People

PI: Amanda Larracuente
Graduate Students:  Xiaolu Wei, Matthew Lindsay
Postdocs:  Cécile Courret, Felix Beaudry
Research associates and technicians: Danna Eickbush, Shaun Jones
Undergraduates:  Sherif Negm, Xuewen Geng, Tuan Pham, Lorraine Zaki, Julia Granato, Miraz Sadi
Former lab members

Larracuente lab- 2019
Larracuente lab 2020
Larracuente lab 2020

Lab members:


Amanda Larracuente, Ph.D. (PI, Associate Professor)

e-mail: alarracu@bio.rochester.edu
Amanda earned her Ph.D. studying Drosophila genomics and sex chromosome evolution in Dr. Andrew Clark’s lab at Cornell University. During her postdoctoral training, she focused on the evolution of selfish DNA including the Segregation Distorter system of Drosophila melanogaster. Amanda was the Stephen Biggar and Elisabeth Asaro Fellow in Data Science from 2017-2020.

Other roles: Amanda is the advisor and track coordinator for the undergraduate major and minor in Computational Biology. She teaches the Applied Genomics capstone for comp bio majors. Amanda is also an active member of the Goergen Institute for Data Science where she advised majors and MS students and co-chairs the working group in Life and Biomedical Data Science.  Outside of the University, she is on the editorial boards for Molecular Biology and Evolution and GENETICS.

Selected publications from before starting the lab. Click here for a full list of Amanda’s publications or see her NCBI bibliography and ORCID.

 

Graduate students

Xiaolu Wei (Genetics, Development, and Stem Cells program URMC Ph.D. candidate)

e-mail: Xiaolu_Wei@URMC.Rochester.edu
Xiaolu is a Biomedical Genetics student studying how satellite DNA is regulated in the Drosophila germline using functional genomics and cytogenetic approaches. She uses the selfish Segregation Distorter system to understand the consequences of misregulating satellite DNA in the male germline. Xiaolu is Agnes M. Messersmith and George Messersmith fellow for 2020-2021.

Selected publications:
Wei,X., Eickbush,D.G., Speece,I., A.M. Larracuente. 2021. Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline. eLife 2021;10:e62375. doi: 10.7554/eLife.62375

 

Matthew Lindsay (E2G2 graduate student)

e-mail: matthew.lindsay@rochester.edu
Matthew joined our lab after finishing his undergraduate work at the University of Toronto as a technician and began as an E2G2 graduate student in Fall 2020. Matthew is working on the population dynamics of Segregation Distorter and satellite DNA fitness.

 

Emiliano Martí (rotating E2G2 graduate student)

Emiliano got his masters at the Sao Paulo State University studying the evolution of repetitive DNA in Schistocerca grasshoppers. He is interested in repetitive elements and their role in genome organization and sex chromosome evolution. Emiliano joined the Larracuente lab as an E2G2 graduate student, and is studying the organization of satellite DNA in populations.

 

Postdocs

Cécile Courret, Ph.D. (Postdoctoral associate)

e-mail: cecile.courret@rochester.edu
Cécile earned her PhD in Evolution at the University Paris Saclay (France) in Catherine Montchamp-Moreau’s lab. During her PhD she was interested in the evolution and genetic basis of the genetic conflict induced by sex-linked meiotic drive in Drosophila simulans. Cécile joined the Larracuente lab as a postdoc to study of the role of retroelements in centromere organization and function in Drosophila.
Publications:

Felix Beaudry, PhD (NSF Postdoctoral fellow, jointly advised by Dr. Nancy Chen)

Felix is interested in the evolution of sex and the evolution of our genomes. Combining quantitative genetics, population genetics and molecular evolution, Felix investigates sex chromosomes and the maintenance of heritable fitness variation in the Florida Scrub Jay. Felix also explores how the genetics of sex is taught, creating teaching plans that clearly distinguish sex from gender in the genetics classroom. For more, see Felix’s website: felixbeaudryresearch.com

Selected publications:

Rifkin JL*, Beaudry FEG*, Humphries Z, Choudhury BI, Barrett SCH, Wright SI. 2021. Widespread recombination suppression facilitates plant sex chromosome evolution. Molecular Biology and Evolution. 38: 1018-1030 bioRxiv.

Beaudry FEG*, Rifkin JL*, Barrett SCH, Wright SI. 2020. Evolutionary Genomics of Plant Gametophytic Selection. Plant Communications. 1:100115

Beaudry FEG and Wright SI. 2020. Chromosome Evolution: Infectious Sex Chromosomes in the African Monarch Butterfly. Current Biology. 30: R657-R659.

Beaudry FEG. 2020. Recombination restriction, degeneration and population divergence on plant sex chromosomes. PhD thesis. University of Toronto. Watch Exit Seminar.

Beaudry FEG, Barrett SCH and Wright SI. 2019. Ancestral and neo-sex chromosomes contribute to population divergence in a dioecious plant. Evolution. 74:256-279. bioRxiv.

Research associates and technicians

Danna Eickbush, Ph.D. (Research associate)

e-mail: danna.eickbush@rochester.eduflowers
Danna Eickbush attended the University of Arizona where she was introduced to the wonders of molecular biology and immediately transferred to the newly formed Department of Cellular and Development Biology. She then joined the Ph.D. program in Cellular and Development Biology at Harvard University, characterizing the molecular structure and transcriptional patterns of the 71C-E region of Drosophila melanogaster while in the lab of Dr. Peter Cherbas. After moving to upstate New York, she did a postdoc with Dr. Jack Werren studying the selfish B-chromosome Paternal Sex Ratio (PSR) in the wasp Nasonia vitripennis. For the last 25 years, she has worked as a research associate with Dr. Tom Eickbush at the University of Rochester. The long tenure with her husband allowed Danna to study many aspects of the life cycle of the retrotransposable element R2, including its regulation and transcription. Danna works on the regulation of satellite DNA expression in Drosophila species.

Selected recent publications. Click here to see Danna’s PubMed list.

 

Shaun Jones (Technician)ShaunJones2

Shaun is a skilled fly wrangler who  maintains the lab’s fly lines and helps the lab with various projects.

 

 

 

Undergraduates

Sherif Negm (undergraduate; Comp Bio/Data Science)

Sherif is using computational methods to study  repeat evolution in Drosophila. He has contributed to several projects ranging from euchromatic satellite DNA evolution to  designing a pipeline called RepeatProfiler to study repeats with short read sequence data.

Selected publications:

 

 

Xuewen Geng (undergraduate; Ecology and

Evolutionary Biology)

Xuewen is studying centromeric retroelements in Drosophilaspecies using phylogenetic approaches.

 

Tuan Pham (undergraduate; Computational Biology)

Tuan is a computational biology major working on various satellite DNA projects in the lab, from detecting homologous repeats across species to building pipelines to annotate revised mappability scores.

 

 

Lorraine Zaki (undergraduate, Molecular Genetics)

Lorraine is a Molecular Gentics major who worked on detecting satellite DNA homologs across species and is now starting to work on Segregation Distorter.

 

 

Julia Granato (undergraduate, Ecology and Evolutionary Biology)

Julia is an EEB/Archaeology double major helping with Segregation Distorter projects. Julia works with our flies that have mutations in their satellite DNA that we made using CRISPR/Cas9.

 

 

Miraz Sadi (undergraduate, Computational Biology)

Miraz is working on centromere evolution in the Drosophila simulans clade.

Former lab members

 

Recently departed lab members:

Former postdocs

John Sproul, Ph.D. (NSF postdoctoral fellow 2018-2020; Assistant Professor University of Nebraska)

e-mail:jsproul@ur.rochester.edu 
John earned his PhD in Integrative Biology at Oregon State University in David Maddison’s lab. John studied species delimitation, phylogenomics, and repetitive DNA dynamics in ground beetles, and developed methods to improve sequencing results from historical specimens. John joined Amanda’s lab thorough a NSF-funded fellowship that aims to improve benchmarking and generate pipelines for transposable element annotation software, as well as to increase participation of underrepresented groups in science. John is now an Assistant Professor at the University of Nebraska, Omaha.

Selected recent publications. See full list of publications on John’s google scholar page.
  • Sproul, J., Khost, D.E.*, Eickbush, D.G., Negm, S., Wei, X., Wong, I., and A.M. Larracuente 2020. Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade. BIORXIV/2019/846238,  Molecular Biology and Evolution,  msaa078, https://doi.org/10.1093/molbev/msaa078 *co-first author
  • Sproul,J.S., Barton, L.M., D.R. Maddison. 2020. Repetitive DNA profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles. BIORXIV https://doi.org/10.1101/2020.01.03.894527
  • Sproul, J.S.; Maddison, D.R. (2017) Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA. Molecular Ecology Resources, 17 (6): 1183-1201.
  • Sproul, J.S.; Maddison, D.R. (2017) Cryptic species in the mountaintops: species delimitation and taxonomy of the breve species group (Carabidae: Bembidion) aided by genomic architecture of a century-old type specimen. Zoological Journal of the Linnean Society, 183 (3): 556-583.
  • Kanda, K.; Pflug, J.M.; Sproul, J.S.; Dasenko, M.; Maddison, D.R. (2015) Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS ONE, 10, e0143929.

Beatriz Navarro-Domínguez, Ph.D. (2018-2021, Postdoc)

e-mail: bnavarr2@ur.rochester.edu
Beatriz earned her PhD  studying B chromosomes in grasshoppers, in the Evolutionary Genetics Group at the University of Granada (Spain). As a postdoc, she has worked in a variety of organisms, from ferns to turtles, trying to understand how genomes evolve. Beatriz is now studying the population genomics of Segregation Distorter and the role of satellite DNA in genetic incompatibilities. She is jointly advised by Daven Presgraves and Amanda Larracuente.

Selected recent publications. See full list of publications on Beatriz’s google scholar page.

 

Lucas Hemmer, Ph.D. (Postdoc 2018-2021, Computational Biologist, Invaio Sciences)

e-mail: lhemmer@ur.rochester.edu
Lucas earned his Ph.D. in Ecology and Evolutionary Biology at the University of Kansas in Justin Blumenstiel’s lab. Lucas studied the evolution of meiotic recombination landscapes in different species of Drosophila in light of selfish genetic elements including transposable elements and centromeres. Lucas joined Amanda’s lab as a postdoc to study centromere evolution in Drosophila.

Recent publications:

Recent graduate students:

Ching-Ho Chang (Ph.D. student 2015-2020)Ching-HoChang

Ching-Ho was an E2G2 student working on Segregation Distorter in Drosophila melanogaster and Y chromosome evolution in  Drosophila. Before coming to Rochester, Ching-Ho worked with Dr. Chau-Ti Ting  at National Taiwan University on neo-sex chromosome evolution in Drosophila albomicans. Ching-Ho was a recipient of the Ernst Caspari Fellowship and the Messersmith Fellowship. He is a current Damon Runyun fellow in Harmit Malik’s lab at the Fred Hutchison Cancer Research Center. In 2021, Ching-Ho received the prestigious Larry Sandler award for his outstanding dissertation work.

Selected publications:

Danielle (Dani) Khost (Ph.D. student 2014-2019)

Dani was an E2G2 student working on the evolution and functional genomics of satellite DNA in Drosophila species. She  used deep real time single molecule sequencing from Pacific Biosciences to study the structural organization of satellite DNA loci in Drosophila genomes. Dani is now in the Harvard University Bioinformatics group.

Publications:

Undergrads, recently graduated:

 

Eddyson Altidor (undergraduate; Biology)

Eddyson used molecular methods to study variation in centromeric retroelements in Drosophila.

 

 

 

Gefei (Vera) Yu (undergraduate; Computational Biology)

Vera used genomic approaches to study patterns of expression in the Segregation Distorter system

 

 

 

Anya Greenberg (undergraduate; Data Science)

Anya was a data science student working on developing a bioinformatic pipeline to study repeats (RepeatProfiler) and using methods in machine learning to study satellite DNA evolution.

Publications:

Sherif Negm, Anya D. Greenberg, Amanda M. Larracuente, John S. Sproul. 2020. RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles. BioRxiv 5/26/2020 doi: https://doi.org/10.1101/2020.05.22.111252

 

Isaac Wong (undergraduate)

Isaac used computational and cytogenetic methods to study repeat evolution in fireflies and Drosophila species.

Publications:

 

 

Taylar Mouton (undergraduate)

Taylar studied the function of multi-copy Y-linked gene families in D. melanogaster and the simulans clade species. Taylar successfully defended her senior thesis and graduated with honors in research. Taylar is a graduate student in the Broderick lab at Johns Hopkins.

 

 

Iain Speece (undergraduate)

Iain is a computational biology major studying the functional genomics of satellite DNAs in D. melanogaster.

Publications:

Complete list of former lab members:

Graduate students: Danielle Khost (Harvard Bioinformatics), Ching-Ho Chang (Damon Runyun fellow, Malik lab, Fred Hutchison Cancer Research Center)

Postdocs: John Sproul (Assistant Professor, University of Nebraska Omaha); Beatriz Navarro-Domínguez (Postdoc Mireia Coscollá Devís lab, Valencia), Lucas Hemmer (Computational Biologist, Invaio Sciences)

Undergraduates: Christian Silva (grad student UC Davis), Thanatcha (Kwan) Khunkhet, Linhe (Alex) Xu (grad student at Vanderbilt ), Danielle Pascua, Arif Kodza (MD student at SUNY Downstate), Taylar Mouton (grad student at Johns Hopkins); Isaac Wong (bioinformatician, Harvard MGH), Vera Yu (Computational Biology, Cornell University), Iain Speece (FMI), Gilbert Giri (UNC graduate student)

Rotating graduate students: Steven Messer, John Bettinger, Omid Saleh Ziabari, Nilima Walunjkar, Yingying Liang, Lauren Gregory, Songeun Lee, Lindsey Perrin, Faye Romero