Williams lab

Cornell campus at dusk
Amy Williams (CV) left Cornell University in December 2022 and is now a Senior Scientist at 23andMe. This HAPI-DNA website hosts several tools the Williams lab produced at Cornell. Below are lists of the students and postdoc that were in the lab and publications (including those published at 23andMe).

Williams lab students and postdoc

Siddharth Avadhanam

Siddharth is a Computational Biology graduate student interested in developing probabilistic models and inference techniques to better understand human genetic variation and demographic history, and to build faster and more accurate tools for annotating genome data. He came to Cornell with a B.E. in Chemical Engineering from the Birla Institute of Technology of Sciences in India and a Masters degree in Biostatistics from Michigan State University.

Jens Sannerud

Jens is a Genetics, Genomics, and Development Ph.D. student interested in studying evolution and genetics at the population scale. He received his Sc.B. in Applied Mathematics and Biology from Brown University.

Sayantani Basu-Roy

Sayantani was a postdoctoral associate in the lab from Feb 2015-Jan 2017 and worked on a method for inferring the parnet-of-origin of haplotypes using data from a set of siblings. She received her Ph.D. in Biology from the University of Paris-SUD XI in Orsay, France.

Ramya Babu

Ramya did research on relatedness inference in the lab and graduated with an M.S. degree in May 2018.

Arjun Biddanda

Arjun graduated from Cornell University with a B.S. in Computer Science in 2015. He was an undergraduate researcher and worked on comparing methods for detecting identity by descent segments.

Yilei Huang

Yilei was an undergraduate student in the lab interested in population genetics and in particular applications of coalescent theory for demographic inference. He worked on demography-aware relatedness inference techniques.

Melissa Hubisz

Melissa received her Ph.D. in Computational Biology in 2019, and was a co-advisee in the lab (also working with Adam Siepel). She has a B.S. in engineering from Caltech and an M.S. in human genetics from the University of Chicago.

Ryan O’Hern

Ryan graduated from Cornell University with a M.Eng. in Computer Science. He was a research assistant in the lab from August 2015-December 2016 and worked on a method for inferring pedigree relationships using large genotype datasets.

Ying Qiao

Ying graduated with a Ph.D. in Computational Biology from Cornell in 2021. She developed several methods for relatedness inference and reconstructing DNA of parents from siblings. Before coming to Cornell, she received her B.S. degree in in Applied Mathematics from Zhejiang University in China.

Monica Ramstetter

Monica began research in the lab in March 2015 and completed a Ph.D. in 2017, having conducted research on methods to infer relationships between individuals.

Daniel N. Seidman

Daniel received his Ph.D. in Computational Biology from Cornell in 2022. His worked focused on algorithmic design and implementation for analysis of genetic data. He received a B.S. in Computational Biology from Brown University.


Preprints and manuscripts under review

Qiao Y, Jewett EM, McManus KF, Freyman WA, Curran JE, Williams-Blangero S, Blangero J, The 23andMe Research Team, Williams AL. Reconstructing parent genomes using siblings and other relatives. (bioRxiv preprint)

Williams CM, O’Connell J, Freyman WA, 23andMe Research Team, Gignoux CR, Ramachandran S, Williams AL. Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin classification of variants. (bioRxiv preprint)

Avadhanam S, Williams AL. Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods. (bioRxiv preprint)

Peer-reviewed Publications

Massarat AR, Lamkin M, Reeve C, Williams AL, D’Antonio M, Gymrek M. Haptools: a toolkit for admixture and haplotype analysis. Bioinformatics 39(3):btad104, Mar. 2023.

Avadhanam S, Williams AL. Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls. Am J Hum Genet 109(1):1405-1420, Aug. 2022.

Smith J, Qiao Y, Williams AL. Evaluating the utility of identity-by-descent segment numbers for relatedness inference via information theory and classification. G3: Genes, Genomes, Genetics, Mar. 2022.

Chan AW, Villwock SS, Williams AL, Jannink JL. Sexual dimorphism and the effect of wild introgressions on recombination in Manihot esculenta. G3: Genes, Genomes, Genetics, Nov. 2021.

Kivisild T, Saag L, Hui R, Biagini SA, Pankratov V, D’Atanasio E, Pagani L, Saag L, Rootsi S, Mägi R, Metspalu E, Valk H, Malve M, Irdt K, Reisberg T, Solnik A, Scheib CL, Seidman DN, Williams AL, Tambets K, Metspalu M. Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population. Am J Hum Genet 108(9):1792-1806, Sep. 2021.

Qiao Y, Sannerud J, Basu-Roy S, Hayward C, Williams AL. Distinguishing pedigree relationships using multi-way identity by descent sharing and sex-specific genetic maps. Am J Hum Genet 108(1):68-83, Jan 2021.

Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLOS Genet 16(8):e1008895, Aug 2020.

Seidman DN, Shenoy SA, Kim M, Babu R, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Williams AL. Rapid, phase-free detection of long identical by descent segments enables effective relationship classification. Am J Hum Genet 106(4):453-466, Apr 2020.

Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Carmi S, Williams AL. Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. PLOS Genet 15(12):e1007979, Dec 2019.

Chan AW, Williams AL, Jannink JL. A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data. BMC Bioinformatics 19:478, Dec 2018.

Ramstetter MD, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Mezey JG, Williams AL. Inferring identical by descent sharing of sample ancestors promotes high resolution relative detection. Am J Hum Genet 103(1):30-44, Jul 2018.
Video of invited webinar presentation from Broad Institute [YouTube]

Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukianinen T, … [18 authors] … Williams AL, … [54 authors] … Altshuler D, Florez JC on behalf of the SIGMA T2D Genetics
Consortium. A loss-of-function splice acceptor variant in IGF2 is protective for type 2 diabetes. Diabetes 66(11):2903-2914, Nov 2017.

Ramstetter MD, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Mezey JG, Williams AL. Benchmarking relatedness inference methods with genome-wide data from thousands of relatives. Genetics 207(1):75-82, Sep 2017.

Palmer ND, Goodarzi MO, Langefeld CD, … [22 authors] … Williams AL, … [21 authors] … Watanabe RM, Wagenknecht LE. Genetic Variants Associated with Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium. Diabetes 64(5):1853-66, May 2015.

Williams AL, Genovese G, Dyer T, et al. for the T2D-GENES Consortium. Non-crossover gene conversions show strong allelic bias and unexpected clustering in humans. eLife 2015;4:e04637, Apr 2015.

The SIGMA Type 2 Diabetes Consortium: Estrada K, Aukrust I, Bjørkhaug L, Burtt NP, Mercader JM, García-Ortiz H, Huerta-Chagoya A, Moreno-Macías H, Walford G, Flannick J, Williams AL*, et al. Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population. JAMA 311(22):2305-14, Jun 2014.
* Preformed sample selection for exome sequencing and contributed to association analyses

The SIGMA Type 2 Diabetes Consortium: Williams AL, Jacobs SBR, Moreno-Macías H, et al. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506:97-101, Feb 2014.
Led the genetics analysis and wrote the genetics portions of paper.

The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65, Nov 2012.
Developed HAPMIX extension and applied it to the Latino populations.

Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D. Phasing Many Thousands of Genotyped Samples. Am J Hum Genet 91:238-51, Aug 2012.

Fejerman L, Chen GK, Eng C, Huntsman S, Hu D, Williams A, Pasaniuc B, John EM, Via M, Gignoux C, Ingles S, Monroe KR, Kolonel LN, Torres-Mejía G, Pérez-Stable EJ, Burchard EG, Henderson BE, Haiman CA, Ziv E. Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas. Hum Mol Genet 21:1907-17, Apr 2012.

Williams AL, Housman DE, Rinard MC, Gifford DK. Rapid Haplotype Inference for Nuclear Families. Genome Biol 11:R108, Oct 2010.

Williams A, Thies W, Ernst MD. Static Deadlock Detection for Java Libraries. European Conference on Object-Oriented Programming (ECOOP). Glasgow, Scotland, UK. Jul 2005.

Williams A, Barrus S, Morley K, Shirley P. An efficient and robust ray-box intersection algorithm. Journal of Graphics Tools 10:49-54, Jun 2005.