Suggested Reading List

Below are a variety of texts selected by the 2019 PiTP Lecturers. All texts are not required, however, be sure to go over the list and familiarize yourself with the topics before your arrival. Please note, this list will continue to be updated as the program draws nearer.

General Reference:
Bruce Alberts et al. Molecular Biology of the Cell (6th edition)

Suggested by Uri Alon:
- Karin and Alon, “Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits” MSB 2016 and 2017 http://msb.embopress.org/content/13/6/933
- Karin et al “Senescent cells and the dynamics of aging” doi: https://doi.org/10.1101/470500

Suggested by Curtis Callan:
- Elhanati Y, Sethna Z, Callan C, Mora T, and Walczak AM, {\sl OLGA: fast computation of generation probability of B- and T-cell receptor amino-acid sequences and motifs}, {Bioinformatics} {\bf NNN} (2018) nnn-mmm
- Elhanati Y, Sethna Z, Callan C, Mora T, and Walczak AM, {\sl Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination}, {Immunological Reviews} {\bf 284} (2018) 167-179
- Elhanati Y, Sethna Z, Dudgeon C, Callan C, Levine A, Mora T, and Walczak A, {\sl Insights into immune system development and function from mouse T cell repertoires}. {Proc. Natl. Acad. Sci USA} {\bf 114} 2253-2258 (2017)
- Callan C, Mora T, and Walczak A, {\sl Repertoire sequencing and the statistical ensemble approach to adaptive immunity.} {Current Opinion in Systems Biology} {\bf 1} 44 (2017)
- Elhanati Y, Sethna Z, Callan C, Mora T, and Walczak AM, {\sl Inferring processes underlying B cell repertoire diversity.} {Phil Trans R Soc London} {\bf B 370} (2016) 1676-
- Elhanati Y, Murugan A, Callan C, Mora T, and Walczak A, {\sl Quantifying selection in immune receptor repertoires.} {Proc. Natl. Acad. Sci. USA} {\bf 111} (2014) 9875-9880
- Murugan A, Callan C, Mora T, and Walczak A, {\sl Statistical inference of the generation probability of T-cell receptors from sequence repertoires.} {Proc. Natl. Acad. Sci. USA} {\bf 109} (2012) 16161-16166

Suggested by Navdeep Chandel:
- Textbook- Navigating Metabolism, Cold Spring Harbor Press. Navdeep Chandel.
- Chandel NS (2015) "Evolution of Mitochondria as Signaling Organelles" Cell Metabolism. 22:204-6

Suggested by Michael Desai:
- Evolutionary Dynamics Fisher, Daniel S. (2007)
- “Progress and open problems in evolutionary dynamics” Neher, Richard A. and Aleksandra M. Walczak (2018)

Suggested by Steve Goff:
Overall reviews on retrovirus replication:
- Varmus HE. 1982. Form and function of retroviral proviruses. Science. 216:812-20.
- Goff, S.P. 2013. Retroviridae: The Retroviruses and their Replication. in Fields Virology, sixth edition. (Knipe, D., and Howley, P., eds.) Lippincott Williams & Wilkins, Philadelphia PA, Chapter 47, pp. 1424-1473.
Cloning of virus receptors:
- Albritton, L.A., Tseng, L., Scadden, D., and Cunningham, J.M. 1989. A putative murine ecotropic retrovirus receptor gene encodes a multiple membrane-spanning protein and confers susceptibility to virus infection. Cell 57: 659-666.
- Rai SK, Duh FM, Vigdorovich V, Danilkovitch-Miagkova A, Lerman MI, Miller AD. 2001. Candidate tumor suppressor HYAL2 is a glycosylphosphatidylinositol (GPI)-anchored cell-surface receptor for jaagsiekte sheep retrovirus, the envelope protein of which mediates oncogenic transformation. Proc Natl Acad Sci U S A. 98:4443-8.
Integration and nuclear Import:
- Brown, P.O., Bowerman, B., Varmus, H.E., and Bishop, J.M. 1987. Correct integration of retroviral DNA in vitro. Cell 49: 347-356.
- Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TL, Roth SL, Hué S, Fletcher AJ, Lee K, KewalRamani VN, Noursadeghi M, Jenner RG, James LC, Bushman FD, Towers GJ. 2011. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog. 7:e1002439.
Virus budding and host factors (first siRNA screen):
- Garrus J.E., von Schwedler U.K., Pornillos O.W., Morham S.G., Zavitz K.H., Wang H.E., Wettstein D.A., Stray K.M., Cote M., Rich R.L., Myszka D.G., and Sundquist W.I. 2001. Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell 107: 55-65.
A classic breakthrough paper on oncogenesis:
- Neel, B.G. Hayward WS, Robinson HL, Fang J, Astrin SM. 1981. Avian leukosis virus-induced tumors have common proviral integration sites and synthesize discrete new RNAs: Oncogenesis by promoter insertion. Cell 23: 323-334.
Reviews on endogenous retroviruses:
- Xu X, Zhao H, Gong Z, Han GZ. 2018. Endogenous retroviruses of non-avian/mammalian vertebrates illuminate diversity and deep history of retroviruses. PLoS Pathog. 14, e1007072.
- Johnson WE. 2015. Endogenous Retroviruses in the Genomics Era. Annu Rev Virol. 2:135-59.
A review on host use of viral genes (exaptation):
- Lavialle C, Cornelis G, Dupressoir A, Esnault C, Heidmann O, Vernochet C, Heidmann T. 2013.
- Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation. Philos Trans R Soc Lond B Biol Sci. 368, 20120507. PMID:2393875
The Koala virus story
- Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV. 2017. Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions. Microbiol Mol Biol Rev. 82. pii: e00044-17. PMID:29237726
- Tarlinton RE, Meers J, Young PR. 2006. Retroviral invasion of the koala genome. Nature 442:79-81
Gene therapy and insertional activation:
- Hacein-Bey-Abina S. et al. 2003. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302:415-9.
- Cavazzana-Calvo M. et al. 2010. Transfusion independence and HMGA2 activation after gene therapy of human b-thalassaemia. Nature 467:318-22.

Suggested by Clyde Hutchison, III:
For historical background see:
- Erwin Schrödinger (1944). What Is Life? The Physical Aspect of the Living Cell.
- The Wikipedia article “What Is Life?”
- J.D. Watson and F.H.C. Crick (1953). A Structure for Deoxyribose Nucleic Acid. Nature 171, 737-738.
- Harold J. Morowitz (1984). The completeness of molecular biology. Isr. J. Med. Sci. 20, 750-753.
In the genomic era:
- Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrman, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merrick, J. M., Tomb, J.-F., Dougherty, B. A., Bott, K. F., Hu, P.-c., Lucier, T. S., Peterson, S. N., Smith, H. O., Hutchison, C. A.III and Venter, J. C. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403
- Hutchison, C.A.III, Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O., and Venter, J.C. (1999). Global transposon mutagenesis and a minimal mycoplasma genome. Science 286, 2165-2169.
-Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A. III, Smith, H.O., and Venter, J.C. (2007). Genome transplantation in bacteria: changing one species to another. Science 317, 632-638.
In the era of synthetic biology:
- Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., Algire, M.A., Benders, G.A., Montague, M.G., Ma, L., Moodie, M.M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E.A., Young, L., Qi, Z.Q., Segall-Shapiro, T.H., Calvey, C.H., Parmar, P.P., Hutchison, C.A. III, Smith, H.O., and Venter, J.C. (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329, 52-56.
- Hutchison CA 3rd, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. (2016) Design and synthesis of a minimal bacterial genome. Science. 2016 Mar 25;351(6280):aad6253. doi: 10.1126/science.aad6253. PMID: 27013737
- Marian Breuer, Tyler M. Earnest, Chuck Merryman, Kim S. Wise, Lijie Sun, Michaela R. Lynott, Clyde A. Hutchison III, Hamilton O. Smith, John D. Lapek Jr., David J. Gonzalez, Valérie de Crécy-Lagard, Drago Haas, Andrew D. Hanson, Piyush Labhsetwar, John I. Glass, and Zan Luthey-Schulten (2019) Essential Metabolism for a Minimal Cell. eLife Jan 18;8. pii: e36842. doi:10.7554/elife.36842. [Epub ahead of print]

Suggested by Edo Kussell:
Highly readable, concise, essential classics:
- The Lac Operon: A Short History of a Genetic Paradigm by Benno Müller-Hill
- A Genetic Switch (3rd ed.): Phage Lambda Revisited by Mark Ptashne
Related papers on adaptation in fluctuating environments:
- Kussell E and Leibler S. Phenotypic diversity, population growth, and information in fluctuating environments. /Science/, 309:2075 (2005).
- Lambert G and Kussell E. Memory and fitness optimization of bacteria under fluctuating environments. /PLoS Genetics/, 77:102602 (2014).
- Lin W-H and Kussell E. Complex interplay of physiology and selection in the emergence of antibiotic resistance. Current Biology, 26:1 (2016).
- Skanata A and Kussell E. Evolutionary phase transitions in random environments. /Physical Review Letters/, 117:038104 (2016).
- Moxon R and Kussell E. The impact of bottlenecks on microbial survival, variation and phenotypic switching in host-pathogen interactions. /Evolution/ 71:2803 (2017).

Suggested by Arnold Levine:
- Textbook - The Biology of Cancer, 2^nd Edition. Robert Weinberg
- Levine AJ, Ting DT, Greenbaum BD 2016, “P53 and the defenses against genome instability caused by transposons and repetitive elements”, Bioessays. 38 508-513
- Levine AJ, Puzio-Kuter AM, 2010, “The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes” Science. 330, 1340-1344
- Levine AJ, Jenkins Na, Copeland NG, 2019 “The Roles of Initiating Truncal Mutations in Human Cancers: The Order of Mutations and Tumor Cell Type Matters” Cancer cell, 35, 10-15

Suggested by Ake T. Lu:
- Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biol. 2013 Oct 21;14(10):R115. PMCID: PMC4015143
- Horvath S, Raj K DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet. 2018 Jun;19(6):371-384. doi: 10.1038/s41576-018-0004-3. PMID: 29643443
- Lu AT, Quach A, Wilson JG, Reiner AP, Aviv A, Raj K, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Assimes TL, Ferrucci L, Horvath (2019) DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging (Albany NY). 2019 Jan 21. doi: 10.18632/aging.101684. PMID: 30669119 https://www.aging-us.com/full/101684

Suggested by Remi Monasson:
- Emergence of compositional representations in restricted Boltzmann machines - J. Tubiana, R. Monasson Physical Review Letters 118, 138501 (2017)
- Inverse Statistical Physics of Protein Sequences: A Key Issues Review - S. Cocco, C. Feinauer, M. Figliuzzi, R. Monasson, M. Weigt Reports on Progress in Physics 81, 032601 (2018).
- Learning protein constitutive motifs from sequence data - J. Tubiana, S. Cocco, R. Monasson eLife 2019;8:e39397 (2019).

Suggested by Nick Patterson:
papers can be found here
-[LWH+15] Stephen Leslie, Bruce Winney, Garrett Hellenthal, Dan Davison, Abdelhamid Boumertit, Tammy Day, Katarzyna Hutnik, Ellen C Royrvik, Barry Cunliffe, Daniel J Lawson, et al. The fine-scale genetic structure of the British population. Nature, 519(7543):309–314, 2015. An interesting example of how haplotype methods may add power to population analysis
-[Nor01] M. Nordborg. Coalescent theory. In D.J. Balding, M. Bishop, and C. Cannings, editors, Handbook of Statistical Genetics, pages 179– 212. John Wiley and Sons. New York., 2001.A Primer on the Coalescent – a basic concept in modern mathematical genetics
-[PML+12] N. Patterson, P. Moorjani, Y. Luo, S. Mallick, N. Rohland, Y. Zhan, T. Genschoreck, T. Webster, and D. Reich. Ancient admixture in human history. Genetics, 192(3):1065–1093, Nov 2012. A set of methods useful for recovering phylogeny from genetic data – this is mostly what I will cover

Suggested by Raul Rabadan:
https://rabadan.c2b2.columbia.edu/pitp - link to datasets, papers, and lecture notes

Suggested by R. Clay Reid:
- Briggman, Kevin L., and Davi D. Bock. “Volume electron microscopy for neuronal circuit reconstruction" Current opinion in neurobiology/ 22.1 (2012): 154-161 https://drive.google.com/file/d/0BwWWE4p0wihlMF9mNGoxOWNSa0k/view?usp=sharing
- Lee, Wei-Chung Allen, Vincent Bonin, Michael Reed, Brett J. Graham, Greg Hood, Katie Glattfelder, and R. Clay Reid. “Anatomy and function of an excitatory network in the visual cortex" Nature/532: 370-374 (2016) https://drive.google.com/open?id=0BwWWE4p0wihlZ3d6VllOa1ZlNDg

Suggested by David Ting:
- A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing - Link to pdf
- Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes - Link to pdf