Arjun Raj - Publications

Bioengineering University of Pennsylvania, Philadelphia, PA, United States 
Cell Biology, Biomedical Engineering

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Kaur A, Ecker BL, Douglass SM, Kugel CH, Webster MR, Almeida FV, Somasundaram R, Hayden J, Ban E, Ahmadzadeh H, Franco-Barraza J, Shah N, Mellis IA, Keeney F, Kossenkov A, ... ... Raj A, et al. Remodeling of the collagen matrix in aging skin promotes melanoma metastasis and affects immune cell motility. Cancer Discovery. PMID 30279173 DOI: 10.1158/2159-8290.CD-18-0193  0.36
2018 Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, ... ... Raj A, et al. Corrigendum: Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature. PMID 29466340 DOI: 10.1038/nature25162  0.68
2018 Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A. Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Cell Systems. PMID 29454938 DOI: 10.1016/j.cels.2018.01.014  0.36
2017 Haimovich G, Ecker CM, Dunagin MC, Eggan E, Raj A, Gerst JE, Singer RH. Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078295 DOI: 10.1073/pnas.1706365114  0.4
2017 Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, ... ... Raj A, et al. Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Immunity. 47: 435-449.e8. PMID 28930659 DOI: 10.1016/j.immuni.2017.08.012  0.4
2017 Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, ... ... Raj A, et al. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature. PMID 28607484 DOI: 10.1038/nature22794  0.68
2017 Mellis IA, Gupte R, Raj A, Rouhanifard SH. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nature Methods. PMID 28604724 DOI: 10.1038/nmeth.4332  0.36
2017 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. The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Molecular Cell. 66: 102-116.e7. PMID 28388437 DOI: 10.1016/j.molcel.2017.02.027  0.48
2017 Casson CN, Doerner JL, Copenhaver AM, Ramirez J, Holmgren AM, Boyer MA, Siddarthan IJ, Rouhanifard SH, Raj A, Shin S. Neutrophils and Ly6Chi monocytes collaborate in generating an optimal cytokine response that protects against pulmonary Legionella pneumophila infection. Plos Pathogens. 13: e1006309. PMID 28384349 DOI: 10.1371/journal.ppat.1006309  0.36
2016 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, ... ... Raj A, et al. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. PMID 27525555 DOI: 10.1038/nature19346  0.4
2016 Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS. Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. Plos One. 11: e0158298. PMID 27467384 DOI: 10.1371/journal.pone.0158298  0.68
2016 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. A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Genes & Development. 30: 1423-39. PMID 27340175 DOI: 10.1101/gad.280859.116  1
2016 Symmons O, Raj A. What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. Molecular Cell. 62: 788-802. PMID 27259209 DOI: 10.1016/j.molcel.2016.05.023  1
2016 Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Molecular Cell. PMID 27067601 DOI: 10.1016/j.molcel.2016.03.007  1
2016 Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A. Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. Genes & Development. 30: 567-78. PMID 26944681 DOI: 10.1101/gad.275958.115  1
2016 Cote 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. Nature Communications. 7: 10865. PMID 26936319 DOI: 10.1038/ncomms10865  1
2016 Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI. Overlapping cell population expression profiling and regulatory inference in C. elegans. Bmc Genomics. 17: 159. PMID 26926147 DOI: 10.1186/s12864-016-2482-z  1
2015 Shah NA, Levesque MJ, Raj A, Sarkar CA. Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue. Journal of Cell Science. 128: 4024. PMID 26527202 DOI: 10.1242/jcs.180653  1
2015 Lee K, Hsiung CC, Huang P, Raj A, Blobel GA. Corrigendum: Dynamic enhancer-gene body contacts during transcription elongation. Genes & Development. 29: 2217. PMID 26494793  0.48
2015 Lee K, Hsiung CC, Huang P, Raj A, Blobel GA. Dynamic enhancer-gene body contacts during transcription elongation. Genes & Development. 29: 1992-7. PMID 26443845 DOI: 10.1101/gad.255265.114  0.48
2015 Mellis IA, Raj A. Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? Genome Research. 25: 1466-72. PMID 26430156 DOI: 10.1101/gr.190579.115  1
2015 Nair G, Abranches E, Guedes AM, Henrique D, Raj A. Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation. Scientific Reports. 5: 13339. PMID 26292941 DOI: 10.1038/srep13339  1
2015 Shah NA, Levesque MJ, Raj A, Sarkar CA. Robust hematopoietic progenitor cell commitment in a noisy environment via suppression of a conflicting signal. Journal of Cell Science. PMID 26159733 DOI: 10.1242/jcs.158436  1
2015 Shaffer SM, Joshi RP, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE, Issadore D, Raj A. Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. Lab On a Chip. PMID 26113495 DOI: 10.1039/c5lc00459d  1
2015 Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular Cell. 58: 339-52. PMID 25866248 DOI: 10.1016/j.molcel.2015.03.005  1
2015 Walton T, Preston E, Nair G, Zacharias AL, Raj A, Murray JI. The Bicoid class homeodomain factors ceh-36/OTX and unc-30/PITX cooperate in C. elegans embryonic progenitor cells to regulate robust development. Plos Genetics. 11: e1005003. PMID 25738873 DOI: 10.1371/journal.pgen.1005003  1
2015 Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biology. 16: 20. PMID 25630241 DOI: 10.1186/s13059-015-0586-4  1
2015 Dunagin M, Cabili MN, Rinn J, Raj A. Visualization of lncRNA by single-molecule fluorescence in situ hybridization. Methods in Molecular Biology (Clifton, N.J.). 1262: 3-19. PMID 25555572 DOI: 10.1007/978-1-4939-2253-6_1  1
2014 Panda D, Pascual-Garcia P, Dunagin M, Tudor M, Hopkins KC, Xu J, Gold B, Raj A, Capelson M, Cherry S. Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 111: E3890-9. PMID 25197089 DOI: 10.1073/pnas.1410087111  1
2014 Abranches E, Guedes AM, Moravec M, Maamar H, Svoboda P, Raj A, Henrique D. Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency. Development (Cambridge, England). 141: 2770-9. PMID 25005472 DOI: 10.1242/dev.108910  1
2014 Ginart P, Raj A. RNA sequencing in situ. Nature Biotechnology. 32: 543-4. PMID 24911498 DOI: 10.1038/nbt.2921  1
2014 Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Molecular Cell. 54: 777-90. PMID 24857549 DOI: 10.1016/j.molcel.2014.04.025  1
2014 Facciponte JG, Ugel S, De Sanctis F, Li C, Wang L, Nair G, Sehgal S, Raj A, Matthaiou E, Coukos G, Facciabene A. Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature. The Journal of Clinical Investigation. 124: 1497-511. PMID 24642465 DOI: 10.1172/JCI67382  1
2014 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, et al. Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood. 123: 1927-37. PMID 24497530 DOI: 10.1182/blood-2013-12-544494  1
2014 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, ... ... Raj A, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nature Structural & Molecular Biology. 21: 198-206. PMID 24463464 DOI: 10.1038/nsmb.2764  1
2013 Shaffer SM, Wu MT, Levesque MJ, Raj A. Turbo FISH: a method for rapid single molecule RNA FISH. Plos One. 8: e75120. PMID 24066168 DOI: 10.1371/journal.pone.0075120  1
2013 Padovan-Merhar O, Raj A. Using variability in gene expression as a tool for studying gene regulation. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 5: 751-9. PMID 23996796 DOI: 10.1002/wsbm.1243  1
2013 Levesque MJ, Ginart P, Wei Y, Raj A. Visualizing SNVs to quantify allele-specific expression in single cells. Nature Methods. 10: 865-7. PMID 23913259 DOI: 10.1038/nmeth.2589  1
2013 Nair G, Walton T, Murray JI, Raj A. Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification. Development (Cambridge, England). 140: 3385-94. PMID 23863485 DOI: 10.1242/dev.098012  1
2013 Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, Behlke MA, Tsourkas A. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Research. 41: e152. PMID 23814183 DOI: 10.1093/nar/gkt561  1
2013 Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes & Development. 27: 1260-71. PMID 23723417 DOI: 10.1101/gad.217018.113  1
2013 Levesque MJ, Raj A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nature Methods. 10: 246-8. PMID 23416756 DOI: 10.1038/nmeth.2372  1
2013 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, ... ... Raj A, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/nature11661  1
2012 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 LS, et al. Global analysis of RNA secondary structure in two metazoans. Cell Reports. 1: 69-82. PMID 22832108 DOI: 10.1016/j.celrep.2011.10.002  1
2012 Mirouze N, Desai Y, Raj A, Dubnau D. Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. Plos Genetics. 8: e1002586. PMID 22412392 DOI: 10.1371/journal.pgen.1002586  0.44
2011 Nair G, Raj A. Molecular biology. Time-lapse transcription. Science (New York, N.Y.). 332: 431-2. PMID 21512026 DOI: 10.1126/science.1205995  1
2011 Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, Jaenisch R, Linhart HG. Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. The Journal of Clinical Investigation. 121: 1748-52. PMID 21490393 DOI: 10.1172/JCI43169  1
2011 Batish M, Raj A, Tyagi S. Single molecule imaging of RNA in situ. Methods in Molecular Biology (Clifton, N.J.). 714: 3-13. PMID 21431731 DOI: 10.1007/978-1-61779-005-8_1  1
2010 Youk H, Raj A, van Oudenaarden A. Imaging single mRNA molecules in yeast. Methods in Enzymology. 470: 429-46. PMID 20946820 DOI: 10.1016/S0076-6879(10)70017-3  1
2010 Raj A, Tyagi S. Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Methods in Enzymology. 472: 365-86. PMID 20580972 DOI: 10.1016/S0076-6879(10)72004-8  1
2010 Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 463: 913-8. PMID 20164922 DOI: 10.1038/nature08781  1
2009 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. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/pnas.0904715106  1
2009 Raj A, van Oudenaarden A. Single-molecule approaches to stochastic gene expression. Annual Review of Biophysics. 38: 255-70. PMID 19416069 DOI: 10.1146/annurev.biophys.37.032807.125928  1
2008 Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 135: 216-26. PMID 18957198 DOI: 10.1016/j.cell.2008.09.050  1
2008 Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods. 5: 877-9. PMID 18806792 DOI: 10.1038/nmeth.1253  1
2007 Maamar H, Raj A, Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science (New York, N.Y.). 317: 526-9. PMID 17569828 DOI: 10.1126/science.1140818  0.44
2006 Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. Plos Biology. 4: e309. PMID 17048983 DOI: 10.1371/journal.pbio.0040309  1
2006 Raj A, Peskin CS. The influence of chromosome flexibility on chromosome transport during anaphase A. Proceedings of the National Academy of Sciences of the United States of America. 103: 5349-54. PMID 16567616 DOI: 10.1073/pnas.0601215103  1
2005 Vargas DY, Raj A, Marras SA, Kramer FR, Tyagi S. Mechanism of mRNA transport in the nucleus. Proceedings of the National Academy of Sciences of the United States of America. 102: 17008-13. PMID 16284251 DOI: 10.1073/pnas.0505580102  0.96
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