramachandran, S

    PLoS Genetics 2019 Vol. 15:e1008293

  • Characterization of prevalence and health consequences of uniparental disomy in four million individuals from the general population

    Nakka, P, Smith, SP, O'Donnell-Luria, AH, McManus, KF, 23andMe Research Team, Mountain, JL, Ramachandran, S, Sathirapongsasuti, JF

    American Journal of Human Genetics 2019 Vol. 105:921-932

  • Bayesian estimation of population size changes by sampling Tajima’s Trees

    Palacios, JA, Veber, A, Cappello, L, Wang, Z, Wakeley, J, Ramachandran, S

    Genetics 2019 Vol. 213:967–986

2018
  • No evidence for recent selection at FOXP2 among diverse human populations

    Atkinson, EG, Audesse, AJ, Palacios, JA, Bobo, D, Webb, AE, Ramachandran, S, Henn, BM

    Cell 2018 Vol. 174:1424-1435

  • Localization of adaptive variants in human genomes using averaged one-dependence estimation

    Sugden, LA, Atkinson, EG, Fischer, AP, Rong, S, Henn, BM, Ramachandran, S

    Nature Communications 2018 Vol. 9:703

  • Missing compared to what? Revisiting heritability, genes and culture

    Feldman, MW, Ramachandran, S

    Philosophical Transactions of the Royal Society B 2018 Vol. 373:20170064

2017
  • Novel gene and network associations found for Acute Lymphoblastic Leukemia using case−control and family-based studies in multiethnic populations

    Nakka, P, Archer, NP, Xu, H, Lupo, PJ, Raphael, BJ, Yang, JJ, and Ramachandran, S

    Cancer Epidemiology, Biomarkers, & Prevention 2017 Vol. 26:1531-1539

2016
  • Gene and network analysis of common variants reveals novel associations in multiple complex diseases

    Nakka, P, Raphael, BJ, and Ramachandran, S

    Genetics 2016 Vol. 204:783-798

  • Integrating the signatures of demic expansion and archaic introgression in studies of human population genomics

    Alpert Sugden, L and Ramachandran, S

    Current Opinion in Genetics and Development 2016 Vol. 41:140-149

  • pong: fast analysis and visualization of latent clusters in population genetic data

    Behr, AA, Liu, KZ, Liu-Fang, G, Nakka, P, and Ramachandran, S

    Bioinformatics 2016 Vol. 32:2817-2823

2015
  • Bayesian nonparametric inference of population size changes from sequential genealogies

    Palacios, JA, Wakeley, J, and Ramachandran, S

    Genetics 2015 Vol. 201:281-304

  • A comparison of worldwide phonemic and genetic variation in human populations

    Creanza, N, Ruhlen, M, Pemberton, TJ, Rosenberg, NA, Feldman, MW, and Ramachandran, S

    Proceedings of the National Academy of Sciences USA 2015 Vol. 112:1265-1272

2014
  • Global diversity and risk of human infectious disease outbreaks

    Smith KF, Goldberg M, Rosenthal S, Carlson L, Chen J, Chen C, Ramachandran S

    J Roy Soc Interface 2014 Vol. 11:20140950

  • Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms

    Soemedi R, Vega H, Belmont JM, Ramachandran S, Fairbrother WG

    In: Systems and molecular perspectives to RNA binding protein biology 2014 ed. G Yeo. Springer

2013
  • Network analysis of GWAS data

    Leiserson MDM, Eldridge J, Ramachandran S, Raphael BJ

    Current Opinion in Genetics and Development 2013 Vol. 23:602-610

2012
  • Gene genealogies within a fixed pedigree, and the robustness of Kingman’s coalescent

    Wakeley J, King L, Low BS, Ramachandran S

    Genetics 2012 Vol. 190:1433-1445

  • The phosphorus content of common rocks - a potential driver of ecosystem P status

    Porder S, Ramachandran S

    Plant and Soil 2012 Vol. 367:41-55

2011
  • A test of the influence of continental axes of orientation on patterns of human gene flow

    Ramachandran S, Rosenberg NA

    American Journal of Physical Anthropology 2011 Vol. 146:515-529

  • Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

    Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Rodríguez-Botiguée L, Ramachandran S, et al.

    Proc Natl Acad Sci USA 2011 Vol. 108:5154-5162

  • Perspectives on human population structure at the cusp of the sequencing era

    Novembre J, Ramachandran S

    Annual Review of Genomics and Human Genetics 2011 Vol. 12:245-274


Papers published before Brown


2010
  • Genetics and genomics of human population structure

    Ramachandran S, Tang H, Gutenkunst R, Bustamante CD

    pp. 589-616. In: Vogel and Motulsky's Human Genetics: Problems and Approaches 2010 4th ed., eds. M Speicher, SE Antonarakis, AG Motulsky. Springer

  • Characterization of X-linked SNP genotypic variation in globally distributed human populations

    Casto AM, Li JZ, Absher D, Myers R, Ramachandran S, Feldman MW

    Genome Biology 2010 Vol. 11:R10

2009
  • Evaluating signatures of sex-specific processes in the human genome

    Bustamante CD, Ramachandran S

    Nature Genetics 2009 (News and Views) Vol. 41:8-10

  • Theory of migration: Implications for linguistic evolution

    Ramachandran S, Feldman MW

    In: Ancient Human Migrations: A Multidisciplinary Approach 2009 eds. PN Peregrine, I Peiros, MW Feldman. University of Utah Press

2008
  • Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci

    Ramachandran S, Rosenberg NA, Feldman MW, Wakeley J

    Theoretical Population Biology 2008 Vol. 74:291-301

  • Worldwide human relationships inferred from genome-wide patterns of variation

    Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM

    Science 2008 Vol. 319:1100-1104

2007
  • Genetic variation and population structure in Native Americans

    Wang S, Lewis Jr. CM, Jakobsson M, Ramachandran S, Ray N, et al.

    PLoS Genetics 2007 Vol. 3:e185

2005
  • Clines, clusters, and the effect of study design on the inference of human population structure

    Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW

    PLoS Genetics 2005 Vol. 1:e70

  • Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

    Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL

    Proc Natl Acad Sci USA 2005 Vol. 102:15942-15947

2004
  • Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites

    Ramachandran S, Rosenberg NA, Zhivotovsky L, Feldman MW

    Human Genomics 2004 Vol. 1:87-97

  • Demographic estimates from Y-chromosome microsatellite polymorphisms: analysis of a worldwide sample

    Macpherson JM, Ramachandran S, Diamond L, Feldman MW

    Human Genomics 2004 Vol. 1:345-354