| Year |
Citation |
Score |
| 2024 |
Niu Z, O'Farrell A, Li J, Reffsin S, Jain N, Dardani I, Goyal Y, Raj A. Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning. Biorxiv : the Preprint Server For Biology. PMID 38352551 DOI: 10.1101/2024.01.31.578123 |
0.675 |
|
| 2024 |
Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A. Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. Cell Systems. PMID 38335955 DOI: 10.1016/j.cels.2024.01.001 |
0.699 |
|
| 2023 |
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, et al. Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer. Biorxiv : the Preprint Server For Biology. PMID 37745397 DOI: 10.1101/2023.09.14.557228 |
0.304 |
|
| 2023 |
Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, ... ... Raj A, et al. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. Nature. PMID 37468627 DOI: 10.1038/s41586-023-06342-8 |
0.786 |
|
| 2023 |
Richman LP, Goyal Y, Jiang CL, Raj A. ClonoCluster: A method for using clonal origin to inform transcriptome clustering. Cell Genomics. 3: 100247. PMID 36819662 DOI: 10.1016/j.xgen.2022.100247 |
0.623 |
|
| 2023 |
Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A. Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. Biorxiv : the Preprint Server For Biology. PMID 36798299 DOI: 10.1101/2023.02.10.527870 |
0.694 |
|
| 2022 |
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, et al. CTCF blocks antisense transcription initiation at divergent promoters. Nature Structural & Molecular Biology. 29: 1136-1144. PMID 36369346 DOI: 10.1038/s41594-022-00855-y |
0.587 |
|
| 2022 |
Dardani I, Emert BL, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A. ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. Nature Methods. PMID 36280724 DOI: 10.1038/s41592-022-01653-6 |
0.799 |
|
| 2022 |
Kiani K, Sanford EM, Goyal Y, Raj A. Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. Molecular Systems Biology. 18: e10979. PMID 36069349 DOI: 10.15252/msb.202210979 |
0.701 |
|
| 2022 |
Jiang CL, Goyal Y, Jain N, Wang Q, Truitt RE, Coté AJ, Emert B, Mellis IA, Kiani K, Yang W, Jain R, Raj A. Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. Genome Biology. 23: 90. PMID 35382863 DOI: 10.1186/s13059-022-02654-6 |
0.655 |
|
| 2021 |
Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, ... ... Raj A, et al. Single cell biology-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34605044 DOI: 10.1111/nyas.14692 |
0.306 |
|
| 2021 |
Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. PMID 34352221 DOI: 10.1016/j.cels.2021.07.003 |
0.82 |
|
| 2021 |
Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A. Variability within rare cell states enables multiple paths toward drug resistance. Nature Biotechnology. PMID 33619394 DOI: 10.1038/s41587-021-00837-3 |
0.742 |
|
| 2021 |
Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A. Genetic screening for single-cell variability modulators driving therapy resistance. Nature Genetics. PMID 33398196 DOI: 10.1038/s41588-020-00749-z |
0.787 |
|
| 2020 |
Sanford EM, Emert BL, Coté A, Raj A. Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals. Elife. 9. PMID 33284110 DOI: 10.7554/eLife.59388 |
0.31 |
|
| 2020 |
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. Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. Cell. PMID 32735851 DOI: 10.1016/J.Cell.2020.07.003 |
0.787 |
|
| 2020 |
Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y. Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. Cell Systems. 10: 363-378.e12. PMID 32325034 DOI: 10.1016/J.Cels.2020.03.004 |
0.715 |
|
| 2020 |
Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Chandra A, Silverman M, Joyce EF, Little SC, Kaestner KH, Naji A, ... Raj A, et al. Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression. Immunity. PMID 32049053 DOI: 10.1016/J.Immuni.2020.01.003 |
0.324 |
|
| 2019 |
Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE. LADL: light-activated dynamic looping for endogenous gene expression control. Nature Methods. PMID 31235883 DOI: 10.1038/S41592-019-0436-5 |
0.363 |
|
| 2019 |
Raj A, Rinn JL. Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harbor Perspectives in Biology. 11. PMID 31043413 DOI: 10.1101/Cshperspect.A032094 |
0.377 |
|
| 2019 |
Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A. Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. Plos Genetics. 15: e1007874. PMID 30625149 DOI: 10.1371/Journal.Pgen.1007874 |
0.81 |
|
| 2019 |
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. Amendments: Author Correction: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nature Biotechnology. 37: 102. PMID 30605160 DOI: 10.1038/Nbt0119-102B |
0.75 |
|
| 2019 |
Shaffer S, Emert B, Torre E, Raj A. Abstract LB-050: Memory sequencing reveals heritable single cell gene expression programs associated with therapy resistance Cancer Research. 79. DOI: 10.1158/1538-7445.Am2019-Lb-050 |
0.791 |
|
| 2018 |
Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A. Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Molecular Cell. PMID 30554946 DOI: 10.1016/J.Molcel.2018.11.004 |
0.813 |
|
| 2018 |
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. Nature Biotechnology. PMID 30418432 DOI: 10.1038/Nbt.4286 |
0.786 |
|
| 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 |
0.674 |
|
| 2018 |
Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR. Gene expression distribution deconvolution in single-cell RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 29946020 DOI: 10.1073/Pnas.1721085115 |
0.791 |
|
| 2018 |
Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. SAVER: gene expression recovery for single-cell RNA sequencing. Nature Methods. PMID 29941873 DOI: 10.1038/S41592-018-0033-Z |
0.806 |
|
| 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 |
0.704 |
|
| 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 |
0.811 |
|
| 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 |
0.415 |
|
| 2017 |
Xu J, Sun Y, Li Y, Ruthel G, Weiss SR, Raj A, Beiting D, López CB. Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence. Nature Communications. 8: 799. PMID 28986577 DOI: 10.1038/S41467-017-00909-6 |
0.316 |
|
| 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 |
0.432 |
|
| 2017 |
Perego M, Maurer M, Wang JX, Shaffer S, Müller AC, Parapatics K, Li L, Hristova D, Shin S, Keeney F, Liu S, Xu X, Raj A, Jensen JK, Bennett KL, et al. A slow-cycling subpopulation of melanoma cells with highly invasive properties. Oncogene. PMID 28925403 DOI: 10.1038/Onc.2017.341 |
0.737 |
|
| 2017 |
Palozola KC, Donahue G, Liu H, Grant GR, Becker JS, Cote A, Yu H, Raj A, Zaret KS. Mitotic transcription and waves of gene reactivation during mitotic exit. Science (New York, N.Y.). PMID 28912132 DOI: 10.1126/Science.Aal4671 |
0.524 |
|
| 2017 |
Ko J, Bhagwat N, Yee SS, Black T, Redlinger C, Romeo J, O'Hara M, Raj A, Carpenter EL, Stanger BZ, Issadore D. A magnetic micropore chip for rapid (<1 hour) unbiased circulating tumor cell isolation and in situ RNA analysis. Lab On a Chip. PMID 28809985 DOI: 10.1039/C7Lc00703E |
0.377 |
|
| 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 |
0.768 |
|
| 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 |
0.8 |
|
| 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 |
0.804 |
|
| 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 |
0.734 |
|
| 2017 |
Coté AJ, Raj A. FISHing Out the Details of CRISPR Genome Tracks. Biophysical Journal. 112: 1045-1046. PMID 28355532 DOI: 10.1016/J.Bpj.2017.02.006 |
0.419 |
|
| 2017 |
Mellis I, Gupte R, Raj A, Rouhanifard S. inoFISH: inosine fluorescence in situ hybridization for visualizing adenosine to inosine RNA editing in single mammalian cells Protocol Exchange. DOI: 10.1038/Protex.2017.056 |
0.78 |
|
| 2016 |
Beck LE, Raj A. Systems biology: Molecular memoirs of a cellular family. Nature. PMID 27974796 DOI: 10.1038/Nature21101 |
0.455 |
|
| 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 |
0.455 |
|
| 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 |
0.737 |
|
| 2016 |
Chen F, Wassie AT, Cote 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. Nature Methods. 13: 679-84. PMID 27376770 DOI: 10.1038/Nmeth.3899 |
0.399 |
|
| 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 |
0.794 |
|
| 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 |
0.748 |
|
| 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 |
0.805 |
|
| 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 |
0.807 |
|
| 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 |
0.453 |
|
| 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 |
0.442 |
|
| 2016 |
Hsu SC, Bartman C, Stonestrom AJ, Edwards CR, Gilgenast T, Emerson D, Huang P, Werner MT, Jahn K, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA. The BET Protein BRD2 Cooperates with CTCF to Enforce a Transcriptional Boundary in Erythroid Cells Blood. 128: 1034-1034. DOI: 10.1182/Blood.V128.22.1034.1034 |
0.812 |
|
| 2016 |
Shaffer SM, Biaesch AG, Torborg S, Krepler C, Herlyn M, Raj A. Abstract B32: Single-cell non-genetic heterogeneity confers drug resistance in melanoma Cancer Research. 76. DOI: 10.1158/1538-7445.Fbcr15-B32 |
0.359 |
|
| 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 |
0.652 |
|
| 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 |
0.793 |
|
| 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 |
0.814 |
|
| 2015 |
Xu J, Mercado-López X, Grier JT, Kim WK, Chun LF, Irvine EB, Del Toro Duany Y, Kell A, Hur S, Gale M, Raj A, López CB. Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I. Mbio. 6. PMID 26443454 DOI: 10.1128/Mbio.01265-15 |
0.374 |
|
| 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 |
0.812 |
|
| 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 |
0.681 |
|
| 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 |
0.793 |
|
| 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 |
0.809 |
|
| 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 |
0.806 |
|
| 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 |
0.825 |
|
| 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 |
0.4 |
|
| 2015 |
Weis B, Schmidt J, Maamar H, Raj A, Lin H, Tóth C, Riedmann K, Raddatz G, Seitz HK, Ho AD, Lyko F, Linhart HG. Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a. Oncogene. 34: 1822-30. PMID 24837369 DOI: 10.1038/Onc.2014.114 |
0.785 |
|
| 2015 |
Blobel GA, Hsiung CC, Huang P, Keller C, Ginart P, Jahn K, Bartman C, Stonestrom AJ, Evans P, Giardine B, Hardison RC, Raj A. A Hyperactive Transcriptional State Marks Genome Reactivation during Mitotic Exit Blood. 126: 48-48. DOI: 10.1182/Blood.V126.23.48.48 |
0.827 |
|
| 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 |
0.416 |
|
| 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 |
0.807 |
|
| 2014 |
Ginart P, Raj A. RNA sequencing in situ. Nature Biotechnology. 32: 543-4. PMID 24911498 DOI: 10.1038/Nbt.2921 |
0.799 |
|
| 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 |
0.331 |
|
| 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 |
0.739 |
|
| 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 |
0.433 |
|
| 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 |
0.34 |
|
| 2014 |
Hsiung CC, Morrissey C, Udugama M, Frank C, Keller CA, Baek S, Giardine B, Crawford GE, Sung M, Raj A, Hardison RC, Blobel GA. Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome Blood. 124: 4342-4342. DOI: 10.1182/Blood.V124.21.4342.4342 |
0.685 |
|
| 2014 |
Bartman C, Blobel GA, Grevet J, Hsiung CC, Rupon JW, Raj A. Mechanistic Insights into Forced Chromatin Looping Mediated Activation of Fetal Globin Gene Expression Blood. 124: 331-331. DOI: 10.1182/Blood.V124.21.331.331 |
0.82 |
|
| 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 |
0.809 |
|
| 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 |
0.823 |
|
| 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 |
0.82 |
|
| 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 |
0.83 |
|
| 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 |
0.505 |
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| 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 |
0.837 |
|
| 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 |
0.667 |
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| 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 |
0.424 |
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| 2013 |
Hsiung CC, Raj A, Blobel GA. Hematopoietic Transcriptional Regulation At The Mitosis-G1 Transition Blood. 122: 2440-2440. DOI: 10.1182/Blood.V122.21.2440.2440 |
0.714 |
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| 2013 |
Padovan-Merhar O, Raj A. Cellular Volume is a Global Controller of MRNA Abundance Biophysical Journal. 104: 328a. DOI: 10.1016/J.Bpj.2012.11.1821 |
0.835 |
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| 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 |
0.403 |
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| 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 |
0.366 |
|
| 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 |
0.816 |
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| 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 |
0.576 |
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| 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 |
0.595 |
|
| 2011 |
Nair G, Raj A. Time-Keeping in the Transcriptional Cascades of the Developing C. elegans Embryo Biophysical Journal. 100: 33a. DOI: 10.1016/J.Bpj.2010.12.383 |
0.822 |
|
| 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 |
0.615 |
|
| 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 |
0.625 |
|
| 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 |
0.757 |
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| 2010 |
Raj A. Variability in Gene Expression Underlies Incomplete Penetrance in C. Elegans: Using Single Molecules To Study the Development of Single Cells Biophysical Journal. 98: 14a. DOI: 10.1016/J.Bpj.2009.12.087 |
0.447 |
|
| 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 |
0.677 |
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| 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 |
0.653 |
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| 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 |
0.647 |
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| 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 |
0.768 |
|
| 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 |
0.799 |
|
| 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 |
0.673 |
|
| 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 |
0.546 |
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