Pre-prints

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Niu Z, O’Farrell A, Li J, Reffsin S, Jain N, Dardani IP, Goyal Y, Raj A
bioRxiv | PDF | bioRxiv | tweetorial

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer

Alexander KA, Yu R, Skuli N, Coffey NJ, Nguyen S, Faunce C, Huang H, Dardani IP, Good AL, Lim J, Li C, Biddle N, Joyce EF, Raj A, Lee D, Keith B, Simon MC, Berger SL
bioRxiv | PDF | bioRxiv

Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states

Reffsin S, Miller J, Ayyanathan K, Dunagin MC, Jain N, Schultz D, Cherry S, Raj A
bioRxiv | PDF | bioRxiv, in review | tweetorial

Metastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation

Kaur A, Cuenca L, Kiani K, Busch GT, Fingerman D, Dunagin MC, Li J, Dardani IP, Sanford EM, Pemberton J, Goyal Y, Weeraratna AT, Herlyn M, Raj A
bioRxiv | PDF | bioRxiv | tweetorial

2024

The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes

Coté A^, O’Farrell A^, Dardani IP, Dunagin MC, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A
^contributed equally
eLife | journal | data & code

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

Jain N, Goyal Y, Dunagin MC, Coté C, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A
Cell Systems | PDF | journal | tweetorial

2023

A subpopulation of lipogenic brown adipocytes drives thermogenic memory

Lundgren P, Sharma PV, Dohnalová L, Coleman K, Uhr GT, Kircher S, Litichevskiy L, Bahnsen K, Descamps HC, Demetriadou C, Chan J, Chellappa K, Cox TO, Heyman Y, Pather SR, Shoffler C, Petucci C, Shalem O, Raj A, Baur JA, Snyder NW, Wellen KE, Levy M, Seale P, Li M, Thaiss CA
Nature Metabolism | journal | pubmed | supplement

Diverse clonal fates emerge upon drug treatment of homogenous cancer cells

Goyal Y, Busch GT, Pillai M, Li J, Boe R, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea G, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A
Nature | journal | supplement | data | code | tweetorial

ClonoCluster: a method for using clonal origin to inform transcriptome clustering

2022

Allelic correlation is a marker of tradeoffs between barriers to transmission of expression variability and signal responsiveness in genetic networks

Boe RH, Ayyappan V, Schuh L, Raj A
Cell Systems | PDF | pubmed | journal | tweetorial

CTCF blocks antisense transcription initiation at divergent promoters

Luan J^, Vermunt MW^, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA
^contributed equally
Nature Structural & Molecular Biology | PDF | pubmed | journal

Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations

Kiani K, Sanford EM, Goyal Y, Raj A
Molecular Systems Biology | PDF | journal | tweetorial

clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

Dardani IP, Emert B, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A
Nature Methods | journal | tweetorial

Systematically quantifying morphological features reveals constraints on organoid phenotypes

Beck LE, Lee J, Cote CJ, Dunagin MC, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Raj A
Cell Systems | PDF | pubmed | journal | tweetorial

Cell type determination for cardiac differentiation occurs soon after seeding of human induced pluripotent stem cells

2021

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity

p53 mediates target gene association with nuclear speckles for amplified RNA expression

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
Molecular Cell | PDF | pubmed | journal

Variability within rare cell states enables multiple paths toward drug resistance

Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM & Raj A
Nature Biotechnology | PDF | pubmed | journal | data & code

Genetic Screening for Single-cell Variability Modulators Driving Therapy Resistance

Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane M, Alicea G, Budinich KA, Weeraratna A, Shi J, Raj A
Nature Genetics | PDF | pubmed | journal | data & code

2020

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

Sanford EM, Emert BL, Coté A, Raj A
eLife | PDF | pubmed | journal

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A
Cell | pubmed | journal

Gene networks with transcriptional bursting recapitulate rare transient coordinated high expression states in cancer

Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y
Cell Syst | PDF | pubmed | journal | model simulations

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression

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
Immunity | pubmed | journal

2019

LADL: light-activated dynamic looping for endogenous gene expression control

Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE
Nat Methods | pubmed | journal | nbci

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A
PLoS Genet | PDF | pubmed | journal | data/analyses

Illuminating Genomic Dark Matter with RNA Imaging

Raj A, Rinn JL
Cold Spring Harbor Perspect Biol | pubmed | journal

Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation

2018

ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification

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
Nat Biotechnol | PDF | pubmed | journal

Remodeling of the collagen matrix in aging skin promotes melanoma metastasis and affects immune cell motility

Kaur A, Ecker BL, Douglass SM, Kugel CH 3rd, Webster MR, Almeida FV, Somasundaram R, Hayden J, Ban E, Ahmadzadeh H, Franco-Barraza J, Shah N, Mellis IA, Keeney F, Kossenkov A, Tang HY, Yin X, Liu Q, Xu X, Fane M, Brafford P, Herlyn M, Speicher DW, Wargo JA, Tetzlaff MT, Haydu LE, Raj A, Shenoy V, Cukierman E, Weeraratna AT
Cancer Discov | PDF | pubmed | journal

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images

Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ
Nat Methods | PDF | pubmed | journal

IL-6 mediates cross-talk between tumor cells and activated fibroblasts in the tumor microenvironment

Karakasheva TA, Lin EW, Tang Q, Qiao E, Waldron TJ, Soni M, Klein-Szanto AJ, Sahu V, Basu D, Ohashi S, Baba K, Giaccone ZT, Walker SR, Frank DA, Wileyto EP, Long Q, Dunagin MC, Raj A, Diehl JA, Wong KK, Bass AJ, Rustgi AK
Cancer Res | PDF | pubmed | journal

Gene expression distribution deconvolution in single-cell RNA sequencing

Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR
Proc Natl Acad Sci U S A | PDF | pubmed | journal

SAVER: gene expression recovery for single-cell RNA sequencing

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR
Nat Methods | PDF | pubmed | journal

Rare cell detection by single-cell RNA sequencing as guided by single-molecule RNA FISH

2017

Visualizing adenosine-to-inosine RNA editing in single mammalian cells

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA
Mol Cell | PDF | pubmed | journal

Neutrophils and Ly6Chi monocytes collaborate in generating an optimal cytokine response that protects against pulmonary Legionella pneumophila infection

Casson CN, Doerner JL, Copenhaver AM, Ramirez J, Holmgren AM, Boyer MA, Siddarthan IJ, Rouhanifard SH, Raj A, Shin S
PLoS Pathog | PDF | pubmed | journal

FISHing Out the Details of CRISPR Genome Tracks

Coté AJ, Raj A
Biophys J. [Perspective] | PDF | pubmed

Systems biology: Molecular memoirs of a cellular family

Beck LE, Raj A
Nature [Perspective] | PDF | pubmed | journal

2016

The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

Kotzin JJ, Spencer SP, McCright SJ, Kumar DB, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CC, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J
Nature | PDF | pubmed | journal

Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels

Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS
PLoS One 11, e0158298 | PDF | pubmed | journal

Nanoscale imaging of RNA with expansion microscopy

Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES
Nat Methods | PDF | pubmed | journal

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition

Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA
Genes Dev | PDF | pubmed | journal

What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism

Symmons O, Raj A
Molecular Cell | PDF | pubmed | journal

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartman CR*, Hsu SC*, Hsiung CCS*, Raj A^, and Blobel GA^
*equal contributions, ^corresponding author
Molecular Cell | PDF | pubmed | journal | slidecast

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Single-cell differences in matrix gene expression do not predict matrix deposition

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI
BMC Genomics | PDF | pubmed | journal

2015

Dynamic enhancer–gene body contacts during transcription elongation

Lee K, Hsiung CCS, Huang P, Raj A, Blobel GA
Genes and Development | PDF | pubmed | journal

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu J, Mercado-López X, Grier JT, Kim W, Chun LF, Irvine EB, Duany YDT, Kell A, Hur S, Gale M, Jr., Raj A, López CB
mBio | PDF | pubmed | journal

Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

Mellis IA, Raj A
Genome Research [Perspective] | PDF | journal

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip

Robust hematopoietic progenitor cell commitment in a noisy environment via suppression of a conflicting signal

Shah NA, Levesque MJ, Raj A, Sarkar CA
J. Cell Sci | PDF | pubmed | journal

Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms

Localization and abundance analysis of human lncRNAs at single cell and single molecule resolution

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton T, Preston E, Nair GP, Zacharias AL, Raj A, Murray JI
PLOS Genetics | PDF | pubmed | journal

Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin MC*, Cabili MN*, Rinn JL^, Raj A^
*equal contributions, ^corresponding authors
Meth in Mol Biology | PDF

2014

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda D, Pascual-Garcia P, Dunagin M, Tudorb M, Hopkins KC, Xua J, Golda B, Raj A, Capelson M, Cherry S
Proc Natl Acad Sci U S A | PDF | pubmed | journal

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T
Molecular Cell | PDF | pubmed

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches E, Guedes AM, Moravec M, Maamar H, Svoboda P, Raj A, Henrique D
Development | PDF | pubmed | journal

Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Weis B, Schmidt J, Maamar H, Raj A, Lin H, Tóth C, Riedmann K, Raddatz G, Seitz HK, Ho AD, Lyko F, Linhart HG
Oncogene | PDF | pubmed | journal

RNA sequencing in situ

Ginart P, Raj A
Nature Biotechnology | PDF | pubmed | journal

An intuitive derivation of the expectation-maximization algorithm

Nair, G
Rajlab, brief communication | PDF

Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature

Facciponte JG, Ugel S, De Sanctis F, Li C, Wang L, Nair G, Sehgal S, Raj A, Matthaiou E, Coukos G, Facciabene A
Journal of Clinical Investigation | PDF | pubmed | journal

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, Dunagin M, Pimkin M, Gore M, Sun D, Konuthula N, Raj A, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ
Blood | PDF | pubmed | journal

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL
Nature SMB | PDF | pubmed | journal

2013

Turbo FISH: A method for rapid single molecule RNA FISH

Using variability in gene expression as a tool for studying gene regulation

Padovan-Merhar O, Raj A
WIREs Syst Biol Med | PDF | pubmed

Visualizing SNVs to quantify allele-specific expression in single cells

Gene transcription is coordinated with but not dependent on cell divisions during C. elegans embryonic fate specification

Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells

Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, Behlke MA, Tsourkas A
Nucleic Acids Research | PDF | pubmed

linc-HOXA1 is a non-coding RNA that represses Hoxa1 in cis

Single chromosome transcriptional profiling reveals chromosome-level regulation of gene expression

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA
Nature | PDF | pubmed | journal

2012

Spo0A-P imposes a temporal gate for the bimodal expression of competence in B. subtilis

Mirouze N, Desai Y, Raj A, Dubnau D
PLoS Genetics | PDF | pubmed | journal

Global Analysis of RNA Secondary Structure in Two Metazoans

Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Bambina S, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang L, Gregory BD
Cell Reports | PDF + supplement | pubmed

2011

Time-lapse transcription

Nair G, Raj A
Science [Perspective] | PDF | pubmed | journal

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, Jaenisch R, Linhart HG
J Clin Invest | PDF | pubmed | journal | supplement

Single molecule imaging of RNA in situ

Batish M, Raj A, Tyagi S
Methods Mol Biol | PDF | pubmed

2010

Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes

Raj A, Tyagi S
Method in Enzymology | PDF | pubmed

Variability in gene expression underlies incomplete penetrance

2009

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL
Proc Natl Acad Sci U S A | PDF | pubmed | journal

Single-Molecule Approaches to Stochastic Gene Expression

Raj A, van Oudenaarden A
Ann Rev Biophysics | PDF | pubmed | journal

2008

Nature, Nurture or Chance: Stochastic Gene Expression and its Consequences

Raj A, van Oudenaarden A
Cell | PDF | pubmed | journal

Imaging individual mRNA molecules using multiple singly labeled probes

2007

Noise in gene expression determines cell fate in Bacillus subtilis

Maamar H* Raj A*, Dubnau D
* Equal contributions
Science | PDF | pubmed | journal | perspective

2006

Stochastic mRNA synthesis in mammalian cells

Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S
PLoS Biol | PDF | pubmed | journal

The influence of chromosome flexibility on chromosome transport during anaphase A

Raj A, Peskin CS
Proc Natl Acad Sci U S A | PDF | pubmed | journal

2005

Mechanism of mRNA transport in the nucleus

Vargas DY, Raj A, Marras SA, Kramer FR, Tyagi S
Proc Natl Acad Sci U S A | PDF | pubmed | journal

2002

Wind survey of high-speed bulk flows and field-aligned beams in the near-Earth plasma sheet

Raj A, Phan T, Lin RP, Angelopoulos V
J Geophys Res | PDF

2001

The finite element method on the sierpinski gasket

Gibbons M, Raj A, Strichartz RS
Constr Approx | PDF