People

PI: Amanda Larracuente
Graduate Students:  Xiaolu Wei
Postdocs: Beatriz Navarro-Domínguez, Lucas Hemmer, John Sproul, Cécile Courret
Research associates and technicians: Danna Eickbush, Shaun Jones, Matthew Lindsay
Undergraduates:  Sherif Negm, Eddyson Altidor, Anya Greenberg, Jim Chaffer, Gefei (Vera) Yu, Xuewen Geng
Former lab members

Larracuente lab- 2019

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.

Selected recent publications. Click here for a full list of Amanda’s publications or see her NCBI bibliography.

Graduate students

Xiaolu Wei (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.

Postdocs

Beatriz Navarro-Domínguez, Ph.D. (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)

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:

John Sproul, Ph.D. (NSF postdoctoral fellow)

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.

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

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:

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.

 

Matthew Lindsay (Technician)

e-mail: matthew.lindsay@rochester.edu
Matthew joined our lab after finishing his undergraduate work at the University of Toronto. Matthew is working on the population dynamics of Segregation Distorter and satellite DNA fitness.

 

 

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 Segregation Distorter and repeat evolution in Drosophila. Sherif, along with his co-authors Anya Greenberg and John Sproul, designed a pipeline called RepeatProfiler to study repeats with short read sequence data.

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

 

 

 

Eddyson Altidor (undergraduate; Biology)

Eddyson is using molecular methods to study variation in centromeric retroelements in Drosophila.

 

 

 

Gefei (Vera) Yu (undergraduate; Computational Biology)

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

 

 

 

 

Xuewen Geng (undergraduate; Ecology and Evolutionary Biology)

Xuewen is studying centromeric retroelements in Drosophilaspecies using phylogenetic approaches.

 

Anya Greenberg (undergraduate; Data Science)

Anya is 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 is using computational and cytogenetic methods to study repeat evolution in fireflies and Drosophila species.

 

 

 

 

Taylar Mouton (undergraduate)

Taylar is studying 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.

 

 

Iain Speece (undergraduate)

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

Former lab members

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)

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

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

Ching-Ho is 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 postdoc in Harmit Malik’s lab at the Fred Hutchison Cancer Research Center.

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: