ArticleCell systems2021
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro.
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Article in Cell systems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14citing papers in PubMed
1.6field-weighted citation impact, top 16% of its field
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Molecular gatekeepers of endogenous adult mammalian cardiomyocyte proliferation.Nature reviews. Cardiology · 2025Review
- Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles.bioRxiv : the preprint server for biology · 2025Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.Genome biology · 2024Article
- Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells.Cell systems · 2024Article
- Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.bioRxiv : the preprint server for biology · 2023Article
- Modeling diabetic endothelial dysfunction with patient-specific induced pluripotent stem cells.Bioengineering & translational medicine · 2023Article
- Article
- Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells.bioRxiv : the preprint server for biology · 2023Article
- BRD9-containing non-canonical BAF complex maintains somatic cell transcriptome and acts as a barrier to human reprogramming.Stem cell reports · 2022Article
- Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.Nature biotechnology · 2022Article
- Article
- Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells.Genome biology · 2022Article
- Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain.Cell systems · 2021Article
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Ian A MellisDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Hailey I EdelsteinInstitute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Rachel TruittInstitute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Yogesh GoyalDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Lauren E BeckDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
Orsolya SymmonsDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
Margaret C DunaginDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
Ricardo A Linares SaldanaDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Parisha P ShahDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Juan A Pérez-BermejoGladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
Arun PadmanabhanGladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Wenli YangInstitute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Rajan JainInstitute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: jainr@pennmedicine.upenn.edu.
Arjun RajDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: arjunrajlab@gmail.com.
University of Pennsylvania · USCalifornia Institute for Regenerative Medicine · USGladstone Institutes · US
Funding
UNIVERSITY OF PENNSYLVANIA CAN CTR SUPPORT GRANTP30CA016520 · NCI · UNIVERSITY OF PENNSYLVANIA · PI Robert H. Vonderheide · 1985 to 2026
$222.3MTargeted Combination Therapy for MelanomaP50CA174523 · NCI · WISTAR INSTITUTE · PI HERLYN, MEENHARD F · 2014 to 2018
$11.1MProject-002RM1HG007743 · NHGRI · UNIVERSITY OF WASHINGTON · PI STAMATOYANNOPOULOS, JOHN A · 2015 to 2019
$10.1MTraining Program in Computational GenomicsT32HG000046 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI JUNHYONG KIM, Mingyao Li · 1999 to 2026
$9.5MDecoding the bridges and barriers to cellular reprogramming and lineage identityR01GM137425 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI JAIN, RAJAN, RAJ, ARJUN · 2019 to 2023
$5.6MEngineering and visualizing genome folding at high spatiotemporal resolutionU01HL129998 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI BLOBEL, GERD A, PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2015 to 2019
$4.2MTraining Program in Biomedical Imaging and Information SciencesT32EB009384 · NIBIB · UNIVERSITY OF PENNSYLVANIA · PI GEE, JAMES C, IVES, ZACHARY · 2009 to 2023
$4.0MA plasticity and reprogramming paradigm for therapy resistance at the single cell levelU01CA227550 · NCI · UNIVERSITY OF PENNSYLVANIA · PI RADHAKRISHNAN, RAVI, RAJ, ARJUN · 2018 to 2022
$3.3MAn integrated approach to melanoma metastasis and therapy resistance: effects of age-related changes in the ECM and the biomechanics of the skinR01CA232256 · NCI · WISTAR INSTITUTE · PI CUKIERMAN, EDNA, RAJ, ARJUN · 2019 to 2023
$3.0MUnderstanding and Overcoming Resistance to BRAF/MEK Kinase Inhibitors in MelanomaR01CA238237 · NCI · UNIVERSITY OF PENNSYLVANIA · PI HERLYN, MEENHARD F, RAJ, ARJUN · 2020 to 2024
$2.9MThe Role of BRD4 in Cardiac SpecificationR01HL139783 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI JAIN, RAJAN · 2019 to 2022
$1.6MPadmanabhan K08 Admin SupplementK08HL157700 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PADMANABHAN, ARUN · 2021 to 2025
$830kNCI NIH HHS P30 CA016520NCI NIH HHS P50 CA174523NCI NIH HHS R01 CA232256NCI NIH HHS R01 CA238237NCI NIH HHS U01 CA227550NHGRI NIH HHS RM1 HG007743NHGRI NIH HHS T32 HG000046NHLBI NIH HHS F31 HL147416NHLBI NIH HHS K08 HL157700NHLBI NIH HHS R01 HL139783NHLBI NIH HHS U01 HL129998NIAID NIH HHS F30NS100595NIBIB NIH HHS T32 EB009384NIGMS NIH HHS R01 GM137425NINDS NIH HHS F30 NS100595
Abstract
Identifying the particular transcription factors that maintain cell type in vitro is important for manipulating cell type. Identifying such transcription factors by their cell-type-specific expression or their involvement in developmental regulation has had limited success. We hypothesized that because cell type is often resilient to perturbations, the transcriptional response to perturbations would reveal identity-maintaining transcription factors. We developed perturbation panel profiling (P
Indexed as
Induced Pluripotent Stem CellsTranscription FactorsCell DifferentiationFibroblastsHumansMyocytes, CardiacTranscription Factorscardiac myocytescell identityfibroblastsgene regulationinduced pluripotent stem cellsreprogrammingsystems biologytransdifferentiation
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