Mustafa Mir
Principal Investigator
Assistant Professor of Cell and Developmental Biology, University of Pennsylvania
Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia
Core Member, Penn Epigenetics Institute
Member, Institute for Regenerative Medicine
Graduate Group Affiliations: CAMB, BE, BMB
HHMI Freeman Hrabowski Scholar (2023 -Present)
NIH Directors New Innovator Award Recipient (2021)
Postdoc, University of California, Berkeley (Tjian and Darzacq Lab)
PhD, Electrical Engineering, University of Illinois, Urbana-Champaign (Quantitative Light Imaging Lab, Gabriel Popescu)
email: Mustafa.Mir at pennmedicine.upenn.edu
Bio | Email | Google Scholar | Twitter | ORCID |
Research Staff
Postdocs
Apratim Mukherjee, PhD
PhD, Mechanical Engineering, Virginia Tech, (STEP Lab)
B.Sc., Mechanical Engineering, Lafayette College
email: mukherjea1 at chop.edu
Projects
Nuclear compartmentalization and dynamics during Zygotic Genome Activation
How do transcription factor hubs facilitate target search and occupancy?
RNA Polymerase II Clustering
Email | Google Scholar | LinkedIn|
Santosh Adhikari, PhD
PhD, Biophysics, University of Minnesota Twin Cities, (Puchner Lab)
B.S., Physics, Southern Methodist University
email: adhikaris2 at chop.edu
Projects
Roles of IDRs in transcription factor search and occupancy
Nucleolar protein kinetics
Live imaging of chromatin compaction
Email | Google Scholar | LinkedIn|
Matthew Fischer, PhD
PhD, Molecular and Cellular Biology (with Leslie Pick)
B.S., Cell/Molecular Biology and Genetics
email: fischerm2 at chop.edu
Projects
Email | Google Scholar | LinkedIn|
Lulu Zhou, PhD
PhD, Analytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
B.E., Material Chemistry, Anhui Normal University, China
email: zhoul4 at chop.edu
Projects
Endoderm fate specification during mammalian development
Email | Google Scholar | LinkedIn|
Graduate Students
Kaeli Mathias
PhD Candidate, Biochemistry and Molecular Biophysics (co-mentored by Dr. Liling Wan)
NCI F31 Predoctoral Fellow (2023-Present), Genetics T32 Fellow (2021-2023)
BA Chemistry, Amherst College
2018-2020 Research Technician in Dr. Charles Roberts Lab, St. Jude Children's Hospital
email: kaelim at pennmedicine.upenn.edu
Projects
Oncogenic transcription factor hub formation and function
Samantha "S" Fallacaro
PhD Candidate, Developmental, Stem Cell, and Regenerative Biology
NSF GRFP Fellow (2023-Present)
B.Sc. Biological Sciences, Carnegie Mellon University
email: samantha.fallacaro at pennmedicine.upenn.edu
Projects
Transcription factor hub formation, function, and dynamics
Transcription factor target search and occupancy
New light-sheet image analysis tools
Gabriela Hayward-Lara
PhD Candidate, Developmental, Stem Cell, and Regenerative Biology
NSF GRFP Fellow (2023-Present)
B.A. Molecular Biology, Princeton University
email: gabriela.hayward-lara at pennmedicine.upenn.edu
Projects
Polycomb body formation and chromatin dynamics during transcription repression
Sena Sarıkaya
PhD Candidate, Developmental, Stem Cell, and Regenerative Biology
Developmental Biology T32 Fellow (2025-Present)
B.S. Cell and Molecular Biology, University of Texas at Austin
B.A Anthropology, University of Texas at Austin
email: sena.sarikaya at pennmedicine.upenn.edu
Projects
Chromatin and transcription factor kinetics during mouse pre-implantation development
Raymond Carter
PhD Candidate, Biochemistry and Molecular Biophysics (co-mentored by Dr. Gerd Blobel)
Hematology T32 Fellow (2025-Present)
Structural Biology and Molecular Biophysics T32 Fellow (2024-2025)
B.S. Neuroscience and Medicine, Health, and Society, Vanderbilt University
email: Raymond.carter at pennmedicine.upenn.edu
Projects
Mechanism of transcription factor target search
Kyle Ferguson
PhD Candidate, Bioengineering
M.S. Medical Physics, Duke University
B.S. Biophysics, Bucknell University.
email: fergusonks at chop.edu
Projects
Modular microscope design and multispectral imaging
Manya Kapoor
PhD Candidate, Bioengineering
B.S. Electrical Engineering, Princeton University.
email: manyak at seas.upenn.edu
Projects
Transcription factor IDR interactions driving nuclear distributions and target occupancy
Alexandria Adigun
MD PhD Candidate, Developmental, Stem Cell, and Regenerative Biology, NIGMS F31 Predoctoral Fellow (2025-Present)
B.S. Biology, Howard University
email: alexandria.adigun at pennmedicine.upenn.edu
Projects
Replication and transcription coordination
Lillian Encarnation
PhD Student, Biology
B.S. Biology, Colorado College
email: elillian at sas.upenn.edu
Projects
Molecular Interpretation of morphogen gradients by enhancers
Undergraduate Researchers
Kareena Shankta
Undergraduate Student in Vagelos Life Sciences and Management and in Computational Biology and Economics at the University of Pennsylvania since 2022. Working with Apratim Mukherjee.
Derene Darkwah- FERBS Scholar
Undergraduate Student in Neuroscience at the University of Pennsylvania since 2023. Working with Matthew Fischer.
Mariacristina Calcagno
Undergraduate Student in Vagelos Life Sciences and Management and in Computational Biology and Economics at the University of Pennsylvania since 2025. Working with Gabriela Hayward-Lara.
Heritage Ayodele
Undergraduate Student in Neuroscience at the University of Pennsylvania since 2024. Working with Alexandria Adigun.
Nneamaka Okolo
Undergraduate Student in Biology at the University of Pennsylvania since 2023. Working with Sena Sarikaya.
Administrative Staff
Samantha Jaworski
CCGM Office Manager
Samantha Jaworski is the Office Manager for the Center for Computational and Genomic Medicine at the Children’s Hospital of Philadelphia. She holds a BS in Biobehavioral Health and academic minors in Health Policy and Administration and Psychology from The Pennsylvania State University, Main. She earned her MBA from Haub School of Business at Saint Joseph’s University in 2019. She has been working at CHOP since 2016 and provides administrative support for the Center.
Email: colest at .chop.edu
Allison Fantauzzi
CCGM Administrative Director
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Allison Fantauzzi is the Administrative Director for the Center for Computational and Genomic Medicine. She holds an Executive MBA from Georgetown University’s McDonough School of Business and a BS in Business Administration from Centenary University. She has worked in business administration, finance, and operations for 25 years, and has been with CHOP for 2 years.
Email: fantauzzia at chop.edu
Alumni
Staff
Yara Haloush - Research Technician 07/2023-11/2025. Last known position: Research Technician at Dartmouth University
Joe Zinski, PhD - Bioinformatician 07/2022-01/2024. Last known position: Senior Research Investigator at the Center for Cytokine Storm Treatment & Laboratory · University of Pennsylvania
Mattisen Dimler - Research Technician 07/2022-03/2023. Last known position: Scientist at Parexel (Merck)
Nicholas Gattone - Research Technician 01/2021-09/2021. Last known position: Scientist at Spark Therapeutics
Graduate Students
Alan Boka - BMB Student 04/2021-04/2023. (did not complete PhD with us). Last known position: BMB PhD student @Penn
Rotation Students
Adam Jabak - BMB Rotation Student 04/2021-06/2021. Last known position: BMB PhD student @Penn
Post-baccalaureate Researchers
Guzel Naik- 05/2021-06/2022. Last known position: Biology Graduate Student at University of Virginia
Undergraduate Researchers
Justin Lee - 03/2025-08/2025. Last known position: Biochemistry Undergraduate student @Penn
Ernesto Gamauf - 02/2022-05/2024. Last known position: Med School Prep Program @Penn
Sarah O'Konski - 10/2021-05/2022. Last known position: Chemistry Undergraduate student @Penn
Cody Eskandarian - 06/2021-04/2022. Last known position: Biochemistry and Biophysics Undergraduate student @Penn
Summer Interns
Leora Day (HS student) -07-08/2025
Anusuya Phuyal (OER student) -06-08/2025
Nihanth Pinnaka (HHMI SURP Summer student) -07-08/2025
Carmine Picone (OER student) -06/2024-08/2024
Siani Elliot (OER student) -06/2023-08/2023
Anna Crow - 06/2022-09/2022. Last known position: Undergraduate student at Univ. Leicester, UK
Sapna Krishnakumar - 07/2022-08/2022. Last known position: Undergraduate student at IISER Mohali, India