Arjun Raj, PhD

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Professor of Bioengineering
Department: Bioengineering

Contact information
Office: 111 Hayden Hall
Mail: 210 S. 33rd Street
Skirkanich Hall, Room 240
Philadelphia, PA 19104
Office: 215-821-7394
Education:
BA (Physics and Mathematics)
University of California, Berkeley, 2000.
PhD (Mathematics)
Courant Institute of Mathematical Sciences, New York University, 2006.
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Description of Research Expertise

Research Interests: RNA systems biology, particular as related to non-coding RNAs and cancer biology.

Keywords: RNA, systems biology, cancer, non-coding RNAs

Research Details:
The Raj lab studies the biology of single cells. The primary motivation for studying biological processes on a cell-by-cell basis is the fact that even genetically identical cells can behave very differently. This variability can have consequences in a variety of biological contexts. We aim to understand these differences at the molecular level. We develop and utilize a mix of experimental tools including individual RNA molecules via fluorescence microscopy, high throughput sequencing and molecular biology to make quantitative measurements of cellular behavior.

Rotation Projects: Please contact Arjun for more details.

Selected Publications

Bartman Caroline R, Hamagami Nicole, Keller Cheryl A, Giardine Belinda, Hardison Ross C, Blobel Gerd A, Raj Arjun: Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Molecular cell 73(3): 519-532.e4, 02 2019.

Kaur Amanpreet, Ecker Brett L, Douglass Stephen M, Kugel Curtis H, Webster Marie R, Almeida Filipe V, Somasundaram Rajasekharan, Hayden James, Ban Ehsan, Ahmadzadeh Hossein, Franco-Barraza Janusz, Shah Neelima, Mellis Ian A, Keeney Frederick, Kossenkov Andrew, Tang Hsin-Yao, Yin Xiangfan, Liu Qin, Xu Xiaowei, Fane Mitchell, Brafford Patricia, Herlyn Meenhard, Speicher David W, Wargo Jennifer A, Tetzlaff Michael T, Haydu Lauren E, Raj Arjun, Shenoy Vivek, Cukierman Edna, Weeraratna Ashani T: Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility. Cancer discovery 9(1): 64-81, 01 2019.

Symmons Orsolya, Chang Marcello, Mellis Ian A, Kalish Jennifer M, Park Jihwan, Suszt√°k Katalin, Bartolomei Marisa S, Raj Arjun: Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. PLoS genetics 15(1): e1007874, 01 2019.

Kim Ji Hun, Rege Mayuri, Valeri Jacqueline, Dunagin Margaret C, Metzger Aryeh, Titus Katelyn R, Gilgenast Thomas G, Gong Wanfeng, Beagan Jonathan A, Raj Arjun, Phillips-Cremins Jennifer E: LADL: light-activated dynamic looping for endogenous gene expression control. Nature methods 16(7): 633-639, 07 2019.

Rouhanifard Sara H, Mellis Ian A, Dunagin Margaret, Bayatpour Sareh, Jiang Connie L, Dardani Ian, Symmons Orsolya, Emert Benjamin, Torre Eduardo, Cote Allison, Sullivan Alessandra, Stamatoyannopoulos John A, Raj Arjun: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nature biotechnology Nov 2018.

Karakasheva Tatiana A, Lin Eric W, Tang Qiaosi, Qiao Edmund, Waldron Todd J, Soni Monica, Klein-Szanto Andres J, Sahu Varun, Basu Devraj, Ohashi Shinya, Baba Kiichiro, Giaccone Zachary T, Walker Sarah R, Frank David A, Wileyto E Paul, Long Qi, Dunagin Margaret C, Raj Arjun, Diehl J Alan, Wong K K, Bass Adam J, Rustgi Anil K: IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment. Cancer research 78(17): 4957-4970, Sep 2018.

Torre Eduardo, Dueck Hannah, Shaffer Sydney, Gospocic Janko, Gupte Rohit, Bonasio Roberto, Kim Junhyong, Murray John, Raj Arjun: Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Cell systems 6(2): 171-179.e5, Feb 2018.

Wang Jingshu, Huang Mo, Torre Eduardo, Dueck Hannah, Shaffer Sydney, Murray John, Raj Arjun, Li Mingyao, Zhang Nancy R: Gene expression distribution deconvolution in single-cell RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America 115(28): E6437-E6446, 07 2018.

Hughes Alex J, Mornin Joseph D, Biswas Sujoy K, Beck Lauren E, Bauer David P, Raj Arjun, Bianco Simone, Gartner Zev J: Quanti.us: a tool for rapid, flexible, crowd-based annotation of images. Nature methods 15(8): 587-590, 08 2018.

Mellis Ian A, Gupte Rohit, Raj Arjun, Rouhanifard Sara H: Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nature methods 14(8): 801-804, Aug 2017.

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Last updated: 10/01/2019
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