Publications

Connie L. Jiang, Yogesh Goyal, Naveen Jain, Qiaohong Wang, Rachel E. Truitt, Allison J. Coté, Benjamin Emert, Ian A. Mellis, Karun Kiani, Wenli Yang, Rajan Jain & Arjun Raj. Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. Genome Biol 23, 90 (2022).

Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL. p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol Cell. 2021 Apr 15;81(8):1666-1681.e6.

Allison Coté, Chris Coté, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, Edward S. Boyden, Shelley Berger, L. Stirling Churchman, Arjun Raj. pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally. bioRxiv 2020.04.06.028092

Sanford EM, Emert BL, Coté A, Raj A. Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. Elife. 2020 Dec 7;9:e59388.

Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Chandra A, Silverman M, Joyce EF, Little SC; HPAP Consortium, Kaestner KH, Naji A, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G. Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression. Immunity. 2020 Feb 18;52(2):257-274.e11.

Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nat Biotechnol. 2018 Nov 12.

Palozola KC, Donahue G, Liu H, Grant GR, Becker JS, Coté A, Yu H, Raj A, Zaret KS. Mitotic transcription and waves of gene reactivation during mitotic exit. Science. 2017 Oct;358(6359):119-122.

Coté, AJ, Raj A. FISHing Out the Details of CRISPR Genome Tracks. [perspective] Biophys. J. 2017 Mar;112(6):1045-1046.

Chen F, Wassie AT, Coté AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES. Nanoscale imaging of RNA with expansion microscopy. Nat Methods. 2016 Aug;13(8):679-84.

Coté AJ*, McLeod CM*, Farrell MJ, McClanahan PD, Dunagin MC, Raj A, Mauck RL. Single-cell differences in matrix gene expression do not predict matrix deposition. Nat Commun. 2016 Mar;7:10865.
* indicates co-first author

SKILLS

LAB SKILLS: RNA FISH, DNA FISH, expansion microscopy, high powered epifluorescent microscopy, HPLC, IF, cell culture, tissue engineering, histology/chromatic staining, STORM, western blots, RNA-seq, ChIP-seq, FACS, qPCR, CRISPR KO, cloning

COMPUTATIONAL SKILLS: R (including tidyverse, single cell RNA seq pipelines, and ggplot2 for data visualization), MATLAB (including GUI development for image processing), python for high throughput sequencing data processing, shell scripting for high throughput sequencing data processing, ImageJ/FIJI for image processing, Adobe Illustrator, version control software (git, mercurial)

Selected Posters/Presentations

“Transcriptional escape: unprocessed RNA away from the site of transcription”
Allison Coté, Sareh Bayetpour, Arjun Raj
Poster, Cold Spring Harbor Eukaryotic mRNA Processing Meeting
August 21, 2019

“Endogenous genes exhibit different intron dispersal patterns that demonstrate independent post-transcriptional splicing”
Allison Coté, Sarah Bayetpour, Arjun Raj
Poster, RNA Society Annual Meeting
June 11, 2019

“Expansion microscopy for super-resolution imaging of transcriptional dynamics”
Allison Coté, Fei Chen, Asmamaw Wassie, Edward S. Boyden, Arjun Raj
Poster, RNA Institute Annual Symposium on RNA Science and its Applications
March 17, 2017

“Expansion microscopy allows for visualization of RNA structure at regions of densely packed RNA”
Allison Coté, Fei Chen, Asmamaw Wassie, Edward S. Boyden, Arjun Raj
Presentation, RNA Institute Annual Symposium on RNA Science and its Applications
March 18, 2016

“Single-cell RNA FISH analysis of mesenchymal stem cell chondrogenesis and chondrocyte dedifferentiation challenges traditional definitions of phenotype“
Allison Coté, Claire McLeod, Robert Mauck, Arjun Raj
Poster, Keystone Symposia on Transcriptional and Epigenetic Influences on Stem Cell States
March 23, 2015

AWARDS

Franklin W. Olin College of Engineering Full Tuition Scholarship - 4 years

Cell and Molecular Biology Training Grant - 1 year

Biomedical Graduate Studies Travel Grant - 1 year

Teaching/Mentoring Experience

Teaching Assistant - Cell Biology graduate level

Tutor - Cell Biology graduate level and Gene Expression graduate level

Mentored high school student (Merin Padovan), rotation students (Ian Mellis and Lauren Beck), younger Cell and Molecular Biology/CPM student (Vineet Kulkarni), and undergraduate student in lab (Stacey Sloate)

Outreach and University Service

• Cell and Molecular Biology Executive Committee

• Cell and Molecular Biology Curriculum Committee

• Cell and Molecular Biology Best Practices Committee

• Association of Women in Science volunteer at the Philadelphia Science Festival

• Cell and Molecular Biology Review Committee

• Coordinated information sessions for younger students regarding non-academic careers, image processing, data analysis, and other topics

• Coordinated interview weekend visit for over 30+ students for Cell and Molecular Biology recruitment efforts

• Coordinated Raj Lab Trainee Seminar Series: Twitter link

References

Arjun Raj, PhD

Professor
Department of Bioengineering
University of Pennsylvania
410S South 33rd Street
Philadelphia, PA 19104
arjunrajlab@gmail.com
215-821-7394

Rebecca Wells, MD

Professor of Medicine
Department of Gastroenterology
421 Curie Boulevard
905 Biomedical Research Building II/III
Philadelphia, PA 19104
rgwells@mail.med.upenn.edu
215-573-1860

Robert Mauck, PhD

Mary Black Ralston Professor for Education and Research
Department of Orthopedic Surgery
McKay Orthopedic Research Laboratory
114A Stemmler Hall
3450 Hamilton Walk
Philadelphia, PA 19104
lemauck@mail.med.upenn.edu
215-898-8653