Mickey Atwal
Mickey Atwal

  Selected Publications

  • Ancient trans-acting siRNAs modulate auxin sensitivity in the moss Physcomitrella patens, Y. Plavskin, A. Nagashima, P. Perroud, M. Hasebe, R. S. Quatrano, G. S. Atwal, M. C. P. Timmermans, Developmental Cell, Volume 36, Issue 3, p276–289, 8 February 2016 bioRxiv/10.1101/024307
  • Learning quantitative sequence–function relationships from massively parallel experiments, G. S. Atwal, J. Kinney, Journal of Statistical Physics, pp 1-41, 29 October 2015 pdf
  • Interactive anaysis and quality assessment of single-cell copy-number variations, T. Garvin, R. Aboukhalil, T. Baslan, J. Kendall, J. Hicks, G.S. Atwal, M. Wigler, M. Schatz, Nature Methods 2015 bioRxiv/10.1101/011346 (software website)
  • Statistical mechanics of multistable perception, G. S. Atwal, bioRxiv/10.1101/008177
  • Proceedings of The Twelfth Annual RECOMB Comparative Genomics Conference L. Parida, G. S. Atwal, B. Mishra, BMC Genomics 2014, 15(Suppl 6):I1 (17 October 2014) pdf
  • Reply to Reshef et al.: Falsifiability or bust, J. Kinney, G. S. Atwal, Proc Nat Acad Sci, 2014; 111(33):E3364 pdf
  • Reply to Murrell et al.: Noise matters, J. Kinney, G. S. Atwal, Proc Nat Acad Sci, 2014; 111(21):E2161 pdf
  • Parametric inference in the large data limit using maximally informative models, J. Kinney, G. S. Atwal, Neural Computation, 2014 Apr;26(4):637-53 pdf
  • Equitability, mutual information, and the maximal information coefficient, J. Kinney, G. S. Atwal, Proc Nat Acad Sci, 2014 Mar 4;111(9):3354-9 pdf
  • Kerfuffle: a web tool for multi-species gene colocalization analysis, R. Aboukhalil, B. Fendler, G. S. Atwal, BMC Bioinformatics, 14:22, (2013). pdf (software website)
  • Maximally informative models and diffeomorphic modes in the analysis of large data sets, J. Kinney, G. S. Atwal, arXiv:1212.3647. pdf
  • Utilizing RNA-Seq data for cancer network inference, Y. Cai, B. Fendler, G. S. Atwal, IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS (2012). pdf
  • Novel Foxo1-dependent transcriptional programs control Treg cell function, W. Ouyang, W. Liao, M. Huse, C. Luo, M. Kim, M. Peng, P. Chan. Q. Ma, Y. Mo, D. Meijer, K. Zhao, A. Rudensky, G. Atwal, M. Zhang, N. Yin, Nature, 491, 554-559 (2012).
  • Systematic deciphering of cancer genome networks, B. Fendler, G. S. Atwal, Yale J Biol Med. 2012 September; 85(3): 339-345. pdf
  • The Inheritance of p53, L. F. Grochola, J. Zeron-Medina, E. Repapi, A. Finlayson, Y. Cai, G. S. Atwal, G. L. Bond, book chapter in "p53 in the Clinics", Springer (2012).
  • Developmental coordination of gene expression between synaptic partners during GABAergic circuit assembly in cerebellar cortex, A. Paul , Y. Cai, G. S. Atwal, J. Huang, Front. Neural Circuits 6:37 (2012). pdf (supp)
  • Identification of PHLPP1 as a tumor suppressor reveals the role of feedback compensation in PTEN-mutant prostate cancer progression and therapy, M. Chen, C. P. Pratt, M. E. Zeeman, N. Schultz, B. S. Taylor, A. O'Neill, M. Castillo-Martin, D. G. Nowak, A. Naguib, N. Navin, D. M. Grace, J. Murn, G. S. Atwal, C. Sander, W. L. Gerald, C. Cordon-Cardo, A. C. Newton, B. S. Carver, L. Trotman, Cancer Cell, 20(2):173-86 (2011). PMID 21840483 pdf (supp)
  • Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes, M. S. Mehta, A. Vazquez, D. A. Kulkarni, J. E.  Kerrigan, G. Atwal, S. Metsugi, D. L. Toppmeyer, A. J. Levine, K. M. Hirshfield, Breast Cancer Res Treat. (2010) Jul 25. pdf
  • Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome, H. Mizuno, G. S. Atwal, H. Wang, A. J. Levine, A. Vazquez, BMC Genetics, 11:27 (2010). PMCID:  PMC2873552. pdf (software website)
  • Single-nucleotide polymorphisms in the p53 pathway regulate fertility in humans, H. J. Kang, F. Zhaohui, Y. Sun, G. S. Atwal, M.E. Murphy, T.R. Rebbeck, Z. Rosenwaks, A.J. Levine, W. Hu, Proc Nat Acad Sci, 106 (24):9761-9766. (2009). PMCID: PMC2700980. pdf
  • Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene, G. S. Atwal, T. Kirchhoff, E. E.  Bond, M. Monagna. C. Menin, R. Bertorelle, M. C. Scaini, F. Bartel, A. Bohnke, C. Pempe, E. Gradhand,S. Hauptmann, K. Offit, A. J. Levine, G. L. Bond, Proc Nat Acad Sci (USA) (2009) PMCID: PMC2700939. pdf
  • An information-theoretic analysis of genetics, gender and age in cancer patients, G. S. Atwal, R. Rabadan, G. Lozano, L. Strong, M. Ruijs, M. Schmidt, L. Veer, H. Nevanlinna, J. Tommiska, K. Aittomaki, G. Bougeard, T. Frebourg, A. Levine, G. Bond, PLoS ONE 3(4): e1951 (2008). PMCID: PMC2276689 pdf
  •  p53: A new player in reproduction, W. Hu, Z. Feng, G. S. Atwal, A. J. Levine, Cell Cycle 7, 7 (2008). pdf
  • Haplotype structure and selection of the MDM2 oncogene in humans, G. S. Atwal, G. Bond, S. Metsuyanim, M. Papa, E. Friedman, T. Distelman-Menachem, E. Ben-Asher, D. Lancet, D. Ross, J. Sninsky, T. White, A. Levine, R. Yarden, Proc Nat Acad Sci (USA) 104, 4524-4529 (2007). PMCID: PMC1838634 pdf
  • Correlations in Complex Disease Association Studies, G. S. Atwal, SIAM Conference on Computational Science and Engineering, (2007).
  • Estimating mutual information and multi-information in large networks, N. Slonim, G. S. Atwal, G. Tkacik, W. Bialek,  cs.IT/0502017 pdf
  • Information based clustering, N. Slonim, G. S. Atwal, G. Tkacik, W. Bialek, Proc Nat Acad Sci (USA) 102, 18297-18302 (2005). pdf  (supp) (software website)
  • Dynamic plasticity in coupled avian midbrain maps, G. S. Atwal, Phys. Rev. E 70, 06194 (2004). pdf
  • Polarization waves and superconducting instabilities in electron systems, G. S. Atwal, N. W. Ashcroft,  Phys. Rev. B 70, 104513 (2004). pdf
  • Ambiguous model learning made unambiguous with 1/f priors, G. S. Atwal, W. Bialek, Neural Information Processing Systems 16, MIT Press, Cambridge (2004). pdf
  • Dynamical local-field factors and effective interactions in the two-dimensional electron liquid, G. S. Atwal, I. G. Khalil, N. W. Ashcroft, Phys. Rev. B 67, 115107 (2003). pdf
  • Correlation effects and the high-frequency spin susceptibility of an electron liquid: Exact limits, G. S. Atwal, N. W. Ashcroft,  Phys. Rev. B 67, 233104 (2003). pdf
  • Dynamical correlation in quantum electron liquids, G. S. Atwal, Ph.D. thesis, Cornell University (2002).
  • Relaxation of an electron system: Conserving approximation, G. S. Atwal, N. W. Ashcroft,  Phys. Rev. B 65, 115109 (2002). pdf
  • Quantum size effects in quasi-two dimensional electron-hole systems, Bull. Am. Phys. Soc., (2000).
  • Order-disorder transitions in nematic elastomers, Cambridge University Technical Report, (1998).