Additional materials of the author at
CSHL Institutional Repository

Su, Q, Kim, SY, Adewale, F, Zhou, Y, Aldler, C, Ni, M, Wei, Y, Burczynski, ME, Atwal, GS, Sleeman, MW, Murphy, AJ, Xin, Y , Cheng, X (2021) Single-cell RNA transcriptome landscape of hepatocytes and non-parenchymal cells in healthy and NAFLD mouse liver. iScience, 24(11) pp. 103233-103233.

Yang, T, Alessandri-Haber, N, Fury, W, Schaner, M, Breese, R, LaCroix-Fralish, M, Kim, J, Adler, C, Macdonald, LE, Atwal, GS , Bai, Y (2021) AdRoit is an accurate and robust method to infer complex transcriptome composition. Communications Biology, 4(1)

Panea, C, Zhang, R, VanValkenburgh, J, Ni, M, Adler, C, Wei, Y, Ochoa, F, Schmahl, J, Tang, Y, Siao, CJ, Poueymirou, W, Espert, J, Lim, WK, Atwal, GS, Murphy, AJ, Sleeman, MA, Hovhannisyan, Z , Haxhinasto, S (2021) Butyrophilin-like 2 regulates site-specific adaptations of intestinal γδ intraepithelial lymphocytes. Communications Biology, 4(1)

Wortman, Juliana C, He, Ting-Fang, Solomon, Shawn, Zhang, Robert Z, Rosario, Anthony, Wang, Roger, Tu, Travis Y, Schmolze, Daniel, Yuan, Yuan, Yost, Susan E, Li, Xuefei, Levine, Herbert, Atwal, Gurinder, Lee, Peter P , Yu, Clare C (2021) Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome.. npj Breast Cancer, 7(1) pp. 84.

Copin, Richard, Baum, Alina, Wloga, Elzbieta, Pascal, Kristen E, Giordano, Stephanie, Fulton, Benjamin O, Zhou, Anbo, Negron, Nicole, Lanza, Kathryn, Chan, Newton, Coppola, Angel, Chiu, Joyce, Ni, Min, Wei, Yi, Atwal, Gurinder S, Hernandez, Annabel Romero, Saotome, Kei, Zhou, Yi, Franklin, Matthew C, Hooper, Andrea T, McCarthy, Shane, Hamon, Sara, Hamilton, Jennifer D, Staples, Hilary M, Alfson, Kendra, Carrion, Ricardo, Ali, Shazia, Norton, Thomas, Somersan-Karakaya, Selin, Sivapalasingam, Sumathi, Herman, Gary A, Weinreich, David M, Lipsich, Leah, Stahl, Neil, Murphy, Andrew J, Yancopoulos, George D , Kyratsous, Christos A (2021) The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies.. Cell,

Zhang, Wen, Hawkins, Peter G, He, Jing, Gupta, Namita T, Liu, Jinrui, Choonoo, Gabrielle, Jeong, Se W, Chen, Calvin R, Dhanik, Ankur, Dillon, Myles, Deering, Raquel, Macdonald, Lynn E, Thurston, Gavin , Atwal, Gurinder S (2021) A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity.. Science Advances, 7(20) pp. eabf5835-eabf5835.

Zhang, R, Atwal, GS , Lim, WK (2021) Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns, 2(3) pp. 100211-100211.

Baum, Alina, Ajithdoss, Dharani, Copin, Richard, Zhou, Anbo, Lanza, Kathryn, Negron, Nicole, Ni, Min, Wei, Yi, Mohammadi, Kusha, Musser, Bret, Atwal, Gurinder S, Oyejide, Adelekan, Goez-Gazi, Yenny, Dutton, John, Clemmons, Elizabeth, Staples, Hilary M, Bartley, Carmen, Klaffke, Benjamin, Alfson, Kendra, Gazi, Michal, Gonzalez, Olga, Dick, Edward, Carrion, Ricardo, Pessaint, Laurent, Porto, Maciel, Cook, Anthony, Brown, Renita, Ali, Vaneesha, Greenhouse, Jack, Taylor, Tammy, Andersen, Hanne, Lewis, Mark G, Stahl, Neil, Murphy, Andrew J, Yancopoulos, George D , Kyratsous, Christos A (2020) REGN-COV2 antibodies prevent and treat SARS-CoV-2 infection in rhesus macaques and hamsters.. Science, 370(6520) pp. 1110-1115.

Yu, C. C., Wortman, J. C., He, T. F., Solomon, S., Zhang, R. Z., Rosario, A., Wang, R., Tu, T., Schmolze, D., Yuan, Y., Yost, S. E., Li, X., Levine, H., Atwal, G. , Lee, P. P. (2020) Physics Approaches to the Spatial Distribution of Immune Cells in Tumors. Rep Prog Phys,

Zhao, Qi, Molina-Portela, Maria Del Pilar, Parveen, Asma, Adler, Alexander, Adler, Christina, E, Hock, Wang, Wei, Ni, Min, Wei, Yi, Atwal, Gurinder, Mohrs, Markus, Thurston, Gavin , Eichten, Alexandra (2020) Heterogeneity and chimerism of endothelial cells revealed by single-cell transcriptome in orthotopic liver tumors.. Angiogenesis, 23(4) pp. 581-597.

Baum, Alina, Fulton, Benjamin O, Wloga, Elzbieta, Copin, Richard, Pascal, Kristen E, Russo, Vincenzo, Giordano, Stephanie, Lanza, Kathryn, Negron, Nicole, Ni, Min, Wei, Yi, Atwal, Gurinder S, Murphy, Andrew J, Stahl, Neil, Yancopoulos, George D , Kyratsous, Christos A (2020) Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies.. Science, 369(6506) pp. 1014-1018.

Benitez, Asiel A, Khalil-Agüero, Sara, Nandakumar, Anjali, Gupta, Namita T, Zhang, Wen, Atwal, Gurinder S, Murphy, Andrew J, Sleeman, Matthew A , Haxhinasto, Sokol (2020) Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses.. Communications Biology, 3(1) pp. 355.

Carter, J. A., Gilbo, P. , Atwal, G. S. (2019) IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma. Nat Med, 25(12) pp. 1833-1835.

Carter, J. A., Preall, J. B. , Atwal, G. S. (2019) Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire. Cell Syst, 9(5) pp. 475-482.

Carter, J. A., Preall, J. B., Grigaityte, K., Goldfless, S. J., Jeffery, E., Briggs, A. W., Vigneault, F. , Atwal, G. S. (2019) Single T Cell Sequencing Demonstrates the Functional Role alpha beta TCR Pairing in Cell Lineage and Antigen Specificity. Frontiers in Immunology, 10 pp. Article Number:1516.

Utama, Raditya, Bastian, Anja, Sadagopan, Narayanan, Jin, Ying, Antoniou, Eric, Gao, Qing, Huang, Yinghui J, Gopalakrishna-Pillai, Sailesh, Lee, Peter P , Atwal, Gurinder S (2019) Cell non-autonomous interactions during non-immune stromal progression in the breast tumor microenvironment. BioRxiv,

Utama, R., Bastian, A., Sadagopan, N., Jin, Y., Antoniou, E., Huang, Y., Lee, P. , Atwal, G. (2018) Transcriptional landscape of stroma progression in the breast tumor microenvironment. Cancer Research, 78(13 S) pp. meeting abstract : LB-357.

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M. , Krasnitz, A. (2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78(2) pp. 348-358.

Atwal, G. S. , Kinney, J. B. (2016) Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments. Journal of Statistical Physics, 162(5) pp. 1203-1243.

Plavskin, Yevgeniy, Nagashima, Akitomo, Perroud, Pierre-François, Hasebe, Mitsuyasu, Quatrano, Ralph S, Atwal, Gurinder S , Timmermans, Marja C P. (2016) Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Developmental Cell, 36(3) pp. 276-289.

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M. , Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12 pp. 1058-1060.

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael , Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12 pp. 1058-1060.

Parida, L., Atwal, G. , Mishra, B. (2014) Proceedings of The Twelfth Annual RECOMB Comparative Genomics Conference. BMC Genomics, 15(Suppl ) pp. I1.

Kinney, J. B. , Atwal, G. S. (2014) Reply to Reshef et al.: Falsifiability or bust. Proceedings of the National Academy of Sciences of the United States of America, 111(33) pp. E3364.

Kinney, J. B. , Atwal, G. S. (2014) Reply to Murrell et al.: Noise matters. Proceedings of the National Academy of Sciences of the United States of America, 111(21) pp. E2161.

Kinney, J. B. , Atwal, G. S. (2014) Equitability, mutual information, and the maximal information coefficient. Proceedings of the National Academy of Sciences of the United States of America, 111(9) pp. 3354-9.

Kinney, J. B. , Atwal, G. S. (2014) Parametric Inference in the Large Data Limit Using Maximally Informative Models. Neural Comput, 26(4) pp. 637-653.

Atwal, Gurinder Singh (2014) Statistical mechanics of multistable perception. BioRxiv,

Aboukhalil, R., Fendler, B. , Atwal, G. S. (2013) Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics, 14

Kinney, J. B. , Atwal, G. S. (2013) Parametric inference in the large data limit using maximally informative models. Arxiv,

Ouyang, W., Liao, W., Luo, C. T., Yin, N., Huse, M., Kim, M. V., Peng, M., Chan, P., Ma, Q., Mo, Y., Meijer, D., Zhao, K., Rudensky, A. Y., Atwal, G., Zhang, M. Q. , Li, M. O. (2012) Novel Foxo1-dependent transcriptional programs control T reg cell function. Nature, 491(7425) pp. 554-559.

Paul, A., Cai, Y., Atwal, G. S. , Huang, Z. J. (2012) Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex. Frontiers in Neural Circuits, 6 pp. 37.

Fendler, B. , Atwal, G. (2012) Systematic deciphering of cancer genome networks. Yale Journal of Biology and Medicine, 85(3) pp. 339-45.

Ying, Cai, Fendler, B. , Atwal, G. S. (2012) Utilizing RNA-Seq data for cancer network inference. 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, (GENSIPS), pp. 46-49.

Chen, M. H., Pratt, C. P., Zeeman, M. E., Schultz, N., Taylor, B. S., O'Neill, A., Castillo-Martin, M., Nowak, D. G., Naguib, A., Grace, D. M., Murn, J., Navin, N., Atwal, G. S., Sander, C., Gerald, W. L., Cordon-Cardo, C., Newton, A. C., Carver, B. S. , Trotman, L. C. (2011) Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression. Cancer Cell, 20(2) pp. 173-186.

Mehta, M. S., Vazquez, A., Kulkarni, D. A., Kerrigan, J. E., Atwal, G. S., Metsugi, S., Toppmeyer, D. L., Levine, A. J. , Hirshfield, K. M. (2011) Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes. Breast Cancer Research and Treatment, 125(3) pp. 861-868.

Mizuno, H., Atwal, G. S., Wang, H., Levine, A. J. , Vazquez, A. (2010) Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome. BMC Genet, 11 pp. 27.

Atwal, G. S., Kirchhoff, T., Bond, E. E., Montagna, M., Menin, C., Bertorelle, R., Scaini, M. C., Bartel, F., Böhnke, A., Pempe, C., Gradhand, E., Hauptmann, S., Offit, K., Levine, A. J. , Bond, G. L. (2009) Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene. Proc Natl Acad Sci U S A, 106(25) pp. 10236-10241.

Kang, H. J., Feng, Z., Sun, Y., Atwal, G., Murphy, M. E., Rebbeck, T. R., Rosenwaks, Z., Levine, A. J. , Hu, W. (2009) Single-nucleotide polymorphisms in the p53 pathway regulate fertility in humans. Proc Natl Acad Sci U S A, 106(24) pp. 9761-6.

Atwal, G. S., Rabadan, R., Lozano, G., Strong, L. C., Ruijs, M. W., Schmidt, M. K., van't Veer, L. J., Nevanlinna, H., Tommiska, J., Aittomaki, K., Bougeard, G., Frebourg, T., Levine, A. J. , Bond, G. L. (2008) An information-theoretic analysis of genetics, gender and age in cancer patients. PLoS ONE, 3(4) pp. e1951.

Hu, W., Feng, Z., Atwal, G. S. , Levine, A. J. (2008) p53: a new player in reproduction. Cell Cycle, 7(7) pp. 848-52.

Atwal, G. S., Bond, G. L., Metsuyanim, S., Papa, M., Friedman, E., Distelman-Menachem, T., Ben Asher, E., Lancet, D., Ross, D. A., Sninsky, J., White, T. J., Levine, A. J. , Yarden, R. (2007) Haplotype structure and selection of the MDM2 oncogene in humans. Proc Natl Acad Sci U S A, 104(11) pp. 4524-9.

Atwal, G. S. (2006) Clustering problems in biological networks. Journal of Classification, 23 pp. 349-352.

Slonim, N., Atwal, G. S., Gasper, T. , Bialek, W. (2005) Information-based clustering. Proc Nat Acad Sci (USA), 102(51) pp. 18297-18302.

Slonim, Noam, Atwal, Gurinder Singh, Tkacik, Gasper , Bialek, William (2005) Estimating mutual information and multi--information in large networks. arXiv,

Atwal, G. S. (2004) Dynamic plasticity in coupled avian midbrain maps. Phys Rev E Stat Nonlin Soft Matter Phys, 70(6 Pt 1) pp. 61904.

Atwal, G. S. , Bialek, W (2004) Ambiguous model learning made unambiguous with 1/f priors. NIPS,

Atwal, G. S. , Ashcroft, N. W. (2004) Polarization waves and superconducting instabilities in electron systems. Physical Review B, 70(10) pp. 104513.

Atwal, G. S., Khalil, I. G. , Ashcroft, N. W. (2003) Dynamical local-field factors and effective interactions in the two-dimensional electron liquid. Physical review B. Condensed matter and materials physics, 67(11) pp. 115107.

Atwal, G. S. , Ashcroft, N. W. (2003) Correlation effects and the high-frequency spin susceptibility of an electron liquid: Exact limits. Physical review B. Condensed matter and materials physics, 67(23) pp. 233104-233104.4.

Atwal, G. S. , Ashcroft, N. W. (2002) Relaxation of an electron system: Conserving approximation. Physical Review B, 65 pp. 115109.

Atwal, G. S. , Terentjev, E. (1998) Order-disorder transitions in nematic elastomers. Cambridge University Technical Report,