Former lab members

Former postdocs

Cécile Courret, Ph.D. (Postdoctoral associate; EGCE – Université Paris-Saclay)

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:

Xiaolu Wei, Ph.D. ( Postdoctoral associate; University of North Texas)

e-mail: xwei10@ur.rochester.edu
Xiaolu was a Biomedical Genetics student who recently graduated from that lab. She is now a postdoc  in the lab 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 was an 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

Chen, T.*, Wei, X.*, Courret, C.*, Cui, M., Cheng, L., Wu, J., Ahmad, K., Larracuente, A.M., Rong, Y. 2022. The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila. BIORXIV 4/22/22. PLoS Genet 18(9): e1010351. https://doi.org/10.1371/journal.pgen.1010351

*co-first authors

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

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 was 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:

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

Former graduate students:

Matthew Lindsay (E2G2 graduate student; MS)

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 worked on the population dynamics of Segregation Distorter and satellite DNA fitness.

 

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:

Recently graduated undergrads:

Julia Granato (undergraduate, Ecology and Evolutionary Biology)

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

 

 

Miraz Sadi (undergraduate, Biochemistry)

Miraz worked on centromere evolution in the Drosophila melanogaster clade. He was a recipient of a DeKiewiet Fellowship for undergraduate research.

 

 

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. He was a recipient of a DeKiewiet Fellowship for undergraduate research.

Selected publications:

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.

 

 

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:

Xuewen Geng (undergraduate; Ecology and Evolutionary Biology)

Xuewen is studying centromeric retroelements in Drosophilaspecies using phylogenetic approaches.

 

 

Lorraine Zaki (undergraduate, Molecular Genetics)

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

 

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), Matthew Lindsay (University of Toronto)

Postdocs: John Sproul (Assistant Professor, Brigham Young University); Beatriz Navarro-Domínguez (Grupo de Genética Evolutiva, Universidad de Granada), Lucas Hemmer (Computational Biologist, Invaio Sciences), Xiaolu Wei (University of North Texas), Cécile Courret (EGCE – Université Paris-Saclay)

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), Tuan Pham (grad student Brown University), Sherif Negm (Human Genetics PhD student, University of Chicago), Miraz Sadi (PhD Biochemistry and Biophysics; University of Rochester)

Rotating graduate students: Steven Messer, John Bettinger, Omid Saleh Ziabari, Nilima Walunjkar, Yingying Liang, Lauren Gregory, Songeun Lee, Lindsey Perrin, Faye Romero, Ruoqiao Wang, Cheyenne Thomas, Riti Kamath, Anushka Jain, James Shaul, Eric Moeller, Yuan Liang, Aishwarya Balakrishnan