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, Mechanical Engineering, Virginia Tech, (STEP Lab)
B.Sc., Mechanical Engineering, Lafayette College
email: mukherjea1 at chop.edu
Projects
Molecular kinetics of transcription initiation
Insulator protein kinetics during ZGA
Email | Google Scholar | LinkedIn|
Santosh Adhikari
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, 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, 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|
Franklin Staback Rodriguez
HHMI Gilliam Fellow
PhD, Immunology, University of Pennsylvania
B.S., Cell and Molecular Biology, University of Puerto Rico
email: stabackrof at chop.edu
Projects
Mechanism regulation NK cell killing behaviors
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
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 (2025-2026)
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), NIDDK F31 Fellow (2026-Present)
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
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.
Graduate and Postdoctoral Alumni
Samantha Fallacaro
Position after leaving Lab: Postdoc with Gillian Griffiths, Yale University
Samantha Fallacaro was in the lab from 2021- 2026. She was a member of the DSRB graduate group and a NSF GRFP graduate fellow. During her time with us she used our light-sheet microscope to study how the binding and cluster formation of the morphogen dorsal is regulated. Her work showed that Dorsal clustering emerges from the number of binding sites at enhancer sequences and the molecular on- and off- rates of Dorsal binding (Sci. Adv, 2026). She also was co- lead of our project exploring how Zelda's IDRs regulate its target search and occupancy (Biorxiv, 2024). She also developed many useful tools to characterize transcription factor clusters and their interactions with gene loci (MIMB 2025, In Prep 2026).
Other Alumni
Staff
Yara Haloush - Research Technician 07/2023-11/2025. Position after Mir Lab: Research Technician at Dartmouth University
Joe Zinski, PhD - Bioinformatician 07/2022-01/2024. Position after Mir Lab: Senior Research Investigator at the Center for Cytokine Storm Treatment & Laboratory · University of Pennsylvania
Mattisen Dimler - Research Technician 07/2022-03/2023. Position after Mir Lab: Scientist at Parexel (Merck)
Nicholas Gattone - Research Technician 01/2021-09/2021. Position after Mir Lab: Scientist at Spark Therapeutics
Post-baccalaureate Researchers
Guzel Naik- 05/2021-06/2022. Position after Mir Lab: Biology Graduate Student at University of Virginia
Undergraduate Researchers
Kareena Shankta - 11/2022-05/2026. Position after Mir Lab: Pursuing MD at Yale Medical School
Justin Lee - 03/2025-08/2025. Position after Mir Lab: Biochemistry Undergraduate student @Penn
Ernesto Gamauf - 02/2022-05/2024. Position after Mir Lab: Med School Prep Program @Penn
Sarah O'Konski - 10/2021-05/2022. Position after Mir Lab: Chemistry Undergraduate student @Penn
Cody Eskandarian - 06/2021-04/2022. Position after Mir Lab: Biochemistry and Biophysics Undergraduate student @Penn
Summer Interns
Alexa Butler (HS student) -06-08/2026
Mohammed Al Azzawi (OER HS student) -06-08/2026
Leora Day (HS student) -07-08/2025 Position after Mir Lab: Undergraduate student Penn
Anusuya Phuyal (OER HS student) -06-08/2025
Nihanth Pinnaka (HHMI SURP Summer student) -07-08/2025
Carmine Picone (OER HS student) -06/2024-08/2024
Siani Elliot (OER HS student) -06/2023-08/2023
Anna Crow - 06/2022-09/2022. Position after Mir Lab: Undergraduate student at Univ. Leicester, UK
Sapna Krishnakumar - 07/2022-08/2022. Position after Mir Lab: Undergraduate student at IISER Mohali, India