FSU Biology - Cell & Molecular Biology

Florida State University | Department of Biological Science

Featured Student

Emily Darrow (Ph.D., 2018)
CMB graduate student in the Chadwick lab.

Emily Darrow (Ph.D., 2018) CMB graduate student in the Chadwick lab. The roles of many tandem-repeat DNA sequences in the human genome are unknown. DXZ4 is a large X-linked macrosatellite implicated in the structure of the inactive X chromosome (Xi). Using cutting-edge genome engineering tools, Emily excised DXZ4 from the Xi, causing large-scale local chromatin changes to the Xi. In collaboration with Dr. Erez Lieberman-Aiden's group, we showed compromised Xi 3D conformation. This work involved three members of the CMB Graduate Program: Emily Darrow, Zhuo Sun and Andrew Seberg. Emily defended her Ph.D. in 2017 and is starting a postdoc in 2018. ARTICLE: Darrow, E. M., M. H. Huntley, O. Dudchenko, E. K. Stamenova, N. C. Durand, Z. Sun, S. C. Huang, A. L. Sanborn, I. Machol, M. Shamim, A. P. Seberg, E. S. Lander, B. P. Chadwick and E. L. Aiden (2016). "Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture." Proc Natl Acad Sci U S A 113(31): E4504-4512.
Katherine Easterling
CMB doctoral candidate in the Bass lab

Katherine Easterling CMB doctoral candidate in the Bass lab Katherine co-first-authored a paper on inheritance in hop in the journal The Plant Genome. She carried out 3D imaging of hop chromosomes, suggesting a chromosomal basis for the non-Mendelian inheritance patterns observed for genomic markers. She also recently presented a talk and poster at the 2nd Annual Brewers Symposium in Corvallis, Oregon at Oregon State University, where she received the First Prize Award for her poster. ARTICLE: (2017) Zhang* D, Easterling* KA, Pitra* NJ, Coles MC, Buckler ES, Bass HW, and Matthews PD. "Non-Mendelian SNP inheritance and atypical meiotic configurations are prevalent in hop (Humulus lupulus L.)" The Plant Genome 10(3):(14 pp). (DOI: 10.3835/plantgenome2017.04.0032).
Vishnu Dileep (Ph.D. 2017)
CMB student in the Gilbert lab

Vishnu Dileep (Ph.D. 2017) CMB student in the Gilbert lab He studied the relationship between DNA replication-timing regulation and 3D chromatin architecture. Vishnuâ€™s doctoral research showed that the re-establishment of interphase-specific chromatin folding from the condensed mitotic chromosomes coincides with the establishment of the replication-timing program. Vishnu was supported by an American Heart Association fellowship and completed his work by studying genome-wide replication timing regulation at the single cell level. ARTICLE: Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program. Genome Res. 2015 Aug;25(8):1104-13. DOI: 10.1101/gr.183699.114.
Ji Huang
Ph.D. student in the McGinnis lab

Ji Huang Ph.D. student in the McGinnis lab Dr. Ji Huang graduated from the McGinnis Lab in 2018. Ji's article, entitled "Construction and Optimization of Large Gene Co-expression Network in Maize Using RNA-Seq Data", was published in Plant Physiology. His paper employed and tested different approaches to the construction of gene coexpression networks. He identified the optimal parameters for processing maize RNAseq data and generated a large, robust network. The maize coexpression database is available through the McGinnis lab web site at mcginnislab/mcn/main_page.php. ARTICLE: Huang, J., et al. (2017). "Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data." Plant Physiol 175(1): 568-583. https://doi.org/10.1104/pp.17.00825
Hardeep Gumber
CMB doctoral candidate in the Bass lab

Hardeep Gumber CMB doctoral candidate in the Bass lab Hardeep won the graduate student oral presentation competition at the Southern Section of the American Society of Plant Biologists Annual Meeting in Orlando, Florida April 2017. She presented a talk titled: â€œThe maize LINC complex componentsâ€. Hardeepâ€™s research focuses on the role of telomeres and the nuclear envelope-associated LINC complex in meiotic chromosome dynamics and segregation.
Jiao Sima (Ph.D., 2018)
CMB graduate student in the Gilbert lab.

Jiao Sima (Ph.D., 2018) CMB graduate student in the Gilbert lab. Using CRISPR-mediated deletions and inversions Jiao discovered the long sought after cis-acting elements regulating DNA replication in mammalian cells. She discovered that these elements control not only replication, but also transcription and 3D genome architecture of entire chromosome domains (~500kb units of chromosome structure and function). Her work is a major breakthrough, making possible the mechanistic dissection of previously enigmatic and impenetrable aspects of large-scale chromosome architecture. In the field of DNA replication, it resolves a 60 year long debate over whether or not specific sequences regulate replication and sets the stage to identify what those sequences are. ARTICLE: Sima J, Chakraborty A, Dileep V, Michalski M, Klein K.N., Holcomb N.P., Turner J.L., Paulsen M.T., Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. (2019) Identifying cis-Elements for Spatiotemporal Control of Mammalian DNA Replication. CELL 176:816-830 (PMID 30595451)

CMB Students Currently in the Graduate Program

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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Sara Akram

ha20be@my.fsu.edu
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Lorea Arambarri

larambarri@bio.fsu.edu
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major professor: Dr. Dennis
second major professor:

B

Daniel Bartlett

dbartlett@bio.fsu.edu
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major professor: Dr. Gilbert
second major professor:

Anandi Batabyal

ab20if@my.fsu.edu
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major professor:
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Shahin Behrouz Sharif

ssharif@bio.fsu.edu
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Tracey Bell

tbell@bio.fsu.edu
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Jane Benoit

My overarching interest is in the innate and adaptive immune responses to viral pathogens on a molecular level. Host cell-pathogen interactions result in changes in chromatin remodeling and architecture in addition to changes in gene expression and other responses. Understanding the molecular processes behind changes in chromatin states on the nucleosomal level is of great importance to molecular biology and immunology.

jbenoit@bio.fsu.edu
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Katherine Bilodeau

kbilodeau@fsu.edu
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Cecilia Bouaichi

cbouaichi@bio.fsu.edu
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Nina Bui

My research investigates the molecular mechanisms of Zika virus pathogenesis in human neural progenitor stem cells. I am interested in Zika virus infection in regards to its high association with congenital birth defects such as infantile Microcephaly.

nbui@bio.fsu.edu
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major professor: Dr. Tang
second major professor:

C

Gabriel Calvin

gcalvin@bio.fsu.edu
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Christopher Carroll

crcarroll@fsu.edu
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Lauren Carson

lacarson@fsu.edu
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Trirupa Chakraborty

tc20cz@my.fsu.edu
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Yichen Cheng

yc14b@my.fsu.edu
phone:
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major professor: Dr. Tang
second major professor:

D

Ishwaree Datta

ishwareedatta94@gmail.com
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Gabrielle Fisher

gtf17@fsu.edu
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major professor: Dr. Jones
second major professor:

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Yashika Garg

ygarg@bio.fsu.edu
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Rubel Hoq

mhoq@bio.fsu.edu
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Mahdi Khadem

mkhadem@bio.fsu.edu
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Kathryn Koirtyohann

kkoirtyohann@fsu.edu
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Linhui Li

lli@bio.fsu.edu
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major professor:
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Ashley Loeven

My research interests lie in understanding intracellular signaling that mediates dietary fat-induced inflammation and irreversible loss of olfactory sensory neurons in mouse models.

aloeven@bio.fsu.edu
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major professor: Dr. Debi Fadool
second major professor:

Jason Lynn

jlynn@bio.fsu.edu
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major professor: Dr. McGinnis
second major professor:

M

Siming Ma

sma@bio.fsu.edu
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major professor: Dr. Zhu
second major professor:

Calvin Mackey

cmackey@bio.fsu.edu
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Dylan Marin

dm19w@my.fsu.edu
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Angelica Medina

mmedina@bio.fsu.edu
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major professor: Dr. Tang
second major professor:

Daniel Murray

My research focus as a member of Stroupe Lab is on microbial enzymes involved in sulfur metabolism, particularly those responsible for sulfur reduction and the biogenesis of associated cofactors. We use a blend of biochemical and structural techniques to answer structure-function mysteries regarding these enzymes.

dmurray@bio.fsu.edu
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major professor: Dr. Stroupe
second major professor:

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Stacey Pierre

spierre@bio.fsu.edu
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Griffin Pratt

gpratt@bio.fsu.edu
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Meizhu Qi

mqi@bio.fsu.edu
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major professor: Dr. Debra Fadool
second major professor:

Maria Quintero Rodriquez

mquintero@bio.fsu.edu
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Hosna Rastegarpouyani

hr18d@my.fsu.edu
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Bryce Redfern

bredfern@bio.fsu.edu
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Juan Reza

During my current research on SARS-CoV-2, I have designed viral mimic constructs, short-interfering RNA constructs and software to assist in design and test. I develop new protocols for viral infection and gene knock-down experiments at the bench. Of particular interest is a technology-based protocol for compiling experiment-specific RNA-generating plasmids without traditional bacterial cloning amplification.
For my doctoral work, I identify open scientific questions and research challenges in biological science where I intend to apply my experience as a software engineer to innovate and form cross-functional science collaborations.

jreza@fsu.edu
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major professor: Dr. Bass
second major professor:

Sayantan Roy

sayantanroybcm@yahoo.com
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major professor: Dr. Yin
second major professor:

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Sadia Sayed

ssayed@bio.fsu.edu
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major professor: Dr. Chadwick
second major professor:

Lauren Schulte

lschulte@bio.fsu.edu
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major professor: Dr. McGinnis
second major professor:

Charlie Seibert

cseibert@bio.fsu.edu
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major professor: Dr. Fraser
second major professor:

Yun Shi

My research interest focuses on understanding how chromosome segregation is regulated during meiosis.

yshi@bio.fsu.edu
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major professor:
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Sixian Song

songsixian_apply@163.com
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major professor:
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Divyaa Srinivasan

dsrinivasan@bio.fsu.edu
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Jesse Turner

I am interested in the 3D organization of chromatin within the nucleus and how that relates to other nuclear functions, such as transcription and DNA replication. My current project in the lab is investigating early replication control elements (ERCEs), a discrete class of cis-regulatory elements that act as "enhancers of early replication," but also have roles in maintaining sub-nuclear compartmentalization, transcription, and TAD structure. (he/him/his)

jturner@bio.fsu.edu
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major professor: Dr. Gilbert
second major professor:

Zachary Turpin

zturpin@bio.fsu.edu
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major professor: Dr. Bass
second major professor:

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Paola Urlich

pu19@my.fsu.edu
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Athanasios Vouzas

avouzas@bio.fsu.edu
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Nick Waddell

nwaddell@bio.fsu.edu
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Nidhi Walia

nwalia@bio.fsu.edu
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major professor:
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Miao Wang

mw18f@my.fsu.edu
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major professor: Dr. Zhu
second major professor:

Natalia Westervelt

Research focus is the role of long tandem repeats on the X chromosome and their involvement in X inactivation and other pathways.

nwestervelt@bio.fsu.edu
phone:
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major professor: Dr. Chadwick
second major professor:

Y

Rui Yang

ryang@bio.fsu.edu
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major professor:
second major professor:

Andrea Yoest

My research interests involve X chromosome inactivation and genes expressed exclusively in the X inactivation center (XIC), mainly the X-inactive specific transcript (XIST). I also study posttranslational modifications of the X chromosome and how they are involved in X inactivation and gene expression.

ayoest@bio.fsu.edu
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major professor:
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Z

Peiyao Zhao

pzhao@bio.fsu.edu
phone:
fax:
major professor: Dr. Gilbert
second major professor:

Yijing Zhao

I am interested in studying the impact of Zika virus on cell cycle progression.

yz18@my.fsu.edu
phone:
fax:
major professor: Dr. Tang
second major professor:

Featured Student

Emily Darrow (Ph.D., 2018)
CMB graduate student in the Chadwick lab.

Emily Darrow (Ph.D., 2018) CMB graduate student in the Chadwick lab. The roles of many tandem-repeat DNA sequences in the human genome are unknown. DXZ4 is a large X-linked macrosatellite implicated in the structure of the inactive X chromosome (Xi). Using cutting-edge genome engineering tools, Emily excised DXZ4 from the Xi, causing large-scale local chromatin changes to the Xi. In collaboration with Dr. Erez Lieberman-Aiden's group, we showed compromised Xi 3D conformation. This work involved three members of the CMB Graduate Program: Emily Darrow, Zhuo Sun and Andrew Seberg. Emily defended her Ph.D. in 2017 and is starting a postdoc in 2018. ARTICLE: Darrow, E. M., M. H. Huntley, O. Dudchenko, E. K. Stamenova, N. C. Durand, Z. Sun, S. C. Huang, A. L. Sanborn, I. Machol, M. Shamim, A. P. Seberg, E. S. Lander, B. P. Chadwick and E. L. Aiden (2016). "Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture." Proc Natl Acad Sci U S A 113(31): E4504-4512.
Katherine Easterling
CMB doctoral candidate in the Bass lab

Katherine Easterling CMB doctoral candidate in the Bass lab Katherine co-first-authored a paper on inheritance in hop in the journal The Plant Genome. She carried out 3D imaging of hop chromosomes, suggesting a chromosomal basis for the non-Mendelian inheritance patterns observed for genomic markers. She also recently presented a talk and poster at the 2nd Annual Brewers Symposium in Corvallis, Oregon at Oregon State University, where she received the First Prize Award for her poster. ARTICLE: (2017) Zhang* D, Easterling* KA, Pitra* NJ, Coles MC, Buckler ES, Bass HW, and Matthews PD. "Non-Mendelian SNP inheritance and atypical meiotic configurations are prevalent in hop (Humulus lupulus L.)" The Plant Genome 10(3):(14 pp). (DOI: 10.3835/plantgenome2017.04.0032).
Vishnu Dileep (Ph.D. 2017)
CMB student in the Gilbert lab

Vishnu Dileep (Ph.D. 2017) CMB student in the Gilbert lab He studied the relationship between DNA replication-timing regulation and 3D chromatin architecture. Vishnuâ€™s doctoral research showed that the re-establishment of interphase-specific chromatin folding from the condensed mitotic chromosomes coincides with the establishment of the replication-timing program. Vishnu was supported by an American Heart Association fellowship and completed his work by studying genome-wide replication timing regulation at the single cell level. ARTICLE: Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program. Genome Res. 2015 Aug;25(8):1104-13. DOI: 10.1101/gr.183699.114.
Ji Huang
Ph.D. student in the McGinnis lab

Ji Huang Ph.D. student in the McGinnis lab Dr. Ji Huang graduated from the McGinnis Lab in 2018. Ji's article, entitled "Construction and Optimization of Large Gene Co-expression Network in Maize Using RNA-Seq Data", was published in Plant Physiology. His paper employed and tested different approaches to the construction of gene coexpression networks. He identified the optimal parameters for processing maize RNAseq data and generated a large, robust network. The maize coexpression database is available through the McGinnis lab web site at mcginnislab/mcn/main_page.php. ARTICLE: Huang, J., et al. (2017). "Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data." Plant Physiol 175(1): 568-583. https://doi.org/10.1104/pp.17.00825
Hardeep Gumber
CMB doctoral candidate in the Bass lab

Hardeep Gumber CMB doctoral candidate in the Bass lab Hardeep won the graduate student oral presentation competition at the Southern Section of the American Society of Plant Biologists Annual Meeting in Orlando, Florida April 2017. She presented a talk titled: â€œThe maize LINC complex componentsâ€. Hardeepâ€™s research focuses on the role of telomeres and the nuclear envelope-associated LINC complex in meiotic chromosome dynamics and segregation.
Jiao Sima (Ph.D., 2018)
CMB graduate student in the Gilbert lab.

Jiao Sima (Ph.D., 2018) CMB graduate student in the Gilbert lab. Using CRISPR-mediated deletions and inversions Jiao discovered the long sought after cis-acting elements regulating DNA replication in mammalian cells. She discovered that these elements control not only replication, but also transcription and 3D genome architecture of entire chromosome domains (~500kb units of chromosome structure and function). Her work is a major breakthrough, making possible the mechanistic dissection of previously enigmatic and impenetrable aspects of large-scale chromosome architecture. In the field of DNA replication, it resolves a 60 year long debate over whether or not specific sequences regulate replication and sets the stage to identify what those sequences are. ARTICLE: Sima J, Chakraborty A, Dileep V, Michalski M, Klein K.N., Holcomb N.P., Turner J.L., Paulsen M.T., Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. (2019) Identifying cis-Elements for Spatiotemporal Control of Mammalian DNA Replication. CELL 176:816-830 (PMID 30595451)

Featured Student

Emily Darrow (Ph.D., 2018)CMB graduate student in the Chadwick lab.

Katherine Easterling CMB doctoral candidate in the Bass lab

Vishnu Dileep (Ph.D. 2017)CMB student in the Gilbert lab

Ji Huang Ph.D. student in the McGinnis lab

Hardeep Gumber CMB doctoral candidate in the Bass lab

Jiao Sima (Ph.D., 2018)CMB graduate student in the Gilbert lab.

CMB Students Currently in the Graduate Program

Sara Akram

Lorea Arambarri

Daniel Bartlett

Anandi Batabyal

Shahin Behrouz Sharif

Tracey Bell

Jane Benoit

Katherine Bilodeau

Cecilia Bouaichi

Nina Bui

Gabriel Calvin

Christopher Carroll

Lauren Carson

Trirupa Chakraborty

Yichen Cheng

Ishwaree Datta

Gabrielle Fisher

Yashika Garg

Rubel Hoq

Mahdi Khadem

Kathryn Koirtyohann

Linhui Li

Ashley Loeven

Jason Lynn

Siming Ma

Calvin Mackey

Dylan Marin

Angelica Medina

Daniel Murray

Stacey Pierre

Griffin Pratt

Meizhu Qi

Maria Quintero Rodriquez

Hosna Rastegarpouyani

Bryce Redfern

Juan Reza

Sayantan Roy

Sadia Sayed

Lauren Schulte

Charlie Seibert

Yun Shi

Sixian Song

Divyaa Srinivasan

Jesse Turner

Zachary Turpin

Paola Urlich

Athanasios Vouzas

Nick Waddell

Nidhi Walia

Miao Wang

Natalia Westervelt

Rui Yang

Andrea Yoest

Peiyao Zhao

Yijing Zhao

Featured Student

Emily Darrow (Ph.D., 2018)CMB graduate student in the Chadwick lab.

Katherine Easterling CMB doctoral candidate in the Bass lab

Vishnu Dileep (Ph.D. 2017)CMB student in the Gilbert lab

Ji Huang Ph.D. student in the McGinnis lab

Hardeep Gumber CMB doctoral candidate in the Bass lab

Jiao Sima (Ph.D., 2018)CMB graduate student in the Gilbert lab.

Emily Darrow (Ph.D., 2018)
CMB graduate student in the Chadwick lab.

Katherine Easterling
CMB doctoral candidate in the Bass lab

Vishnu Dileep (Ph.D. 2017)
CMB student in the Gilbert lab

Ji Huang
Ph.D. student in the McGinnis lab

Hardeep Gumber
CMB doctoral candidate in the Bass lab

Jiao Sima (Ph.D., 2018)
CMB graduate student in the Gilbert lab.

Emily Darrow (Ph.D., 2018)
CMB graduate student in the Chadwick lab.

Katherine Easterling
CMB doctoral candidate in the Bass lab

Vishnu Dileep (Ph.D. 2017)
CMB student in the Gilbert lab

Ji Huang
Ph.D. student in the McGinnis lab

Hardeep Gumber
CMB doctoral candidate in the Bass lab

Jiao Sima (Ph.D., 2018)
CMB graduate student in the Gilbert lab.