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.

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.

• Beatriz Navarro-Domínguez, Francisco J Ruiz-Ruano, Josefa Cabrero, José María Corral, María Dolores López-León, Timothy F Sharbel, Juan Pedro M Camacho. 2017. Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Scientific reports 7, 45200.
• Beatriz Navarro-Domínguez, Josefa Cabrero, Juan Pedro M Camacho, María Dolores López-León. 2016. B-chromosome effects on Hsp70 gene expression does not occur at transcriptional level in the grasshopper Eyprepocnemis plorans. Molecular Genetics and Genomics 291 (5), 1909-1917.
• Josefa Cabrero, Mohammed Bakkali, Beatriz Navarro-Domínguez, Francisco J Ruíz-Ruano, Rubén Martín-Blázquez, María Dolores López-León, Juan Pedro M Camacho.  2013. The Ku70 DNA-repair protein is involved in centromere function in a grasshopper species. Chromosome research 21 (4), 393-406.

 

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:

• Hemmer L.W. and Blumenstiel J.P.. 2016. Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila. BMC Evolutionary Biology. 16:91. https://doi.org/10.1186/s12862-016-0670-8.
• Blumenstiel J.P., A.A. Erwin, L.W. Hemmer 2016. What Drives Positive Selection in the Drosophila piRNA machinery? The Genomic Autoimmunity Hypothesis. Yale J Biol Med. 2016 Dec; 89(4): 499–512.
• Hemmer L.W. and J.P. Blumenstiel 2018. BioRxiv Preprint 6/8/18. The Recombination Landscape of Drosophila virilis is Robust to Transposon Activation in Hybrid Dysgenesis. https://doi.org/10.1101/342824

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:

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

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:

• Chang, C-H, Chavan, A, Palladino, J., Wei, X., Martins, N.M.C., Santinello, B., Chen, C-C, Erceg, J., Beliveau, B.J., Wu, C-T, Larracuente, A.M., and Mellone, B.G. 2019. Islands of retroelements are major components of Drosophila melanogaster centromeres.  BioRxiv Epub 2/1/2019. PLoS Biology https://doi.org/10.1371/journal.pbio.3000241.
• Chang, C-H. and A.M. Larracuente. 2019. Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome. BioRxiv 7/25/18. GENETICS 211: 333-348. doi: 10.1534/genetics.118.301765.  featured in GENETICS highlights 1/1/2019 http://www.genetics.org/content/211/1/NP
• Chang, C-H. and A.M. Larracuente. 2017. Structural changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Evolution. Advanced Access 3/21/17. http://dx.doi.org/10.1111/evo.13229.
• Chang C-c, Ting C-T, Chang C-H, Fang S, Chang H-y (2014) The Persistence of Facultative Parthenogenesis in Drosophila albomicans. PLoS ONE 9(11): e113275. doi:10.1371/journal.pone.0113275
• Chia-Hao Cheng, Ching-Ho Chang, and Hwei-yu Chang (2011) Early-stage evolution of the neo-Y chromosome in Drosophila albomicans. Zoological Studies 50(3): 338-349.

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:

• 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
• Khost, D.E., D. Eickbush, A.M. Larracuente. 2017. Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster.  Genome Research . Advanced Access. 4/3/17. http://www.genome.org/cgi/doi/10.1101/gr.213512.116.

Recently graduated undergrads:

 

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:

• 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. Molecular Ecology Resources. 12/2020 https://doi.org/10.1111/1755-0998.13305
• 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 autho

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:

• 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

 

 

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:

• 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

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 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.

 

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), Tuan Pham (grad student Brown University), Sherif Negm (Human Genetics PhD student, University of Chicago)

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