Recommended Readings: Li Zhao, Ph.D. Monday April 15, 2019

Monday Lectures

Monday, April 15, 2019  4:00 p.m.

Carson Family Auditorium

Li Zhao, Ph.D.

Assistant Professor and Head

Laboratory of Evolutionary Genetics and Genomics

The Rockefeller University

The Origin and Evolution of De Novo Genes


Recommended Readings:

Empirical Articles

Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; et al. (2018). Improved reference genome of Aedes aegypti informs arbovirus vector control. NATURE. 563 (7732): 501-+

Zhao, Li; Begun, David J. (2017). Genomics of parallel adaptation at two timescales in Drosophila. PLOS GENETICS. 13 (10)

Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; et al. (2016). The adaptive significance of natural genetic variation in the DNA damage response of Drosophila melanogaster. PLOS GENETICS. 12 (3)

Li, Xueyan; Fan, Dingding; Zhang, Wei; et al. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. NATURE COMMUNICATIONS. 6

Zhao, Li; Wit, Janneke; Svetec, Nicolas; et al. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS GENETICS. 11 (5)

Zhao, Li; Saelao, Perot; Jones, Corbin D.; et al. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. SCIENCE. 343 (6172): 769–772

Ding, Yun; Zhao, Li; Yang, Shuang; et al. (2010). A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y- Linked Male Fertility Genes. PLOS GENETICS. 6 (12)

Recommended Readings: David Baker, Ph.D. Friday January 11, 2019

Friday Lectures

Friday, January 11, 2018  3:45 p.m

Caspary Auditorium

David Baker Ph.D.

Professor of Biochemistry and Director of the Institute for Protein Design

University of Washington

The Coming of Age of De Novo Protein Design


Recommended Readings:

Science News

Scientists program proteins to pair exactly. December 19, 2018. Science Daily

Empirical Articles

Shen, Hao; Fallas, Jorge A.; Lynch, Eric; et al. (2018). De novo design of self-assembling helical protein filaments. SCIENCE. 362 (6415): 705-709

Marcos, Enrique; Chidyausiku, Tamuka M.; McShan, Andrew C.; et al. (2018). De novo design of a non-local beta-sheet protein with high stability and accuracy. NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 25 (11): 1028-1030

Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William; et al. (2018). De novo design of a fluorescence-activating beta-barrel. NATURE. 561 (7724): 485-+

Lu, Peilong; Min, Duyoung; DiMaio, Frank; et al. (2018). Accurate computational design of multipass transmembrane proteins. SCIENCE. 359 (6379): 1042-1046

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; et al. (2017). Comprehensive computational design of ordered peptide macrocycles. SCIENCE. 358 (6369): 1461-1466

Review Paper

Huang, Po-Ssu; Boyken, Scott E.; Baker, David. (2016). The coming of age of de novo protein design. NATURE. 537 (7620): 320-327

Fleishman, Sarel J.; Baker, David. (2012). Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution. CELL. 149 (2): 262-273

Book Chapter

Thyme, Summer; Baker, David. (2014). Redesigning the Specificity of Protein-DNA Interactions with Rosetta. HOMING ENDONUCLEASES: METHODS AND PROTOCOLS. 1123: 265-282

Whitehead, Timothy A.; Baker, David; Fleishman, Sarel J. (2013). Computational Design of Novel Protein Binders and Experimental Affinity Maturation. METHODS IN PROTEIN DESIGN. 523: 1-19

 Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; et al. (2011). Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules. METHODS IN ENZYMOLOGY. 487: 545-574


Recommended Readings: Peter Reddien, Ph.D. Friday September 28, 2018

Friday Lectures

Friday, September 28, 2018  3:45 p.m.

Caspary Auditorium

Peter Reddien Ph.D.

Professor and Associate Department Head

Department of Biology

Massachusetts Institute of Technology

How Stem Cells and Positional Information Lead to Planarian Regeneration

Recommended Readings:

Science News

Lisa Girard. A blueprint for regeneration. March 15, 2018. MIT News

Empirical Articles

Fincher, Christopher T.; Wurtzel, Omri; de Hoog, Thom; et al. (2018). Cell type transcriptome atlas for the planarian Schmidtea mediterranea. SCIENCE.  360 (6391): 874-+

Atabay KD, LoCascio SA, de Hoog T, Reddien PW. (2018). Self-organization and progenitor targeting generate stable patterns in planarian regeneration. SCIENCE. 360 (6387):404-409

Scimone, M. Lucila; Cote, Lauren E.; Reddien, Peter W. (2017). Orthogonal muscle fibres have different instructive roles in planarian regeneration. NATURE. 551 (7682): 623-+  

Raz, Amelie A.; Srivastava, Mansi; Salvamoser, Ranja; et al. (2017). Acoel regeneration mechanisms indicate an ancient role for muscle in regenerative patterning. NATURE COMMUNCATIONS. 8

Wurtzel, Omri; Oderberg, Isaac M.; Reddien, Peter W. (2017). Planarian Epidermal Stem Cells Respond to Positional Cues to Promote Cell-Type Diversity. DEVELOPMENTAL CELL. 40 (5): 491-504  

Scimone, M. Lucila; Kravarik, Kellie M.; Lapan, Sylvain W.; et al. (2014). Neoblast Specialization in Regeneration of the Planarian Schmidtea mediterranea. STEM CELLS REPORTS. 3 (2): 339-352

van Wolfswinkel, Josien C.; Wagner, Daniel E.; Reddien, Peter W. (2014). Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment. CELL STEM CELL. 15 (3): 326-339

Wagner, Daniel E.; Wang, Irving E.; Reddien, Peter W. (2011). Clonogenic Neoblasts Are Pluripotent Adult Stem Cells That Underlie Planarian Regeneration. SCIENCE. 332 (6031): 811-816  

Review Paper

Tanaka, Elly M.; Reddien, Peter W. (2011). The Cellular Basis for Animal Regeneration. DEVELOPMENTAL CELL. 21 (1): 172-185

Reddien, Peter W. (2011). Constitutive gene expression and the specification of tissue identity in adult planarian biology.  TRENDS IN GENETICS. 27 (7): 277-285  

Book Chapter

Wang IE, Wagner DE, Reddien PW. (2018). Clonal Analysis of Planarian Stem Cells by Subtotal Irradiation and Single-Cell Transplantation. Planarian Regeneration. 1774:479-495

Recommended Readings: Erich Jarvis, Ph.D. Friday March 2nd, 2018

Friday Lectures

Friday, March 2nd, 2018  3:45 p.m.

Caspary Auditorium

Erich Jarvis, Ph.D.

Professor and Head

Laboratory of Neurogenetics of Language

The Rockefeller University

Insights from non-human animals into the neurobiology of spoken language 

Recommended Readings:

Science News

Jordana Cepelewicz. In Birds’ Songs, Brains and Genes, He Finds Clues to Speech. (2018, Jan 30). Quanta Magazine

Empirical Articles

Lei, Huimeng; Yan, Zhangming; Sun, Xiaohong; et al. (2017). Axon guidance pathways served as common targets for human speech/language evolution and related disorders. BRAIN AND LANGUAGE. 174: 1-8

Korlach, Jonas; Gedman, Gregory; Kingan, Sarah B.; et al. (2017). De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. GIGASCIENCE. 6 (10)

Chabout, Jonathan; Jones-Macopson, Joshua; Jarvis, Erich D. (2017). Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS. 123  

Chabout, Jonathan; Sarkar, Abhra; Patel, Sheel R.; et al. (2016). A Foxp2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice. FRONTIERS IN BEHAVIORAL NEUROSCIENCE. 10   

Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; et al. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. SCIENCE. 346 (6215): 1320-1331

Pfenning, Andreas R.; Hara, Erina; Whitney, Osceola; et al. (2014). Convergent transcriptional specializations in the brains of humans and song-learning birds. SCIENCE. 346 (6215): 1333-+

Review Papers

Theofanopoulou, Constantina; Boeckx, Cedric; Jarvis, Erich D. (2017). A hypothesis on a role of oxytocin in the social mechanisms of speech and vocal learning. PNAS. 284 (1861)

Simonyan, Kristina; Horwitz, Barry; Jarvis, Erich D. (2012). Dopamine regulation of human speech and bird song: A critical review. BRAIN AND LANGUAGE. 122 (3): 142-150

Book Chapter

Jarvis, Erich D. (2016). Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. ANNUAL REVIEW OF ANIMAL BIOSCIENCES. 4: 45-59


Recommended Readings: Vamsi Mootha, M.D. Friday November 17th, 2017

Friday Lectures

Friday, November 17, 2017  3:45 p.m.

Caspary Auditorium

Vamsi Mootha, M.D.


Systems Biology and Medicine

Harvard Medical School and Massachusetts General Hospital

Genome-scale Approaches to Mitochondrial Disease

Recommended Readings:

Science News

Howard Hughes Medical Institute. (2017, May 8). Low oxygen reverses mitochondrial disease in mice. ScienceDaily

Empirical Articles

Ferrari, Michele; Jain, Isha H.; Goldberger, Olga; et al. (2017). Hypoxia treatment reverses neurodegenerative disease in a mouse model of Leigh syndrome. PNAS. 114 (21): E4241-E4250

Jain, Isha H.; Zazzeron, Luca; Goli, Rahul; et al. (2016). Hypoxia as a therapy for mitochondrial disease. SCIENCE. 352 (6281): 54-61  

Titov, Denis V.; Cracan, Valentin; Goodman, Russell P.; et al. (2016). Complementation of mitochondrial electron transport chain by manipulation of the NAD(+)/NADH ratio. SCIENCE. 352 (6282): 231-235

Calvo, Sarah E.; Clauser, Karl R.; Mootha, Vamsi K. (2016). MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.  NUCLEIC ACIDS RESEARCH. 44 (D1): D1251-D1257

Lake, Nicole J.; Bird, Matthew J.; Isohanni, Pirjo; et al. (2015). Leigh Syndrome: Neuropathology and Pathogenesis. JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY. 74 (6): 482-492  

Lieber, Daniel S.; Calvo, Sarah E.; Shanahan, Kristy; et al. (2013). Targeted exome sequencing of suspected mitochondrial disorders. NEUROLOGY. 80 (19): 1762-1770

Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; et al. (2012). Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing. SCIENCE TRANSLATIONAL MEDICINE. 4 (118)

Calvo, S; Jain, M; Xie, XH; et al. (2006). Systematic identification of human mitochondrial disease genes through integrative genomics. NATURE GENETICS. 38 (5): 576-582

Review Papers

Kamer, Kimberli J.; Mootha, Vamsi K. (2015). The molecular era of the mitochondrial calcium uniporter.  NATURE REVIEWS MOLECULAR CELL BIOLOGY. 16 (9): 545-553

Vafai, Scott B.; Mootha, Vamsi K. (2012). Mitochondrial disorders as windows into an ancient organelle. NATURE. 491 (7424): 374-383

Book Chapter

Calvo, Sarah E.; Mootha, Vamsi K. (2010). The Mitochondrial Proteome and Human Disease. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 11: 25-44


Recommended Readings: Jack W. Szostak, Ph.D., Friday April 24, 2017

Friday Lectures

Friday, April 28, 2017   3:45 p.m.

Caspary Auditorium

Jack W. Szostak, Ph.D.

Professor of Genetics, Chemistry and Chemical Biology

Harvard University

Distinguished Investigator

Department of Molecular Biology and Center for Computational and Integrative Biology

Massachusetts General Hospital

The Surprising Chemistry of Nonenzymatic RNA Replication

Recommended Readings:

Li, Li; Prywes, Noam; Tam, Chun Pong; et al. (2017). Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139(5): 1810-1813

Prywes, Noam; Blain, J. Craig; Del Frate, Francesca; et al. (2016). Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides. ELIFE.  Article Number: e17756


Adamala, Katarzyna; Szostak, Jack W. (2013). Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells. SCIENCE. 342(6162): 1098-1100

Jack W Szostak. (2012). The eightfold path to non-enzymatic RNA replication. Journal of systems chemistry. 3(2) DOI: 10.1186/1759-2208-3-2

Wochner, Aniela; Attwater, James; Coulson, Alan; et al. (2011). Ribozyme-Catalyzed Transcription of an Active Ribozyme. SCIENCE. 332(6026): 209-212


Recommended Readings: David Kingsley, Ph.D.

Friday Lecture Series

The Fairfield Osborn Memorial Lecture

Fishing for the Secrets of Vertebrate Evolution

David Kingsley, Ph.D., professor, developmental biology, Stanford University;

investigator, Howard Hughes Medical Institute

April 18, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

han, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr., G., Shapiro, M. D., Brady, S. D., . . . Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a pitxl enhancer. Science, 327(5963), 302-305

Haussler, D., O’Brien, S. J., Ryder, O. A., Keith Barker, F., Clamp, M., Crawford, A. J., . . . Turner, S. (2009). Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6), 659-674

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., . . . Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61

Kingsley, D. M., Zhu, B., Osoegawa, K., De Jong, P. J., Schein, J., Marra, M., . . . Myers, R. (2004). New genomic tools for molecular studies of evolutionary change in threespine sticklebacks. Behaviour, 141(11-12), 1331-1344

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., . . . Haussler, D. (2011). Three periods of regulatory innovation during vertebrate evolution. Science, 333(6045), 1019-1024

Shapiro, M. D., Bell, M. A., & Kingsley, D. M. (2006). Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 103(37), 13753-13758


Recommended Readings: Ila R. Fiete, Ph.D. April 7

Monday, April 7, 2014
4:00 p.m., Carson Family Auditorium

Ila R. Fiete, Ph.D.
Associate Professor, Department of Neuroscience
Fellow, The Institute for Neuroscience
The University of Texas at Austin

Neural Codes and Dynamics for Representation and Memory

Recommended Readings:

Empirical Papers

Burak, Y., & Fiete, I. R. (2012). Fundamental limits on persistent activity in networks of noisy neurons. Proceedings of the National Academy of Sciences, 109(43), 17645–17650. doi:10.1073/pnas.1117386109

Fiete, I. R., Burak, Y., & Brookings, T. (2008). What grid cells convey about rat location. The Journal of Neuroscience, 28(27), 6858–6871. doi:10.1523/JNEUROSCI.5684-07.2008

Sreenivasan, S., & Fiete, I. (2011). Grid cells generate an analog error-correcting code for singularly precise neural computation. Nature Neuroscience, 14(10), 1330–1337. doi:10.1038/nn.2901

Yoon, K., Buice, M. a, Barry, C., Hayman, R., Burgess, N., & Fiete, I. R. (2013). Specific evidence of low-dimensional continuous attractor dynamics in grid cells. Nature Neuroscience, 16(8), 1077–1084. doi:10.1038/nn.3450

Review Articles

Burak, Y. (2006). Do We Understand the Emergent Dynamics of Grid Cell Activity? Journal of Neuroscience, 26(37), 9352–9354. doi:10.1523/JNEUROSCI.2857-06.2006

Recommended Readings: Eran Segal Ph.D. October 9, 2013

Special Seminar Series
Deciphering the Code of Gene Regulation
Eran Segal, Ph.D.
Incumbent of the Soretta and Henry Shapiro Career Development Chair
Department of Computer Science and Applied Mathematics
4:00 p.m. – 5:00 p.m. Carson Family Auditorium (CRC)
Refreshments: 3:45 p.m. – 4:00 p.m., Lower Level Greenberg Building (CRC)

Recommended Readings:

Review Papers

Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013). Eukaryotic transcriptional dynamics: from single molecules to cell populationsNature Reviews Genetics14(8), 572-584. doi: 10.1038/nrg3484.

De Smet, R., & Marchal, K. (2010). Advantages and limitations of current network inference methodsNature Reviews Microbiology8(10), 717-729. doi: 10.1038/nrmicro2419

Segal, E., & Widom, J. (2009). From DNA sequence to transcriptional behaviour: a quantitative approachNature Reviews Genetics10(7), 443-456. doi: 10.1038/nrg2591

Jiang, C., & Pugh, B. F. (2009). Nucleosome positioning and gene regulation: advances through genomicsNature Reviews Genetics10(3), 161-172. doi: 10.1038/nrg2522

Empirical Articles

Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … & Segal, E. (2008). The DNA-encoded nucleosome organization of a eukaryotic genomeNature458(7236), 362-366. doi: 10.1038/nature07667

Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., … & Zhao, K. (2008). Dynamic regulation of nucleosome positioning in the human genomeCell132(5), 887-898. doi: 10.1016/j.cell.2008.02.022

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., … & Widom, J. (2006). A genomic code for nucleosome positioningNature,442(7104), 772-778. doi: 10.1038/nature04979

Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics34(2), 166-176. doi: 10.1038/ng1165

Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., & Sidow, A. (2011). Determinants of nucleosome organization in primary human cellsNature474(7352), 516-520. doi: 10.1038/nature10002

The State of Vaccine Development: Toughest Problems Remain Unsolved

Accelerating Next-Generation Vaccine Development for Global Disease Prevention

Koff, W. C. et all    Science  v. 340, 2013

Recent technological advances in molecular genetics, molecular and cellular immunology, structural biology, bioinformatics, computational biology, nanotechnology, formulation methods, and systems biology are ushering in a new era of discovery. However, translation of these advances into vaccines remains impeded by major gaps in our knowledge of human immune responses.