Publications

KAlignedoscope: An interactive visualization tool for aligned clustering results from population structure analyses

Guo, A, Ramachandran, S, Liu, X

Human Population Genetics and Genomics 2026 Vol. 6(2):0006

Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King

Ramachandran, S, Rosenberg, NA

GENETICS 2026 Vol. 232:iyaf273

Clumppling 2.0: A Clustering Alignment Program for Population Structure Analyses

Liu, X, Rosenberg, NA, Ramachandran, S

Human Population Genetics and Genomics 2026 Vol. 6:0004

ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage

Liu, X, Crawford, L, Ramachandran, S

Genome Research 2025 Vol. 35:2691-2700

Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses

Williams, CM, O'Connell, J, Jewett, E, Freyman, WA, 23andMe Research Team, Gignoux, CR, Ramachandran, S, Williams, AL

HGG Advances 2025 Vol. 7:100526

A rapid accurate approach to inferring pedigrees in endogamous populations

Williams, CM, Scelza, BA, Slack, SD, Font-Porterias, N, Al-Hindi, DR, Mathias, RA, Watson, H, Barnes, KC, Lange, E, Johnson, RK, Gignoux, CR, Ramachandran, S, Henn, BM

GENETICS 2025 Vol. 230:iyaf094

Genetic Data Governance in Crisis: Policy Recommendations for Safeguarding Privacy and Preventing Discrimination

Ramanan, V (joint first), Vinod, R (joint first), Williams, C (joint first), Ramachandran, S, Venkatasubramanian, S

STAIG@CHI2025 2025 1st CHI workshop on Sociotechnical AI Governance

Population Genetics Meets Ecology: A Guide to Individual-Based Simulations in Continuous Landscapes

Chevy, ET (joint first), Min, J (joint first), Caudill, V, Champer, SE, Haller, BC, Rehmann, CT, Smith, CCR, Tittes, S, Messer, PW, Haller, BC, Kern, AD, Ramachandran, S, Ralph, PL

Ecology and Evolution 2025 Vol. 15:e71098

Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense

Moody, NM, Williams, CM, Ramachandran, S, Fuxjager, MJ

PLoS Computational Biology 2025 Vol. 21:e1012740

Principles and Policy Recommendations for Comprehensive Genetic Data Governance

Ramanan, V (joint first), Vinod, R (joint first), Williams, C (joint first), Ramachandran, S, Venkatasubramanian, S

AIES 2025 2025 Proceedings of the Eighth AAAI/ACM Conference on AI, Ethics, and Society

Discovering non-additive heritability using additive GWAS summary statistics

Smith, SP (joint first), Darnell, G (joint first), Udwin, D, Stamp, J, Harpak, A, Ramachandran, S, Crawford, L

eLife (original model: review, then publish) 2024 Vol. 13:e90459

Genetic and molecular architecture of complex traits

Lappalainen, T, Li, YI, Ramachandran, S, Gusev, A

Cell 2024 Vol. 187:1059-1075

Deceptive learning in histopathology

Shahamatdar, S, Saeed-Vafa, D, Linsley D, Khalil, F, Lovinger, K, Li, L, McLeod, HT, , Serre, T

Histopathology 2024 Vol. 85:116-132

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

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

Counter the weaponization of genetics research by extremists

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

Nature 2022 Vol. 610:444-447

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 (joint first), Cheng, W (joint first), Darnell, G, Zhou, X, Ramachandran, S, Crawford L

PLoS Genetics 2021 Vol. 17:e1009754

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

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

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

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

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

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

Missing compared to what? Revisiting heritability, genes and culture

Feldman, MW, Ramachandran, S

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

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

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

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

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

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

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

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

Bayesian nonparametric inference of population size changes from sequential genealogies

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

Genetics 2015 Vol. 201:281-304

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

Network analysis of GWAS data

Leiserson MDM, Eldridge J, Ramachandran S, Raphael BJ

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

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

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

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

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

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

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

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

Evaluating signatures of sex-specific processes in the human genome

Bustamante CD, Ramachandran S

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

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

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

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

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

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