Top 10 Papers Reading List

Papers are not listed in any particular order.

  • Quantitative modeling of transcription factor binding specificities using DNA shape, Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R. PNAS 2015 Apr 14;112(15):4654-9. PMID: 26103224
  • Deconvolving the recognition of DNA shape from sequence, Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Cell 2015 Apr 9;161(2):307-18. PMID: 25843630
  • A method to predict the impact of regulatory variants from DNA sequence, D. Lee, D.U. Gorkin, M. Baker, B.J. Strober, A.L. Asoni, A.S. McCallion, M.A. Beer. Nat Genet. 2015 Aug;47(8):955-61. PMID: 26075791
  • Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning, Alipanahi B, Delong A, Weirauch MT, Frey BJ. Nat Biotechnol 33(8):831-8. PMID: 26213851
  • Inferring interaction type in gene regulatory networks using co-expression data, Khosravi P, Gazestani V, Pirhaji L, Law B, Sadeghi M, Goliaei B , Bader G. Algorithms for Molecular Biology 2015, 10:23. PMID: 26265933
  • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells, Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature Biotechnology 33, 155-160, 2015. PMID: 25599176
  • Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression, Libbrecht, M. W., Ay, F., Hoffman, M. M., Gilbert, D. M., Bilmes, J. A., & Noble, W. S. Genome research 25(4), 544-557. PMID: 25677182
  • Elucidating Compound Mechanism of Action by Network Perturbation Analysis, Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Cell/em>.. 2015 Jul 16;162(2):441-51. PMID: 26186195
  • Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues, Ernst J, Kellis M. Nature Biotechnology/em> 33, 364-376, 2015. PMID: 25690853
  • The human splicing code reveals new insights into the genetic determinants of disease, Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K., ... & Frey, B. J. Science /em>3347(6218), 1254806. PMID: 25525159
  • Integration of genomic data enables selective discovery of breast cancer drivers, Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, Pe'er D. Cellem> 159(6):1461-7. PMID: 25433701