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Rahul Satija

Assistant Professor

    20042020

    Research output per year

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    Research Output

    A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

    Wurtzel, O., Cote, L. E., Poirier, A., Satija, R., Regev, A. & Reddien, P. W., 2015, In : Developmental Cell. 35, 5, p. 632-45

    Research output: Contribution to journalArticle

    A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

    Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., Shalem, O., Satija, R., Raychowdhury, R., Mertins, P., Carr, S. A., Zhang, F., Hacohen, N. & Regev, A., Aug 1 2015, In : Cell. 162, 3, p. 675-686 12 p.

    Research output: Contribution to journalArticle

    A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

    Velasco, S., Ibrahim, M. M., Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M. A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., Mahony, S. & Mazzoni, E. O., Feb 2 2017, In : Cell Stem Cell. 20, 2, p. 205-217.e8

    Research output: Contribution to journalArticle

    A single-cell transcriptional roadmap for cardiopharyngeal fate diversification

    Wang, W., Niu, X., Stuart, T., Jullian, E., Mauck, W. M., Kelly, R. G., Satija, R. & Christiaen, L., Jun 1 2019, In : Nature Cell Biology. 21, 6, p. 674-686 13 p.

    Research output: Contribution to journalArticle

    Author Correction: The bone marrow microenvironment at single-cell resolution (Nature, (2019), 569, 7755, (222-228), 10.1038/s41586-019-1104-8)

    Tikhonova, A. N., Dolgalev, I., Hu, H., Sivaraj, K. K., Hoxha, E., Cuesta-Domínguez, Á., Pinho, S., Akhmetzyanova, I., Gao, J., Witkowski, M., Guillamot, M., Gutkin, M. C., Zhang, Y., Marier, C., Diefenbach, C., Kousteni, S., Heguy, A., Zhong, H., Fooksman, D. R., Butler, J. M. & 6 others, Economides, A., Frenette, P. S., Adams, R. H., Satija, R., Tsirigos, A. & Aifantis, I., Aug 1 2019, In : Nature. 572, 7767, p. E6

    Research output: Contribution to journalComment/debate

    BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    Satija, R., Novk, Á., Miklás, I., Lyngsø, R. & Hein, J., 2009, In : BMC Evolutionary Biology. 9, 1, 217.

    Research output: Contribution to journalArticle

    Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

    Stoeckius, M., Zheng, S., Houck-Loomis, B., Hao, S., Yeung, B. Z., Mauck, W. M., Smibert, P. & Satija, R., Dec 19 2018, In : Genome biology. 19, 1, 224.

    Research output: Contribution to journalArticle

    Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

    Satija, R., Pachter, L. & Hein, J., May 2008, In : Bioinformatics. 24, 10, p. 1236-1242 7 p.

    Research output: Contribution to journalArticle

    Comparative analysis of RNA sequencing methods for degraded or low-input samples

    Adiconis, X., Borges-Rivera, D., Satija, R., Deluca, D. S., Busby, M. A., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., Gnirke, A., Pochet, N., Regev, A. & Levin, J. Z., Jul 2013, In : Nature methods. 10, 7, p. 623-629 7 p.

    Research output: Contribution to journalArticle

    Comprehensive Integration of Single-Cell Data

    Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P. & Satija, R., Jun 13 2019, In : Cell. 177, 7, p. 1888-1902.e21

    Research output: Contribution to journalArticle

    Corrigendum: Landscape of X chromosome inactivation across human tissues

    Tukiainen, T., Villani, A. C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., Aguirre, M., Gauthier, L., Fleharty, M., Kirby, A., Cummings, B. B., Castel, S. E., Karczewski, K. J., Aguet, F., Byrnes, A., Consortium, GTE., Lappalainen, T., Regev, A., Ardlie, K. G., Hacohen, N. & 1 others, MacArthur, D. G., Mar 7 2018, In : Nature. 555, 7695, 1 p.

    Research output: Contribution to journalComment/debate

    Open Access

    Deconstructing transcriptional heterogeneity in pluripotent stem cells

    Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., Keyser, A. D., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., Ferrante, T. C., Regev, A., Daley, G. Q. & Collins, J. J., Dec 4 2014, In : Nature. 516, 729, p. 56-61 6 p.

    Research output: Contribution to journalArticle

    Developmental diversification of cortical inhibitory interneurons

    Mayer, C., Hafemeister, C., Bandler, R. C., Machold, R., Batista Brito, R., Jaglin, X., Allaway, K., Butler, A., Fishell, G. & Satija, R., Mar 22 2018, In : Nature. 555, 7697, p. 457-462 6 p.

    Research output: Contribution to journalArticle

    Dynamic profiling of the protein life cycle in response to pathogens

    Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., Mumbach, M. R., Eisenhaure, T., Rabani, M., Gennert, D., Lu, D., Delorey, T., Weissman, J. S., Carr, S. A., Hacohen, N. & Regev, A., Mar 6 2015, In : Science. 347, 6226, 1259038.

    Research output: Contribution to journalArticle

    Dynamic regulatory network controlling TH17 cell differentiation

    Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., Gennert, D., Satija, R., Shakya, A., Lu, D. Y., Trombetta, J. J., Pillai, M. R., Ratcliffe, P. J., Coleman, M. L., Bix, M., Tantin, D. & 3 others, Park, H., Kuchroo, V. K. & Regev, A., 2013, In : Nature. 496, 7446, p. 461-8

    Research output: Contribution to journalArticle

    Dynamic regulatory network controlling TH 17 cell differentiation

    Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., Gennert, D., Satija, R., Shakya, A., Lu, D. Y., Trombetta, J. J., Pillai, M. R., Ratcliffe, P. J., Coleman, M. L., Bix, M., Tantin, D. & 3 others, Park, H., Kuchroo, V. K. & Regev, A., Apr 25 2013, In : Nature. 496, 7446, p. 461-468 8 p.

    Research output: Contribution to journalArticle

    Erratum: Pathogen cell-to-cell variability drives heterogeneity in host immune responses ((Cell (2015) 162 (1309-1321))

    Avraham, R., Haseley, N., Brown, D., Penaranda, C., Jijon, H. B., Trombetta, J. J., Satija, R., Shalek, A. K., Xavier, R. J., Regev, A. & Hung, D. T., Oct 8 2015, In : Cell. 163, 2, 1 p.

    Research output: Contribution to journalComment/debate

    Erratum: Comparative analysis of RNA sequencing methods for degraded or low-input samples (Nature Methods (2013) 10 (623-629 )

    Adiconis, X., Borges-Rivera, D., Satija, R., DeLuca, D. S., Busby, M. A., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., Gnirke, A., Pochet, N., Regev, A. & Levin, J. Z., 2014, In : Nature Protocols. 9, 4, 1 p.

    Research output: Contribution to journalComment/debate

    Erratum: The genome of the sea urchin Strongylocentrotus purpuratus (Science (2006) (941))

    Elsik, C. G., Hibino, T., Vacquier, V. D., Kitts, P., Landrum, M. J., Maglott, D., Pruitt, K., Souvorov, A., Fedrigo, O., Primus, A., Satija, R., Adams, N., Flytzanis, C., Galindo, B. E., Goldstone, J. V., Manning, G., Mellott, D., Song, J., Terwilliger, D. P. & Wikramanayake, A., Feb 9 2007, In : Science. 315, 5813, 1 p.

    Research output: Contribution to journalComment/debate

    Erratum: Comparative analysis of RNA sequencing methods for degraded or low-input samples (Nature Methods (2013) 10 (623-629))

    Adiconis, X., Borges-Rivera, D., Satija, R., Deluca, D. S., Busby, M. A., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., Gnirke, A., Pochet, N., Regev, A. & Levin, J. Z., Feb 2014, In : Nature methods. 11, 2, 1 p.

    Research output: Contribution to journalComment/debate

    Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells (Nature (2014) 516 (5661) DOI:10.1038/nature13920)

    Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., DaleyKeyser, A. J., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., Ferrante, T. C., Regev, A., Daley, G. Q. & Collins, J. J., Mar 5 2015, In : Nature. 519, 7541, 1 p.

    Research output: Contribution to journalComment/debate

    Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques

    Satija, R., Hein, J. & Lunter, G. A., Jul 7 2010, In : Bioinformatics. 26, 17, p. 2116-2120 5 p., btq360.

    Research output: Contribution to journalArticle

    Heterogeneity in immune responses: From populations to single cells

    Satija, R. & Shalek, A. K., May 2014, In : Trends in Immunology. 35, 5, p. 219-229 11 p.

    Research output: Contribution to journalReview article

    Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

    Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., Trombetta, J. J., Weitz, D. A., Sanes, J. R., Shalek, A. K., Regev, A. & McCarroll, S. A., May 30 2015, In : Cell. 161, 5, p. 1202-1214 13 p.

    Research output: Contribution to journalArticle

    High-Resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis

    Schwartz, S., Agarwala, S. D., Mumbach, M. R., Jovanovic, M., Mertins, P., Shishkin, A., Tabach, Y., Mikkelsen, T. S., Satija, R., Ruvkun, G., Carr, S. A., Lander, E. S., Fink, G. R. & Regev, A., Dec 5 2013, In : Cell. 155, 6, p. 1409-1421 13 p.

    Research output: Contribution to journalArticle

    Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs

    Breton, G., Zheng, S., Valieris, R., da Silva, I. T., Satija, R. & Nussenzweig, M. C., Dec 12 2016, In : Journal of Experimental Medicine. 213, 13, p. 2861-2870 10 p.

    Research output: Contribution to journalArticle

    In situ neutron imaging technique for evaluation of water management systems in operating PEM fuel cells

    Satija, R., Jacobson, D. L., Arif, M. & Werner, S. A., Apr 22 2004, In : Journal of Power Sources. 129, 2, p. 238-245 8 p.

    Research output: Contribution to journalArticle

    Integrating single-cell transcriptomic data across different conditions, technologies, and species

    Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R., Jun 1 2018, In : Nature Biotechnology. 36, 5, p. 411-420 10 p.

    Research output: Contribution to journalArticle

    Integrative single-cell analysis

    Stuart, T. & Satija, R., May 1 2019, In : Nature Reviews Genetics. 20, 5, p. 257-272 16 p.

    Research output: Contribution to journalReview article

    Kinetics of adult hematopoietic stem cell differentiation in vivo

    Upadhaya, S., Sawai, C. M., Papalexi, E., Rashidfarrokhi, A., Jang, G., Chattopadhyay, P., Satija, R. & Reizis, B., Nov 1 2018, In : Journal of Experimental Medicine. 215, 11, p. 2815-2832 18 p.

    Research output: Contribution to journalArticle

    Landscape of X chromosome inactivation across human tissues

    GTEx Consortium, Oct 11 2017, In : Nature. 550, 7675, p. 244-248 5 p.

    Research output: Contribution to journalArticle

    MERFISHing for spatial context

    Shalek, A. K. & Satija, R., Jul 1 2015, In : Trends in Immunology. 36, 7, p. 390-391 2 p.

    Research output: Contribution to journalShort survey

    Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue

    Accelerating Medicines Partnership RA/SLE Network, Jul 11 2018, In : Arthritis Research and Therapy. 20, 1, 139.

    Research output: Contribution to journalArticle

    Molecular transitions in early progenitors during human cord blood hematopoiesis

    Zheng, S., Papalexi, E., Butler, A., Stephenson, W. & Satija, R., Mar 2018, In : Molecular systems biology. 14, 3, e8041.

    Research output: Contribution to journalArticle

    Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

    Mimitou, E. P., Cheng, A., Montalbano, A., Hao, S., Stoeckius, M., Legut, M., Roush, T., Herrera, A., Papalexi, E., Ouyang, Z., Satija, R., Sanjana, N. E., Koralov, S. B. & Smibert, P., May 1 2019, In : Nature methods. 16, 5, p. 409-412 4 p.

    Research output: Contribution to journalArticle

    Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

    Hafemeister, C. & Satija, R., Dec 23 2019, In : Genome biology. 20, 1, 296.

    Research output: Contribution to journalArticle

    Open Access

    Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

    Avraham, R., Haseley, N., Brown, D., Penaranda, C., Jijon, H. B., Trombetta, J. J., Satija, R., Shalek, A. K., Xavier, R. J., Regev, A. & Hung, D. T., Sep 10 2015, In : Cell. 162, 6, p. 1309-1321 13 p.

    Research output: Contribution to journalArticle

    Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites

    Schwartz, S., Mumbach, M. R., Jovanovic, M., Wang, T., Maciag, K., Bushkin, G. G., Mertins, P., Ter-Ovanesyan, D., Habib, N., Cacchiarelli, D., Sanjana, N. E., Freinkman, E., Pacold, M. E., Satija, R., Mikkelsen, T. S., Hacohen, N., Zhang, F., Carr, S. A., Lander, E. S. & Regev, A., Jul 10 2014, In : Cell Reports. 8, 1, p. 284-296 13 p.

    Research output: Contribution to journalArticle

    Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features

    Konstantinides, N., Kapuralin, K., Fadil, C., Barboza, L., Satija, R. & Desplan, C., Jul 26 2018, In : Cell. 174, 3, p. 622-635.e13

    Research output: Contribution to journalArticle

    Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

    Trombetta, J. J., Gennert, D., Lu, D., Satija, R., Shalek, A. K. & Regev, A., 2014, In : Curr Protoc Mol Biol. 107, p. 4.22.1-4.22.17

    Research output: Contribution to journalArticle

    Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions

    Efroni, I., Mello, A., Nawy, T., Ip, P. L., Rahni, R., Delrose, N., Powers, A., Satija, R. & Birnbaum, K. D., Jun 16 2016, In : Cell. 165, 7, p. 1721-1733 13 p.

    Research output: Contribution to journalArticle

    Seq-Well: Portable, low-cost rna sequencing of single cells at high throughput

    Gierahn, T. M., Wadsworth, M. H., Hughes, T. K., Bryson, B. D., Butler, A., Satija, R., Fortune, S., Christopher Love, J. & Shalek, A. K., Feb 13 2017, In : Nature methods. 14, 4, p. 395-398 4 p.

    Research output: Contribution to journalArticle

    Simultaneous epitope and transcriptome measurement in single cells

    Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., Satija, R. & Smibert, P., Aug 31 2017, In : Nature methods. 14, 9, p. 865-868 4 p.

    Research output: Contribution to journalArticle

    Single-cell analysis reveals key roles for Bcl11a in regulating stem cell fate decisions

    Powers, A. N. & Satija, R., Sep 21 2015, In : Genome biology. 16, 1, 199.

    Research output: Contribution to journalArticle

    Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

    Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., Kuchroo, V. K., Park, H. & Regev, A., 2015, In : Cell. 163, 6, p. 1400-1412

    Research output: Contribution to journalArticle

    Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

    Stephenson, W., Donlin, L. T., Butler, A., Rozo, C., Bracken, B., Rashidfarrokhi, A., Goodman, S. M., Ivashkiv, L. B., Bykerk, V. P., Orange, D. E., Darnell, R. B., Swerdlow, H. P. & Satija, R., Dec 1 2018, In : Nature communications. 9, 1, 791.

    Research output: Contribution to journalArticle

    Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

    Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., Schwartz, S., Fowler, B., Weaver, S., Wang, J., Wang, X., Ding, R., Raychowdhury, R., Friedman, N., Hacohen, N., Park, H. & 2 others, May, A. P. & Regev, A., 2014, In : Nature. 510, 7505, p. 363-369 7 p.

    Research output: Contribution to journalArticle

    Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

    Villani, A. C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., Jardine, L., Dixon, D., Stephenson, E., Nilsson, E., Grundberg, I., McDonald, D., Filby, A., Li, W., De Jager, P. L., Rozenblatt-Rosen, O. & 4 others, Lane, A. A., Haniffa, M., Regev, A. & Hacohen, N., Apr 21 2017, In : Science. 356, 6335, eaah4573.

    Research output: Contribution to journalArticle

    Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

    Tirosh, I., Venteicher, A. S., Hebert, C., Escalante, L. E., Patel, A. P., Yizhak, K., Fisher, J. M., Rodman, C., Mount, C., Filbin, M. G., Neftel, C., Desai, N., Nyman, J., Izar, B., Luo, C. C., Francis, J. M., Patel, A. A., Onozato, M. L., Riggi, N., Livak, K. J. & 18 others, Gennert, D., Satija, R., Nahed, B. V., Curry, W. T., Martuza, R. L., Mylvaganam, R., Iafrate, A. J., Frosch, M. P., Golub, T. R., Rivera, M. N., Getz, G., Rozenblatt-Rosen, O., Cahill, D. P., Monje, M., Bernstein, B. E., Louis, D. N., Regev, A. & Suvà, M. L., Nov 10 2016, In : Nature. 539, 7628, p. 309-313 5 p.

    Research output: Contribution to journalArticle

    Single-cell RNA sequencing to explore immune cell heterogeneity

    Papalexi, E. & Satija, R., Jan 1 2018, In : Nature Reviews Immunology. 18, 1, p. 35-45 11 p.

    Research output: Contribution to journalReview article