BioSci D145 Winter 2020 - Reading list for presentations


Week 1 papers Dear and Cook, 1993, Jiang et al, 2011 (Angela)


Week 2 papers (1) Geisler et al., 1999 (2) Redon et al., 2006 (3) Venter et al., 2004,


Week 3 papers (4) Bentley et al., 2008 (5) Lindblad-Toh et al., 2011 (6) Sessions et al., 2016


Week 4 papers (7) Kapranov et al., 2007 (8) Morrison et al., 2017 (9) Owens et al., 2016


Week 5 papers (10) Cheng et al., 2019 (11) Chen et al., 2012 (12) Silvert et al., 2019


Week 6 papers Midterm, no presentations


Week 7 papers (13) Flyamer et al., 2017 (14) Buenrostro et al., 2012 (15) Argelaget et al., 2019


Week 8 papers (16) Gilbert et al., 2014 (17) Anzalone et al., 2019 (18) Luo et al., 2009


Week 9 papers (19) Ito et al., 2001 (20) Dejardin and Kingston, 2009 (21) Gavin et al., 2002


Week 10 papers (22) David et al., 2014 (23) Rampelli et al., 2015 (24) Tang et al., 2019

Specific references


Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature.576 (7785):149-57 PDF


Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, et al. (2019) Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature. 576(7787):487-91 PDF


Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59. PDF


Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. (20131) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 10(12):1213-8. PDF


Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., Cheng, Y. et al. (2012). Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293-307. PDF


Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PPL, et al. (2019) Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. Cell Rep. 26(10):2593-607 e3. PDF


David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563. PDF


Dear, P. H. and P. R. Cook (1993). Happy mapping: linkage mapping using a physical analogue of meiosis. Nucleic Acids Res 21, 13-20. PDF

Dejardin, J. and Kingston, R. E. (2009). Purification of proteins associated with specific genomic Loci. Cell 136, 175-86. PDF


Flyamer IM, Gassler J, Imakaev M, Brandao HB, Ulianov SV, Abdennur N, et al. (2017) Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. ;544(7648):110-4. PDF


Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M. et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147. PDF PDF PDF PDF PDF PDF PDF


Geisler, R., Rauch, G. J., Baier, H., van Bebber, F., Bross, L., Dekens, M. P., Finger, K., Fricke, C., Gates, M. A., Geiger, H. et al. (1999). A radiation hybrid map of the zebrafish genome. Nat Genet 23, 86-9. PDF


Gilbert, L.A., Horlbeck, M.A., Adamson, B., Villalta, J.E., et al. (2014). Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation Cell 159, 647-661. PDF


Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98, 4569-74. PDF PDF


Jiang, Z., Michal, J. J., Beckman, K. B., Lyons, J. B., Zhang, M., Pan, Z., Rokhsar, D. S. and Harland, R. M. (2011). Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome. Int J Biol Sci 7, 1037-1044. PDF


Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermuller, J., Hofacker, I. L., et al. (2007). RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488. PDF SUPP


Lindblad-Toh et al., (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478,476482. PDF SUPP


Luo, J., Emanuele, M. J., Li, D., Creighton, C. J., Schlabach, M. R., Westbrook, T. F., Wong, K. K. and Elledge, S. J. (2009). A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 137, 835-48. PDF


Morrison JA, McLennan R, Wolfe LA, Gogol MM, Meier S, McKinney MC, et al. (2017) Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions. Elife. 2. PDF


Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, et al. (2016) Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep. 2016;14(3):632-47 PDF.


Rampelli, S., Schnorr, S. L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., Brigidi, P., Crittenden, A. N., Henry, A. G. and Candela, M. (2015). Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota. Curr Biol 25, 1682-93. PDF


Redon et al. (2006) Global variation in copy number in the human genome. Nature 444, 444-454. PDF S1 S2 S3 S4 S5 S6 S7 S8 N&V


Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538(7625):336-43. PDF


Silvert M, Quintana-Murci L, Rotival M. (2019) Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation. Am J Hum Genet.104(6):1241-50. PDF


Tang ZZ, Chen G, Hong Q, Huang S, Smith HM, Shah RD, et al. (2019) Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites. Front Genet. 2019;10:454. PDF SUPP


Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W. et al. (2004). Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304, 66-74. PDF PDF