BioSci D145 – Winter 2017 - Reading list for presentations


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


Week 2 papers – (1) Geisler et al., 1999 (2) Redon et al., 2006 (3)  Myers et al., 2000


Week 3 papers – (4) Iyer et al., 1999 (5) Venter et al., 2004, (6) Bentley et al., 2008


Week 4 papers – (7) RIKEN, 2005 (8) Kapranov et al., 2007 (9) Lindblad-Toh et al., 2011 


Week 5 – Midterm, no presentations


Week 6 papers – (10) Horak et al., 2002 (11) Chen et al., 2012 (12) Dewey et al., 2016


Week 7 papers – (13)  Seisenberger et al, 2012 (14)  Siklenka et al., 2015 (15) Donkin et al., 2016


Week 8 papers – (16) Gilbert et al., 2014 (17) Liu et al., 2017 (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)  Breton et al., 2016 (24) Rampelli et al., 2015 

Specific references

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

Breton, J., Tennoune, N., Lucas, N., Francois, M., Legrand, R., Jacquemot, J., Goichon, A., Guerin, C., Peltier, J., Pestel-Caron, M., et al. (2016). Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth. Cell Metabolism 23, 324-334. 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


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


Dewey, F. E., Murray, M. F., Overton, J. D., Habegger, L., Leader, J. B., Fetterolf, S. N., O'Dushlaine, C., Van Hout, C. V., Staples, J., Gonzaga-Jauregui, C., et al. (2016). Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science 354, 1549. PDF

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

Donkin, I., Versteyhe, S., Ingerslev, Lars R., Qian, K., Mechta, M., Nordkap, L., Mortensen, B., Appel, Emil Vincent R., Jψrgensen, N., Kristiansen, Viggo B., et al. (2016). Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans. Cell Metabolism, in press 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


Horak, C. E., Luscombe, N. M., Qian, J., Bertone, P., Piccirrillo, S., Gerstein, M. and Snyder, M.  (2002). Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16, 3017-33. PDF S1

Iyer, V. R., Eisen, M. B., Ross, D. T., Schuler, G., Moore, T., Lee, J. C., Trent, J. M., Staudt, L. M., Hudson, J., Jr., Boguski, M. S. et al. (1999). The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-7. 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

Lindblad-Toh et al., (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478,476–482. PDF  SUPP


Liu, S. J., Horlbeck, M. A., Cho, S. W., Birk, H. S., Malatesta, M., He, D., Attenello, F. J., Villalta, J. E., Cho, M. Y., Chen, Y., et al. (2017). CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355. PDF

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


Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K. H., Remington, K. A. et al. (2000). A whole-genome assembly of Drosophila. Science 287, 2196-204. 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


RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium (2005) The Transcriptional landscape of the mammalian genome. Science 309, 1559-1563 PDF PDF

 Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W. and Reik, W. (2012). The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells. Mol Cell 48, 849-62. PDF S1 ST1 ST2 ST3 ST4 ST5 ST6

Siklenka, K., Erkek, S., Godmann, M., Lambrot, R., McGraw, S., Lafleur, C., Cohen, T., Xia, J., Suderman, M., Hallett, M., et al. (2015). Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 350, 6261 PDF.


Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B. et al. (2012). The accessible chromatin landscape of the human genome. Nature 489, 75-82.  PDF


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