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Research Group

Computational & statistical human genetics — how germline and somatic evolution shape genome function, reproduction, and development.

The McCoy Lab

Johns Hopkins University
The McCoy Lab

Overview

Genetic differences in DNA sequence underlie much of the variation in traits we see in nature, both within and between species. Even within a single individual, genetic differences can arise among cells over time, contributing to variation in traits and, in some cases, to conditions such as pregnancy loss and cancer.

The McCoy Lab uses tools from computational and statistical human genetics to study how germline and somatic evolution shape genome function and reproduction and development. Our work spans diverse biological systems but is unified by a common goal: developing methods to uncover the fundamental evolutionary forces that influence our genomes, from individual cells to entire populations.

Research

We combine diverse datasets and concepts from population and complex-trait genetics to achieve quantitative perspectives on human evolution, reproduction, and development, developing and applying computational and statistical methods to this end.

Tree of life illustration linking blood to organs and microbes

Human Evolution

Patterns of variation in human genomes carry a record of key evolutionary events and processes, from archaic introgression to local adaptation.

Read more →Show less ←

Much of this signal lies in complex regions of the genome that we can now resolve by pairing new computational methods with complete, telomere-to-telomere assemblies. Using a graph-based method, we genotyped structural variants across 2,504 globally diverse individuals and found loci with extreme allele-frequency differentiation, including an immunoglobulin-locus insertion that reached high frequency in parts of southeast Asia after being introgressed from Neanderthals ~50,000 years ago.

As part of the Telomere-to-Telomere (T2T) Consortium, we contributed to the first complete human genome (T2T-CHM13) and the first complete Y chromosome, showing the new reference offers universal improvements for analyzing human variation in diverse populations.

Representative papers
Aganezov, S., et al. (2022). A complete reference genome improves analysis of human genetic variation. Science.
Yan, S. M., et al. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife.
Embryo development illustration
Credit: Maayan Harel

Reproduction & Development

Using prenatal and preimplantation genetic testing data, we investigate the genetic causes of aneuploidy and pregnancy loss, from meiotic recombination errors to chromosomal mosaicism in early embryos.

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Fewer than half of all conceptions survive to birth, much of this loss driven by chromosomal errors arising early in development. We showed that a common maternal-effect allele of PLK4 is associated with mosaic aneuploidy, and that severe mosaic forms frequently arise during the first embryonic divisions, causing arrest before implantation, whereas low-level mosaicism appears to be a normal feature of preimplantation development.

To overcome the very low coverage of conventional genetic testing, we developed haplotype-aware methods that distinguish meiotic from mitotic trisomies, map crossovers, and reveal abnormalities that evade standard detection. Expanding upon this work, we recently leveraged genetic testing data from ~140,000 IVF embryos to map the genetic basis of recombination and meiotic-origin aneuploidy. Our study revealed that common variation in meiosis genes, including the meiosis-specific cohesin gene SMC1B, shapes recombination phenotypes and aneuploidy risk.

Beyond embryos, we are extending these themes into other developmental systems, such as spermatogenesis and clonal hematopoiesis.

Representative papers
Carioscia, S. A., et al. (2026). Common variation in meiosis genes shapes human recombination and aneuploidy risk. Nature.
McCoy, R. C., et al. (2023). Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Medicine.
McCoy, R. C., et al. (2015). Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science.

Genome Function

We analyze data from globally diverse populations to understand the genetic basis and evolution of gene expression and splicing, addressing long-standing diversity bias in human genetics.

Read more →Show less ←

Non-coding, regulatory variation influencing gene expression and splicing is a primary source of phenotypic variation, yet human datasets have long been biased toward European ancestries. To address this, we generated an open-access RNA-seq dataset from 731 individuals across 26 populations of the 1000 Genomes Project and mapped expression and splicing QTLs at high resolution, including many that are private to or locally enriched in underrepresented populations.

Notably, when allowing for multiple causal variants per gene, genetic effects on expression are remarkably consistent across ancestries, an encouraging sign for the portability of genetic findings in precision medicine.

Representative papers
Taylor, D. J., et al. (2024). Sources of gene expression variation in a globally diverse human cohort. Nature.
McCoy, R. C., et al. (2017). Impacts of Neanderthal-introgressed sequences on the human transcriptome. Cell.

People

Rajiv McCoy
Principal Investigator

Rajiv McCoy

Associate Professor, Department of Biology

Rajiv's research program uses computational and statistical approaches to study how germline and somatic evolution shape human genome function, reproduction, and development. Before Johns Hopkins, he received his PhD in Biology from Stanford and conducted postdoctoral work at Princeton and the University of Washington.

Postdoctoral Fellows
Michael Tassia
Michael Tassia
Somatic evolution in blood. More →Less ←

Michael is broadly interested in the evolution of animal genomes and how their structure and function change over time. He received his PhD at Auburn University, studying the evolution of immune systems. His current research investigates somatic evolution in the blood by applying phylogenetics over developmental timescales. He is supported by a Scholar Award from the American Society of Hematology and an NIH T32 fellowship in Hematology at the Johns Hopkins School of Medicine.

Website →
Arjun Biddanda
Arjun Biddanda
Population genetics of disease and fertility. More →Less ←

Arjun's research spans theoretical and applied population genetics, particularly to understand human disease, evolution, and fertility. He received his PhD in Human Genetics from the University of Chicago and was a postdoctoral researcher at Oxford. He is supported by a Lalor Foundation fellowship for developing new statistical methods to understand diverse types of aneuploidy in early development.

Website →
Margaret Starostik
Margaret Starostik
Genetic basis of mRNA isoform diversity. More →Less ←

Margaret uses new genomic technologies to achieve an accurate view of the extent, distribution, and genetic basis of mRNA isoform diversity in humans. She received her PhD at Johns Hopkins, working with John Kim and Mike Schatz on post-transcriptional regulation of gene expression by small RNAs.

Website →
Graduate Students
Graydon Moorhead
Graydon Moorhead
Centromeres in embryonic aneuploidy. More →Less ←

Graydon is a PhD student in the CMDB program. He received his BA in Applied Mathematics from Harvard College and worked at the Broad Institute researching cancer genomics. He is currently interested in understanding centromeres in the context of embryonic aneuploidy.

Joshua Bauman
Joshua Bauman
Accuracy of genetic prediction across populations. More →Less ←

Josh is a PhD student in the CMDB program. He received his BS in Cellular, Molecular, and Developmental Biology from the University of Michigan, where he studied AMPK signaling in the lab of Anuj Kumar. He is currently interested in improving the accuracy of genetic predictions across human populations.

Betty Huang
Betty Huang
Genetic basis of expression & splicing variation. More →Less ←

Betty is a PhD student in the CMDB program. She received her BS in Molecular and Cellular Biology from Johns Hopkins. Her current research focuses on understanding the genetic mechanisms shaping variation in human gene expression and splicing.

Undergraduate Researchers
Angela Yang
Angela Yang
Simulations of chromosome mis-segregation. More →Less ←

Angela majors in Molecular & Cellular Biology and Computer Science, applying her CS background to genomic analysis. Her project uses simulations to infer the rates of meiotic and mitotic chromosome mis-segregation that best explain clinical genetic-testing data from embryo biopsies. She is a recipient of a Provost's Undergraduate Research Award (PURA) and will begin a computational biology PhD at Weill Cornell Medicine.

Lana Cheng
Lana Cheng
Simulating hematopoietic stem cell dynamics. More →Less ←

Lana Cheng is a junior undergraduate majoring in Applied Mathematics & Statistics and Biology. Her current project uses SLiM to simulate hematopoietic stem cell populations and track their evolutionary dynamics.

Alumni

PhD & postdoctoral   Andrew Bortvin (PhD 2026) · Sara Carioscia (PhD 2025; Data Scientist, Valo Health) · Dylan Taylor (PhD 2024; Bioinformatics Scientist, Zephyr AI) · Stephanie Yan (PhD 2024; Scientist, Genomics plc) · Kate Isaac (PhD 2023; Postdoc, Fred Hutchinson Cancer Center) · Daniel Ariad (Postdoc 2020–2022; Applied Scientist, Evidium)

View profiles & full bios ↓Hide profiles ↑
Andrew Bortvin
Andrew Bortvin
PhD 2026

BA in Biology from the University of Pennsylvania; previously a research technician at Princeton and Dana-Farber. His thesis developed reference-free population genomic methods that overcome reference-genome bias. Held a Dean's Teaching Fellowship from Johns Hopkins.

Website →
Sara Carioscia
Sara Carioscia
PhD 2025; Data Scientist, Valo Health

BS in Biology and Classics from Georgetown; previously worked in science policy in Washington, DC. Her thesis discovered genetic variants in maternal genomes that influence the risk of aneuploidy in embryos, the leading cause of pregnancy loss. NSF Graduate Research Fellow.

Website →
Dylan Taylor
Dylan Taylor
PhD 2024; Bioinformatics Scientist, Zephyr AI

BS in Biological Sciences from the University of Maryland. His thesis developed functional genomic resources and tested hypotheses about gene-expression evolution in diverse human populations. NIH/NHGRI F31 predoctoral fellow.

Website →
Stephanie Yan
Stephanie Yan
PhD 2024; Scientist, Genomics plc

BA in Biological Sciences from Cornell; summer research student at the Moffitt Cancer Center. Her thesis investigated the role of structural variation in human divergence and adaptation. NIH/NHGRI F31 predoctoral fellow.

Website →
Kate Isaac
Kate Isaac
PhD 2023; Postdoc, Fred Hutchinson Cancer Center

BS in Biochemistry & Molecular Biology and BS in Mathematics from Bethel University. Her research developed statistical models to test hypotheses about human meiosis, embryo implantation, and hematopoiesis. Dean's Teaching Fellow at Johns Hopkins.

Website →
Daniel Ariad
Daniel Ariad
Postdoc 2020–2022; Applied Scientist, Evidium

A physicist by training, with experience in condensed matter and astrophysics, Daniel adapts theory and analytical approaches from these fields to human genomics and evolution. PhD from Ben-Gurion University of the Negev; previously a postdoc at Indiana University Bloomington.

Website →

Undergraduate & MS   Sukriti Gupta (Master's) · Arta Seyedian (Master's 2018–2020; Bioinformatics Data Engineer, Children's Hospital of Philadelphia) · Ameena Beg (Bachelor's, 2024) · Hao Pan (Bachelor's, 2022–2024) · Divya Nair (Bachelor's, 2020–2023) · Katherine Gilbert (Bachelor's, 2022) · Joel Espinoza (Bachelor's, 2018–2020) · Peter Huang (Bachelor's, 2019–2020) · Nicholas Parente (Bachelor's, 2019–2020) · Vincent Huang (Bachelor's, 2018)

News

June 2026
Award

Next Generation Pregnancy Initiative Award

The lab receives a Next Generation Pregnancy Initiative Award from the Burroughs Wellcome Fund, supporting work on the genetic mechanisms of pregnancy loss and fetal genomes.

2026
People
Andrew Bortvin thesis defense

Andrew Bortvin defends his PhD

Andrew, the lab's most recent doctoral graduate, completes his PhD developing reference-free population genomic methods that overcome reference-genome bias.

Jan 2026
Paper

Common variation in meiosis genes shapes recombination and aneuploidy risk

Published in Nature. Analyzing PGT data from more than 139,000 embryos, the lab links common maternal genetic variation to recombination and aneuploidy, a leading cause of pregnancy loss.

2025
Paper

A high incidence of chromosomal mosaicism in human embryos

Published in Genetics. Angela Yang and colleagues use approximate Bayesian computation to show that chromosomal mosaicism is common in blastocyst-stage human embryos, with implications for preimplantation genetic testing.

2025
People
Sara Carioscia's thesis defense

Two PhDs defended, with Oppenheimer Thesis Awards

Sara Carioscia and Dylan Taylor complete their PhDs and receive Oppenheimer Thesis Awards, heading on to Valo Health and Zephyr AI. Congratulations!

Jul 2024
Paper

Sources of gene expression variation in a globally diverse cohort

Published in Nature. The MAGE resource, RNA-seq from 731 individuals across 26 populations, helps address long-standing diversity bias in human genetics.

2024–2026
People

Welcoming new graduate students

Betty Huang (2024), Joshua Bauman (2025), and Graydon Moorhead (2026) join the lab as PhD students in the CMDB program.

View full news archive (2019–2026) ↓Hide full archive ↑
2026
Jun
Lab Retreat in DC. We held our annual retreat at the Bloomberg Center in Washington, DC. Then we checked out the National Gallery of Art across the street.
May
JHU Graduation 2026. Andrew earned his PhD and Angela earned her BS from JHU Biology. Angela also received the McElroy Award for outstanding undergraduate research. Andrew… More →Less ←

Andrew earned his PhD and Angela earned her BS from JHU Biology. Angela also received the McElroy Award for outstanding undergraduate research. Andrew will be heading to Juilliard for music school, and Angela will be pursuing her PhD in computational biology at Weill Cornell Medicine. Congratulations to you both! Screenshot

May
PRISM Conference in Japan. Margaret presented her research on long-read transcriptomes from globally diverse human populations at the PacBio PRISM conference in Fukuoka.
May
Graydon joins the lab. Graydon Moorhead joins the McCoy Lab as a PhD student from the CMDB program. Welcome, Graydon!
Feb
Andrew's thesis defense. Andrew Bortvin delivered his public thesis defense, presenting computational approaches in population genetics that do not rely on a reference genome.… More →Less ←

Andrew Bortvin delivered his public thesis defense, presenting computational approaches in population genetics that do not rely on a reference genome. These “reference-free” methods are especially valuable for studying complex, repetitive, or hyperdiverse loci, as well as species lacking high-quality reference genomes. Congratulations to Dr. Bortvin!

2025
Dec
ASH conference in Orlando. Michael attended the annual conference of the American Society of Hematology in Orlando and gave a talk about his latest work using phylogenetic metho… More →Less ←

Michael attended the annual conference of the American Society of Hematology in Orlando and gave a talk about his latest work using phylogenetic methods to uncover surprising examples of recurrent somatic evolution during hematopoiesis. Check out his abstract, published in Blood .

Oct
ASHG 2025 in Boston. Rajiv, Arjun, and Margaret attended the American Society of Human Genetics Conference in Boston. Arjun and Rajiv presented posters, and Margaret prese… More →Less ←

Rajiv, Arjun, and Margaret attended the American Society of Human Genetics Conference in Boston. Arjun and Rajiv presented posters, and Margaret presented a talk about her work using long-read RNA-seq to study isoform diversity across global human populations.

Aug
JHU turns 150. Sara, Michael, and Rajiv were featured for a fraction of a second in a video celebrating the 150th anniversary of Johns Hopkins University. See if you… More →Less ←

Sara, Michael, and Rajiv were featured for a fraction of a second in a video celebrating the 150th anniversary of Johns Hopkins University. See if you can find us chatting with President Daniels!

Jul
Lab retreat in DC. We had our annual lab retreat at the new JHU Bloomberg Center building in Washington, D.C. We enjoyed some good science, as well as good food and view… More →Less ←

We had our annual lab retreat at the new JHU Bloomberg Center building in Washington, D.C. We enjoyed some good science, as well as good food and views of the city.

May
Sara's thesis defense. Sara Carioscia gave her public thesis defense talk describing her research investigating mechanisms and genetic influences on the accuracy of chromoso… More →Less ←

Sara Carioscia gave her public thesis defense talk describing her research investigating mechanisms and genetic influences on the accuracy of chromosome segregation during the formation of human eggs and sperm. Her research helped uncover how common genetic variation in maternal genome influences risk of chromosome abnormalities that underlie pregnancy loss. Congrats to Dr. Carioscia!

May
Biology of Genomes at Cold Spring Harbor. Rajiv and Sara attended the Biology of Genomes conference at Cold Spring Harbor in New York. Sara presented a poster about her research studying the g… More →Less ←

Rajiv and Sara attended the Biology of Genomes conference at Cold Spring Harbor in New York. Sara presented a poster about her research studying the genetic basis of human aneuploidy.

May
Joshua Bauman joins the lab. Joshua Bauman joins the McCoy lab as a PhD student from the CMDB program. Welcome Josh!
Apr
Mutations in Time and Space conference in Boston. Sara and Michael attended the Mutations in Time and Space conference at the Broad Institute in Boston. Michael presented a poster about the applicatio… More →Less ←

Sara and Michael attended the Mutations in Time and Space conference at the Broad Institute in Boston. Michael presented a poster about the application of Bayesian phylogenetic methods for studying complex histories of somatic evolution. Sara gave a prize-winning talk about her work studying the genetic basis of aneuploidy and recombination!

Apr
PGDIS and Origins of Aneuploidy conferences in Belgium. Rajiv and Arjun attended back-to-back meetings of the Preimplantation Genetic Diagnosis International Society (PGDIS) and Origins of Aneuploidy Resear… More →Less ←

Rajiv and Arjun attended back-to-back meetings of the Preimplantation Genetic Diagnosis International Society (PGDIS) and Origins of Aneuploidy Research Consortium (OARC) in Leuven, Belgium. Rajiv presented at PGDIS and Arjun presented at OARC about the lab's research using data from in vitro fertilized human embryos to study the genetic basis of aneuploidy and recombination.

2024
Dec
Chromosomes and Chromatin Workshop. Our lab participated in the JHU Chromatin and Chromosomes Workshop hosted by the BDP Epigenome Sciences Cluster. Sara gave a talk about her work inves… More →Less ←

Our lab participated in the JHU Chromatin and Chromosomes Workshop hosted by the BDP Epigenome Sciences Cluster. Sara gave a talk about her work investigating the genetic basis of variation in risk for embryonic aneuploidy.

Dec
Margaret wins prize at holiday party. Her Snoopy chocolate Swiss roll cake won "best theme" dessert!
Nov
ASHG 2024 in Denver. Rajiv and Margaret attended the American Society of Human Genetics conference in Denver. Rajiv presented a plenary talk describing Arjun and Sara's re… More →Less ←

Rajiv and Margaret attended the American Society of Human Genetics conference in Denver. Rajiv presented a plenary talk describing Arjun and Sara's research about the genetic basis of aneuploidy and recombination. Margaret chaired a session about the use of new sequencing technologies for transcriptomic analysis.

Oct
CMDB Retreat in Pennsylvania. Our lab participated in the annual retreat at Liberty Mountain Resort, hosted by the Johns Hopkins graduate program in Cell, Molecular, Developmental … More →Less ←

Our lab participated in the annual retreat at Liberty Mountain Resort, hosted by the Johns Hopkins graduate program in Cell, Molecular, Developmental Biology, and Biophysics (CMDB). Sara gave a talk and others presented posters about their research.

Oct
Dylan's thesis defense. Dylan Taylor gave his public thesis defense talk describing his research studying the sources of functional genomic variation across diverse human pop… More →Less ←

Dylan Taylor gave his public thesis defense talk describing his research studying the sources of functional genomic variation across diverse human populations. Congrats to Dr. Taylor!

Sep
MD-GEM Genetics Research Day. Sara and Arjun each presented posters at the Maryland Genetics, Epidemiology, and Medicine research day. Both won first place in their respective cate… More →Less ←

Sara and Arjun each presented posters at the Maryland Genetics, Epidemiology, and Medicine research day. Both won first place in their respective categories (Graduate Student, Postdoc)!

Jul
Summer party at Rajiv's house. The lab tries a Baltimore classic: pepperment lemon sticks.
Jul
Michael receives T32 fellowship. Michael Tassia was awarded an NIH T32 fellowship from the Division of Hematology. Congratulations to Michael!
Jun
JHU Catalyst Award. The lab received a Catalyst Award in support of early career faculty. Read more here: . A celebration was held at the Peabody Library. Thank you to Jo… More →Less ←

The lab received a Catalyst Award in support of early career faculty. Read more here: . A celebration was held at the Peabody Library. Thank you to Johns Hopkins!

Jun
MIRA renewal is funded. Our lab was awarded an R35 fellowship from the National Institute of General Medical Sciences of the NIH, funding our research through 2029. We are ve… More →Less ←

Our lab was awarded an R35 fellowship from the National Institute of General Medical Sciences of the NIH, funding our research through 2029. We are very grateful for the support!

Jun
Margaret Starostik joins the lab. Margaret joins the McCoy lab as a postdoc. Welcome, Margaret!
May
CMDB Hooding Ceremony. Congratulations to the CMDB graduates! Stephanie received the Oppenheimer Thesis Award in recognition of her work.
May
Betty Huang joins the lab. Betty joins the McCoy lab as a PhD student from the CMDB program. Welcome Betty!
May
Biology of Genomes 2024 at CSHL. Our lab attended the Biology of Genomes conference at Cold Spring Harbor Laboratory. Rajiv, Sara, and Michael presented talks, while Steph, Andrew, an… More →Less ←

Our lab attended the Biology of Genomes conference at Cold Spring Harbor Laboratory. Rajiv, Sara, and Michael presented talks, while Steph, Andrew, and Arjun presented posters!

May
Steph’s thesis defense. Stephanie held her public thesis defense where she talked about her work using long-read sequencing and other technologies to study the evolution of s… More →Less ←

Stephanie held her public thesis defense where she talked about her work using long-read sequencing and other technologies to study the evolution of structural variation in human genomes. Congrats, Dr. Yan!

Apr
Lab door re-decoration
Mar
Arjun receives Lalor Foundation Fellowship. Arjun Biddanda received a postdoctoral fellowship from the Lalor Foundation, in support of his research about the genetic causes of human pregnancy lo… More →Less ←

Arjun Biddanda received a postdoctoral fellowship from the Lalor Foundation, in support of his research about the genetic causes of human pregnancy loss. Read more about this program here: . Congratulations to Arjun, and thank you to the Lalor Foundation!

Mar
Angela receives PURA. Angela Yang received the Provost's Undergraduate Research Award (PURA) from JHU, in support of her research using simulations to study the meiotic and… More →Less ←

Angela Yang received the Provost's Undergraduate Research Award (PURA) from JHU, in support of her research using simulations to study the meiotic and mitotic errors that generate aneuploidy in human embryos. Congrats to Angela!

Mar
TAGC 2024 in Washington, DC. The McCoy Lab attended The Allied Genetics Conference (TAGC) in Washington, DC. Sara, Dylan, Arjun, and Angela presented posters about their research!
2023
Dec
Michael receives ASH Scholar Award. Michael Tassia received a Scholar Award from the American Society of Hematology in support of his postdoctoral research. Congrats to Michael, and than… More →Less ←

Michael Tassia received a Scholar Award from the American Society of Hematology in support of his postdoctoral research. Congrats to Michael, and thank you to ASH!

Dec
Lab purchases matching holiday sweaters
Nov
Andrew receives Dean's Teaching Fellowship. Andrew Bortvin was awarded a Dean's Teaching Fellowship from the Kreiger School of Arts and Sciences at Johns Hopkins. The award will support him in d… More →Less ←

Andrew Bortvin was awarded a Dean's Teaching Fellowship from the Kreiger School of Arts and Sciences at Johns Hopkins. The award will support him in developing his own course that he will teach to undergraduates next fall. Congrats to Andrew!

Nov
ASHG 2023 in Washington, DC. The McCoy Lab attended the American Society of Human Genetics conference in Washington, DC. Arjun gave a talk, others give posters, and we saw Macklem… More →Less ←

The McCoy Lab attended the American Society of Human Genetics conference in Washington, DC. Arjun gave a talk, others give posters, and we saw Macklemore at the PacBio concert.

Oct
Lab retreat. The lab held its first ever retreat at the FastForward space at JHU. The retreat was followed by a thrilling game of Gartic Phone.
Aug
Sara gets clock'd
Jul
SMBE 2023. Michael and Steph presented virtual posters at the annual meeting of the Society for Molecular Biology and Evolution.
Mar
New lab tradition. The lab spectates Andrew’s Joint Lab Meeting presentation from the lab space, starting a new tradition.
Feb
Arjun Biddanda joins the lab. Arjun joins the lab as a postdoc. Welcome, Arjun!
Jan
Angela Yang joins the lab. Angela joins the lab as an undergraduate researcher. Welcome, Angela!
Jan
Dylan awarded F31 Fellowship. Dylan Taylor was awarded an F31 predoctoral fellowship from the National Human Genome Research Institute of the NIH. Congrats to Dylan!
2022
Nov
Re-decorating Rajiv's office. The lab left some gifts in Rajiv’s office while he attended the Origins of Aneuploidy conference.
Aug
Steph awarded F31 fellowship. Stephanie Yan was awarded an F31 predoctoral fellowship from the National Human Genome Research Institute of the NIH. Congrats to Steph!
Aug
T2T-F2F in Santa Cruz. Rajiv, Steph, and Dylan attended the Telomere-to-Telomere Face-to-Face (T2T-F2F) conference in Santa Cruz. Dylan gave a talk and Steph gave a flash ta… More →Less ←

Rajiv, Steph, and Dylan attended the Telomere-to-Telomere Face-to-Face (T2T-F2F) conference in Santa Cruz. Dylan gave a talk and Steph gave a flash talk!

May
Discovery Award. The McCoy lab receives a Discovery Award for a collaboration with Winston Timp and Alexis Battle’s labs to use long-read sequencing to study human tra… More →Less ←

The McCoy lab receives a Discovery Award for a collaboration with Winston Timp and Alexis Battle’s labs to use long-read sequencing to study human transcriptome diversity. Read more here:

May
Rajiv becomes Twitter famous
Feb
Kate receives Dean's Teaching Fellowship. Kate Weaver was awarded a Dean’s Teaching Fellowship from the Kreiger School of Arts and Sciences at Johns Hopkins. The award will support her in deve… More →Less ←

Kate Weaver was awarded a Dean’s Teaching Fellowship from the Kreiger School of Arts and Sciences at Johns Hopkins. The award will support her in developing her own course that she will teach to undergraduates. Congrats to Kate!

Feb
Michael Tassia joins the lab. Michael joins the McCoy lab as a postdoc. Welcome Michael!
2021
Jul
Andrew Bortvin joins the lab. Andrew joins the McCoy lab as a PhD student from the CMDB program. Welcome, Andrew!
Apr
CTEI Technology Fellowships. Two separate teams from the lab (Dylan and Sara; Kate, Steph, and Rajiv) were awarded Technology Fellowships from the Johns Hopkins Center for Teachin… More →Less ←

Two separate teams from the lab (Dylan and Sara; Kate, Steph, and Rajiv) were awarded Technology Fellowships from the Johns Hopkins Center for Teaching Excellence and Innovation. The awards will support them in developing innovative technology-based teaching strategies for undergraduate courses. Thank you to CTEI, and congrats to all!

Mar
Sara awarded NSF fellowship. Sara Carioscia received an award from the NSF Graduate Research Fellowship Program (GRFP), and Dylan Taylor received an honorable mention. Congratulat… More →Less ←

Sara Carioscia received an award from the NSF Graduate Research Fellowship Program (GRFP), and Dylan Taylor received an honorable mention. Congratulations to Sara and Dylan!

Feb
Lab movie night. The lab watches Space Jam and learns that Rajiv used to have a burned CD of songs called “Jock Jams”.
2020
Jun
Sara Carioscia and Dylan Taylor join the lab. Sara and Dylan join the McCoy lab as PhD students from the CMDB program. Welcome!
Apr
Kate Weaver joins the lab. Kate joins the McCoy lab as a PhD student from the CMDB program. Welcome Kate!
Mar
Daniel Ariad joins the lab. Daniel joins the lab as a postdoctoral fellow. Welcome, Daniel!
2019
Aug
Lab discovers Rajiv’s middle name
May
Stephanie Yan joins the lab. Steph joins the McCoy lab as a PhD student from the CMDB program. Welcome, Steph!

Selected Publications

RCM corresponding / co-corresponding author Bold = lab member, links to profile * co-first author Full publication list ↓

A selection of the lab's recent work. Lab members are shown in bold and link to their profile.

2026
*Carioscia, S. A., *Biddanda, A., Starostik, M. R., Tang, X., Hoffmann, E. R., Demko, Z. P., McCoy, R. C. Common variation in meiosis genes shapes human recombination and aneuploidy risk. Nature, 651: 146–153.
2025
Yang, Q., Carioscia, S. A., Isada, M., McCoy, R. C. Approximate Bayesian computation supports a high incidence of chromosomal mosaicism in blastocyst-stage human embryos. Genetics, 231(2): iyaf149.
2024
Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Yan, S. M., Wojcik, G. L., Battle, A., McCoy, R. C. Sources of gene expression variation in a globally diverse human cohort. Nature, 632: 122–130.
2023
McCoy, R. C., Summers, M. C., McCollin, A., Ottolini, C. S., Ahuja, K., Handyside, A. H. Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Medicine, 15: 77.
2023
*DeBoy, E. A., *Tassia, M. G., Schratz, K. E., Yan, S. M., … McCoy, R. C., Armanios, M. Familial clonal hematopoiesis in a long telomere syndrome. New England Journal of Medicine, 388: 2422–2433.
2022
*Aganezov, S., *Yan, S. M., … Taylor, D. J., … McCoy, R. C., Dennis, M. Y., Zook, J. M., Schatz, M. C. A complete reference genome improves analysis of human genetic variation. Science, 376: eabl3533.
2021
Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., McCoy, R. C. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10: e67615.
Show full publication list ↓Hide full list ↑
Research articles
2026
Das, A., Biddanda, A., McCoy, R. C., Schatz, M. C. Assembling unmapped reads reveals hidden variation in South Asian genomes. Nature Communications, 17: 5095.
2026
*Carioscia, S. A., *Biddanda, A., Starostik, M. R., Tang, X., Hoffmann, E. R., Demko, Z. P., McCoy, R. C. Common variation in meiosis genes shapes human recombination and aneuploidy risk. Nature, 651: 146–153.
2025
Yang, Q., Carioscia, S. A., Isada, M., McCoy, R. C. Approximate Bayesian computation supports a high incidence of chromosomal mosaicism in blastocyst-stage human embryos. Genetics, 231(2): iyaf149.
2025
McDaniel, J. H., Patel, V., Olson, N. D., … McCoy, R. C., … Liss, A. S., Zook, J. M. Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor–normal pair for somatic benchmarks. Scientific Data, 12: 1195.
2025
Wang, D., Cearlock, A., Lane, K., Jan, I., McCoy, R. C., Yang, M. Chromosomal instability in human trophoblast stem cells and placentas. Nature Communications, 16: 3918.
2025
Yoo, D., Rhie, A., Hebbar, P., … McCoy, R. C., … Phillippy, A. M., Eichler, E. E. Complete sequencing of ape genomes. Nature, 641: 401–418.
2025
Liang, S., Ren, T., Zhang, J., … McCoy, R. C., … Mao, Y., Chen, L. A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome. Genome Biology, 26: 32.
2024
Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Yan, S. M., Wojcik, G. L., Battle, A., McCoy, R. C. Sources of gene expression variation in a globally diverse human cohort. Nature, 632: 122–130.
2024
Xiang, G., He, X., Giardine, B. M., … Taylor, D. J., McCoy, R. C., … Li, Q., Mahony, S., Hardison, R. C. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Research, 34: 1089–1105.
2024
Makova, K. D., Pickett, B. D., Harris, R. S., … Biddanda, A., … McCoy, R. C., … Eichler, E. E., Phillippy, A. M. The complete sequence and comparative analysis of ape sex chromosomes. Nature, 630: 401–411.
2024
Hadyniak, S. E., Eldred, K. C., Brenerman, B., Hussey, K. A., McCoy, R. C., Sauria, M. E. G., … Johnston, R. J. Retinoic acid signaling regulates spatiotemporal specification of human green and red cones. PLoS Biology, 22(1): e3002464.
2024
Ariad, D., Madjunkova, S., Madjunkov, M., Chen, S., Abramov, R., Librach, C., McCoy, R. C. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Research, 34: 70–84.
2023
Sun, S., Aboelenain, M., Ariad, D., Haywood, M. E., … McCoy, R. C., Schindler, K., Xing, J. Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing. American Journal of Human Genetics, 110(12): 2092–2102.
2023
McCoy, R. C., Summers, M. C., McCollin, A., Ottolini, C. S., Ahuja, K., Handyside, A. H. Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Medicine, 15: 77.
2023
*Rhie, A., *Nurk, S., *Cechova, M., *Hoyt, S., *Taylor, Da., … McCoy, R. C. (44/81), … Miga, K. H., Makova, K. D., Phillippy, A. M. The complete sequence of a human Y chromosome. Nature, 621(7978): 344–354.
2023
Yang, X., Wang, X., Zou, Y., … Taylor, D. J., McCoy, R. C., Schatz, M. C., … Lu, Q., Mao, Y. Characterization of large-scale genomic differences in the first complete human genome. Genome Biology, 24(1): 157.
2023
Giraldo, D., Rankin-Turner, S., Corver, A., … McCoy, R. C., … Simulundu, E., McMeniman, C. J. Human scent guides mosquito thermotaxis and host selection under naturalistic conditions. Current Biology, 33(12): 2367–2382.e7.
2023
*DeBoy, E. A., *Tassia, M. G., Schratz, K. E., Yan, S. M., … McCoy, R. C., Armanios, M. Familial clonal hematopoiesis in a long telomere syndrome. New England Journal of Medicine, 388(26): 2422–2433.
2022
*Carioscia, S. A., *Weaver, K. J., Bortvin, A. N., Pan, H., Ariad, D., Bell, A. D., McCoy, R. C. A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel's first law across a large sample of human sperm. eLife, 11: e76383.
2022
Griffin, D. K., Brezina, P. R., Tobler, K., Silvestri, G., McCoy, R. C., Anchan, R., … Kearns, W. G. The human embryonic genome is karyotypically complex, with chromosomally abnormal cells preferentially located away from the developing fetus. Human Reproduction, 38(1): 180–188.
2022
*Aganezov, S., *Yan, S. M., *Soto, D. C., *Kirsche, M., *Zarate, S., … Taylor, D. J., … McCoy, R. C., Dennis, M. Y., Zook, J. M., Schatz, M. C. A complete reference genome improves analysis of human genetic variation. Science, 376(6588): eabl3533.
2022
Nurk, S., Koren, S., Rhie, A., … Yan, S. M., … McCoy, R. C. (89/99), … Eichler, E. E., Miga, K. H., Phillippy, A. M. The complete sequence of a human genome. Science, 376(6588): eabj6987.
2021
Ariad, D., Yan, S. M., Victor, A. R., Barnes, F. L., Zouves, C. G., Viotti, M., McCoy, R. C. Haplotype-aware inference of human chromosome abnormalities. PNAS, 118(46): e2109307118.
2021
Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., McCoy, R. C. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10: e67615.
2021
Ranallo-Benavidez, T. R., Lemmon, Z. H., Soyk, S., Aganezov, S., Salerno, W. J., McCoy, R. C., Lippman, Z. B., Schatz, M. C., Sedlazeck, F. J. SVCollector: optimized sample selection for cost-efficient long-read population sequencing. Genome Research, 31(5): 910–918.
2020
Starostik, M. R., Sosina, O. A., McCoy, R. C. Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism. Genome Research, 30(6): 814–825.
2020
Tyc, K. M., McCoy, R. C., Schindler, K., Xing, J. Mathematical modeling of human oocyte aneuploidy. PNAS, 117(19): 10455–10464.
2020
Sharma, R., Singh, P., McCoy, R. C., … Truman, R. W., Adams, L. B. Isolation of Mycobacterium lepromatosis and development of molecular diagnostic assays to distinguish M. leprae and M. lepromatosis. Clinical Infectious Diseases, 71(8): e262–e269.
2019
Gruhn, J. R., Zielinska, A., Shukla, V., … McCoy, R. C. (23/28), … Hoffmann, E. R. Chromosome errors in human eggs shape natural fertility over reproductive lifespan. Science, 365(6460): 1466–1469.
2019
Victor, A. R., Tyndall, J. C., Brake, A. J., … Griffin, D. K., McCoy, R. C., Barnes, F. L., Zouves, C. G., Viotti, M. One hundred mosaic embryos transferred prospectively in a single clinic: exploring when and why they result in normal pregnancies. Fertility & Sterility, 111(2): 280–293.
2019
Victor, A. R., Griffin, D. K., Brake, A. J., … McCoy, R. C., Viotti, M. Assessment of aneuploidy concordance between clinical trophectoderm biopsy and blastocyst. Human Reproduction, 34(1): 181–192.
Review articles
2025
*Moya, N., *Yan, S. M., McCoy, R. C., Andersen, E. C. The long and short of hyperdivergent regions. Trends in Genetics, 41(4): 303–314.
2024
Taylor, D. J., Eizenga, J. M., Li, Q., Das, A., Jenike, K. M., Kenny, E. E., Miga, K. H., Monlong, J., McCoy, R. C., Paten, B., Schatz, M. C. Beyond the Human Genome Project: the age of complete human genome sequences and pangenome references. Annual Review of Genomics and Human Genetics, 25: 77–104.
2023
Muter, J., Lynch, V. J., McCoy, R. C., Brosens, J. J. Human embryo implantation. Development, 150(10): dev201507.
2022
Brosens, J. J., Bennett, P. R., Abrahams, V., Ramhorst, R., Coomarasamy, A., Quenby, S., Lucas, E. S., McCoy, R. C. Maternal selection of human embryos in early gestation: insights from recurrent miscarriage. Seminars in Cell and Developmental Biology, 131: 14–24.
2021
Quenby, S., Gallos, I. D., Dhillon-Smith, R. K., … McCoy, R. C., … Petrou, S., Coomarasamy, A. Miscarriage matters: the epidemiological, physical, psychological, and economic costs of early pregnancy loss. The Lancet, 397(10285): 1658–1667.
2021
Levy, B., Hoffmann, E. R., McCoy, R. C., Grati, F. R. Chromosomal mosaicism: origins and clinical implications in preimplantation and prenatal diagnosis. Prenatal Diagnosis, 41(5): 631–641.
2021
Wartosch, L., Schindler, K., Schuh, M., Gruhn, J. R., Hoffmann, E. R., McCoy, R. C., Xing, J. Origins and mechanisms leading to aneuploidy in human eggs. Prenatal Diagnosis, 41(5): 620–630.
2020
Yan, S. M., McCoy, R. C. Archaic hominin genomics provides a window into gene expression evolution. Current Opinion in Genetics & Development, 62: 44–49.
Editorials & commentaries
2024
Carioscia, S., McCoy, R. C. A rare genetic variant biases maternal meiotic recombination toward risk of pregnancy loss. Nature Structural & Molecular Biology, 31: 584–585.
2021
Viotti, M., McCoy, R. C., Griffin, D. K., Spinella, F., Greco, E., Madjunkov, M., Madjunkova, S., Librach, C. L., Victor, A. R., Barnes, F. L., Zouves, C. G. Let the data do the talking: the need to consider mosaicism during embryo selection. Fertility & Sterility, 116(5): 1212–1219.
2019
Yan, S. M., McCoy, R. C. Functional divergence among hominins. Nature Ecology & Evolution, 3(11): 1507–1508.
2019
McCoy, R. C., Kort, J. D. Quantifying the transcriptional impacts of aneuploidy in human blastocysts. Fertility & Sterility, 111(5): 888–889.
Preprints & under review
2025
Lalli, J. L., Bortvin, A. N., McCoy, R. C., Werling, D. M. A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation. bioRxiv: 2025.02.24.639687.
2026
Riahi, P., Raghupathy, S., Le, B., Taylor-Brill, S., Taylor, D., McCoy, R. C., Ramdas, S., Zaidi, A. A. Beyond copy number: the regulatory architecture of mitochondrial DNA gene expression. bioRxiv: 2026.05.27.728277.
2025
Cechova, M., Potapova, T. A., Rechtsteiner, A., … Yan, S. M., … McCoy, R. C., … Greider, C. W., Miga, K. H. Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance. bioRxiv: 2025.12.14.693655.
2023
DeGorter, M. K., Goddard, P. C., Karakoc, E., … Yan, S. M., … McCoy, R. C., … Gurdasani, D., Montgomery, S. B. Transcriptomics and chromatin accessibility in multiple African population samples. bioRxiv: 2023.11.04.564839.
Prior to faculty position
Postdoctoral (Princeton University · University of Washington) and doctoral (Stanford University) research.
2018
Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., … Visscher, P. M., Akey, J. M., Green, R. E. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science, 361(6401): 511–516.
2018
Press, M. O., McCoy, R. C., Hall, A. N., Akey, J. M., Queitsch, C. Short tandem repeats with massive variation and functional consequences across strains of Arabidopsis thaliana. Genome Research, 28(8): 1169–1178.
2018
*McCoy, R. C., *Newnham, L. J., Ottolini, C. S., … Sigurjonsson, S., Handyside, A. H. Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos. Human Molecular Genetics, 27(14): 2573–2585.
2018
Kort, J. D., McCoy, R. C., Demko, Z. P., Lathi, R. B. Are blastocyst aneuploidy rates different between fertile and infertile populations?. Journal of Assisted Reproduction and Genetics, 35(3): 403–408.
2017
McCoy, R. C. Mosaicism in preimplantation human embryos: when chromosomal abnormalities are the norm. Trends in Genetics, 33(7): 448–463.
2017
McCoy, R. C., Akey, J. M. Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation. Genome Biology, 18(1): 139.
2017
Adashi, E. Y., McCoy, R. C. Technology versus biology: the limits of pre-implantation genetic screening. EMBO Reports, 18(5): 670–672.
2017
McCoy, R. C., Wakefield, J., Akey, J. M. Impacts of Neanderthal-introgressed sequences on the landscape of human gene expression. Cell, 168(5): 916–927.e12.
2016
Vernot, B., Tucci, S., Kelso, J., … McCoy, R. C., … Pääbo, S., Akey, J. M. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, 352(6282): 235–239.
2016
McCoy, R. C., Akey, J. M. Patterns of deleterious variation between human populations reveal an unbalanced load. PNAS, 113(4): 809–811.
2016
Demko, Z. P., Simon, A. L., McCoy, R. C., Petrov, D. A., Rabinowitz, M. Effects of maternal age on euploidy in a large cohort of embryos analyzed with 24-chromosome SNP-based preimplantation genetic screening. Fertility & Sterility, 105(5): 1307–1313.
2015
McCoy, R. C., Demko, Z., Ryan, A., … Rabinowitz, M., Petrov, D. A. Evidence of selection against complex mitotic-origin aneuploidy during preimplantation development. PLoS Genetics, 11(10): e1005601.
2015
McCoy, R. C., Demko, Z., Ryan, A., … Fraser, H. B., Petrov, D. A. Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science, 348(6231): 235–238.
2014
Ahola, V., Lehtonen, R., Somervuo, P., … McCoy, R. C. (18/45), … Hanski, I. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications, 5: 4737.
2014
McCoy, R. C., Taylor, R., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., Fiston-Lavier, A. S. Illumina TruSeq synthetic long reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE, 9(9): e106689.
2014
McCoy, R. C., Garud, N. R., Kelley, J. L., Boggs, C. L., Petrov, D. A. Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population. Molecular Ecology, 23(1): 136–150.

Software & Resources

We develop open-source methods and release open datasets to support the wider community. A few highlights are below; the rest live on the lab's GitHub.

MAGE

RNA-seq and expression/splicing QTL maps from 731 individuals across 26 globally diverse populations of the 1000 Genomes Project. Data archived on Zenodo.

GitHub & data →

karyoHMM

Hidden Markov models for detecting aneuploidy and inferring its parental and cell-division origin from preimplantation genetic testing data.

GitHub →

rhapsodi

Haplotype phasing, imputation, and recombination inference from low-coverage sequencing of large samples of single gametes.

GitHub →

LD-PGTA

Linkage-disequilibrium–aware inference of chromosome abnormalities from low-coverage preimplantation genetic testing data, using external haplotype reference panels.

GitHub →

Teaching

Graduate

Quantitative Biology Bootcamp & Lab

Each fall, Rajiv teaches the week-long Quantitative Biology Bootcamp and the subsequent Lab to first-year CMDB graduate students (co-instructors: Frederick Tan and Michael Sauria). Through active-learning exercises, students build the fundamental computational and statistical skills now essential across modern biology, performing real data analysis that reinforces core bioinformatic concepts alongside the molecular- and cell-biology core curricula.

Undergraduate

Human Genome Variation & Computational Lab

Each spring, Rajiv teaches Human Genome Variation (co-instructor: Kyle Cunningham) and its Computational Lab to upper-level undergraduates. Lectures span personalized medicine, evolutionary genetics and ancient DNA, and the social and ethical implications of human genetic research, with students presenting and discussing primary literature. In the lab, which is open to a wide range of computational experience, students analyze public human genomic datasets on a cloud platform to test hypotheses about evolution and human phenotypes.

Course materials were enhanced with a Technology Fellowship from the Johns Hopkins Center for Teaching Excellence and Innovation (with graduate students Stephanie Yan and Kathryn Weaver) to build an open online textbook and cloud-based modules: mccoy-lab.github.io/hgv_modules →

Funding

Our research is supported by federal agencies, private foundations, and professional societies, enabling work at the intersection of human genetics, evolution, and reproductive biology.

National Institutes of Health National Science Foundation Burroughs Wellcome Fund American Society of Hematology Lalor Foundation Johns Hopkins University

Join the Lab

We are recruiting trainees interested in using computational and statistical approaches to study human genome function and evolution. See the Research directions for areas your interests may intersect. Informal inquiries are always welcome.

How to apply, by career stage ↓Hide details ↑
Postdoctoral fellows
Email Rajiv with a CV, a description of past and future research interests, and contact information for three references.
Graduate students
Prospective PhD students should apply to the CMDB program. Rajiv is also a faculty preceptor for the Human Genetics and Genomics program. Students in either program can contact Rajiv to discuss rotation projects; current master's students are welcome to reach out with a CV and statement of interests.
Undergraduates
Email Rajiv with a description of academic interests, relevant coursework, and any past research or programming experience.