Recommended Readings: Bing Ren, Ph.D., Friday May 19th, 2017

Friday Lectures

Friday, May 19, 2017  3:45 p.m.

Caspary Auditorium

Bing Ren, Ph.D.

Professor of Cellular and Molecular Medicine and Director of the Center for Epigenomics

University of California, San Diego

Organization and Regulation of the Human Genome

Recommended Readings:

Schmitt, Anthony D.; Hu, Ming; Ren, Bing (2016). Genome-wide mapping and analysis of chromosome architecture. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 17(12): 743-755

Dixon, Jesse R.; Gorkin, David U.; Ren, Bing (2016). Chromatin Domains: The Unit of Chromosome Organization. MOLECULAR CELL. 62(5): 668-680

Zuin, Jessica; Dixon, Jesse R.; van der Reijden, Michael I. J. A.; et al. (2014). Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 111(3): 996-1001

Smallwood, Andrea; Ren, Bing (2013). Genome organization and long-range regulation of gene expression by enhancers. CURRENT OPINION IN CELL BIOLOGY. 25(3): 387-394

Dunham, Ian; Kundaje, Anshul; Aldred, Shelley F.; et al. (2012). An integrated encyclopedia of DNA elements in the human genome. NATURE. 489(7414): 57-74


Recommended Readings: Michael P. Rout, Ph.D., Monday May 15th, 2017

Monday Lectures

Monday, May 15, 2017  3:45 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.

 Professor and Head,

Laboratory of Cellular and Structural Biology

The Rockefeller University

Getting the Hole Picture: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Timney, Benjamin L.; Raveh, Barak; Mironska, Roxana; et al. (2016). Simple rules for passive diffusion through the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 215(1): 57-76

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA . 113(18): E2489-E2497

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; et al. (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. CELL. 167(5): 1215-+

Tu, Li-Chun; Fu, Guo; Zilman, Anton; et al. (2013). Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins.EMBO JOURNAL. 32(24): 3220-3230

Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; et al. (2012). Structure-function mapping of a heptameric module in the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 196(4): 419-434

Grossman, Einat; Medalia, Ohad; Zwerger, Monika (2012). Functional Architecture of the Nuclear Pore Complex. ANNUAL REVIEW OF BIOPHYSICS. 41: 557-584

Recommended Readings: James P. Allison, Ph.D., Friday May 12th, 2017

Friday Lectures

Friday, May 2, 2017  3:45 p.m.

Caspary Auditorium

James P. Allison, Ph.D.

Professor and Vivian L. Smith Distinguished Chair of Immunology,

Executive Director of the Immunotherapy Platform

The University of Texas MD Anderson Cancer Center

Immune Checkpoint Blockade in Cancer Therapy: New Insights, Opportunities, and Prospects for a Cure

Recommended Readings:

Hazarika M; Chuk MK; Theoret MR; et al. (2017). U.S. FDA Approval Summary: Nivolumab for Treatment of Unresectable or Metastatic Melanoma Following Progression on Ipilimumab.CLINICAL CANCER RESEARCH. doi: 10.1158/1078-0432

Medina, Patrick J.; Adams, Val R. (2016). PD-1 Pathway Inhibitors: Immuno-Oncology Agents for Restoring Antitumor Immune Responses. PHARMACOTHERAPY. 36(3): 317-334

Sharma, Padmanee; Allison, James P. (2015). Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential. CELL. 161(2): 205-214

Robert, Caroline; Schachter, Jacob; Long, Georgina V.; et al. (2015). Pembrolizumab versus Ipilimumab in Advanced Melanoma. NEW ENGLAND JOURNAL OF MEDICINE    372(26): 2521-2532

Sharma, Padmanee; Allison, James P. (2015). The future of immune checkpoint therapy. SCIENCE. 348(6230): 56-61

Gubin, Matthew M.; Zhang, Xiuli; Schuster, Heiko; et al. (2014). Checkpoint blockage cancer immunotherapy targets tumour-specific mutant antigens. NATURE. 515(7528): 577-+

Lipson, Evan J.; Drake, Charles G. (2011). Ipilimumab: An Anti-CTLA-4 Antibody for Metastatic Melanoma. CLINICAL CANCER RESEARCH. 17(22): 6958-6962


Recommended Readings: Sue Biggins, Ph.D., Friday May 5th, 2017

Friday Lectures

Friday, May 5th, 2017   3:45 p.m.

Caspary Auditorium

Sue Biggins, Ph.D.

Member and Associate Director

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

Sensing Tension at Kinetochores

Recommended Readings: 

Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. CELL. 165(6): 1428-1439

Musacchio, Andrea (2015). The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics. CURRENT BIOLOGY.  25(20): R1002-R1018

Biggins, Sue (2015). Under tension: Kinetochores and Basic Research. GENETICS. 200(3): 681-682

London, Nitobe; Biggins, Sue (2014). Signalling dynamics in the spindle checkpoint response. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 15 (11): 735-747

Sarangapani, Krishna K.; Duro, Eris; Deng, Yi; et al. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. SCIENCE. 346(6206): 248-251

Biggins, Sue (2013). The Composition, Functions, and Regulation of the Budding Yeast Kinetochore. GENETICS. 194(4): 817-846

Gonen, Shane; Akiyoshi, Bungo; Iadanza, Matthew G.; et al. (2012). The structure of purified kinetochores reveals multiple microtubule-attachment sites. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 19( 9): 925-929







Recommended Readings: Alipasha Vaziri, Ph.D., Monday May 1, 2017

Monday Lectures

Monday, May 1, 2017  3:45 p.m.

Carson Family Auditorium

Alipasha Vaziri, Ph.D.

Associate Professor and Head,

Laboratory of Neurotechnology and Biophysics

The Rockefeller University

Optical Tools for Unraveling Whole-brain Neuronal Circuit Dynamics Underlying Behavior

Recommended Readings:

Prevedel, Robert; Verhoef, Aart J.; Pernia-Andrade, Alejandro J.; et al. (2016).  Fast volumetric calcium imaging across multiple cortical layers using sculpted light. NATURE METHODS. 13(12): 1021-U215

Rupprecht, Peter; Prevedel, Robert; Groessl, Florian; et al. (2015). Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. BIOMEDICAL OPTICS EXPRESS. 6(2): 353-368

Prevedel, Robert; Yoon, Young-Gyu; Hoffmann, Maximilian; et al. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. NATURE METHODS. 11(7): 727-U161

Schrodel, Tina; Prevedel, Robert; Aumayr, Karin; et al. (2013). Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. NATURE METHODS. 10(10)1013-+

Fenno, Lief; Yizhar, Ofer; Deisseroth, Karl. (2011). The Development and Application of Optogenetics.  ANNUAL REVIEW OF NEUROSCIENCE. 34: 389-412

Andrasfalvy, Bertalan K.; Zemelman, Boris V.; Tang, Jianyong; et al. (2010).Two-photon single-cell optogenetic control of neuronal activity by sculpted light. PNAS. 107(26): 11981-11986







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: Edith Heard, Ph.D., Friday, April 21, 2017

Friday Lectures

Friday, April 21, 2017   3:45 p.m.

Caspary Auditorium

Edith Heard, Ph.D.

Professor and Chair, Epigenetics and Cellular Memory, Collège de France

Director, Department of Genetics and Developmental Biology

Institut Curie

The Epigenetic Dynamics of X-chromosome Inactivation: Fine-tuning Gene Dosage during Development

Recommended Readings:

da Rocha, Simao T.; Heard, Edith (2017). Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 197-204

Borensztein, Maud; Syx, Laurene; Ancelin, Katia; et al. (2017). Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 226-+

Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; et al. (2016). Structural organization of the inactive X chromosome in the mouse. NATURE. 535(7613): 575-+

Wu, Hao; Luo, Junjie; Yu, Huimin; et al. (2014). Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease. NEURON. 81(1): 103-119

Gendrel, Anne-Valerie; Heard, Edith (2014). Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation.  ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 561-580

Nora, Elphege P.; Lajoie, Bryan R.; Schulz, Edda G.; et al. (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre. NATURE. 485(7398): 381-385

Recommended Readings: Vincent A. Fischetti, Ph.D. April 24, 2017

Monday Lectures

Monday, April 17, 2017  3:45 p.m.

Carson Family Auditorium

Vincent A. Fischetti, Ph.D.

Professor and Head,

Laboratory of Bacterial Pathogenesis and Immunology

The Rockefeller University

Exploiting phage evolution for the development of novel therapeutics

Recommended Readings:

David Bautz. March 20th 2017. CFRX: Phase 2 Trial of CF-301 to Initiate in mid-2017.

Czaplewski, Lloyd; Bax, Richard; Clokie, Martha; et al. (2016). Alternatives to antibiotics-a pipeline portfolio review. LANCET INFECTIOUS DISEASES. 16(2): 239-251

Diez-Martinez, Roberto; De Paz, Hector D.; Garcia-Fernandez, Esther; et al. (2015). A novel chimeric phage lysin with high in vitro and in vivo bactericidal activity against Streptococcus pneumoniae. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 70(6): 1763-1773

Bikard, David; Euler, Chad W.; Jiang, Wenyan; et al. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. NATURE BIOTECHNOLOGY. 32(11): 1146-1150

Schuch, Raymond; Lee, Han M.; Schneider, Brent C.; et al. (2014). Combination Therapy With Lysin CF-301 and Antibiotic Is Superior to Antibiotic Alone for Treating Methicillin-Resistant Staphylococcus aureus-Induced Murine Bacteremia. JOURNAL OF INFECTIOUS DISEASES. 209(9): 1469-1478

Pastagia, Mina; Schuch, Raymond; Fischetti, Vincent A.; et al. (2013). Lysins: the arrival of pathogen-directed anti-infectives. JOURNAL OF MEDICAL MICROBIOLOGY. 62:1506-1516

Gilmer, Daniel B.; Schmitz, Jonathan E.; Euler, Chad W.; et al. (2013). Novel Bacteriophage Lysin with Broad Lytic Activity Protects against Mixed Infection by Streptococcus pyogenes and Methicillin-Resistant Staphylococcus aureus. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. 57(6): 2743-2750


Recommended Readings: Peter Campbell, Ph.D. March 31, 2017

Friday Lectures

Friday, March 31, 2017   3:45 p.m.

Caspary Auditorium

Peter Campbell, Ph.D.

Head of Cancer Genetics and Genomics,

The Wellcome Trust Sanger Institute

Interrogating the Architecture of Cancer Genomes

Recommended Readings:

The Past, Present and Future of Genome Sequencing

Forbes, Simon A.; Beare, David; Gunasekaran, Prasad; et al. (2015). COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. NUCLEIC ACIDS RESEARCH. 43(D1): D805-D811

Martincorena, Inigo; Campbell, Peter J. (2015). Somatic mutation in cancer and normal cellsSCIENCE.  349(6255): 1483-1489

Alioto, Tyler S.; Buchhalter, Ivo; Derdak, Sophia; et al. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencingNATURE COMMUNICATIONS. 6(10001)

Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C.; et al. (2013). Signatures of mutational processes in human cancer. NATURE. 500(7463): 415-+

Yates, Lucy R.; Campbell, Peter J. (2012). Evolution of the cancer genome. NATURE REVIEWS GENETICS. 13(11): 795-806  



Recommended Readings: Jon Clardy, Ph.D. March 24, 2017

Friday Lectures

Friday, March 24, 2017   3:45 p.m.

Caspary Auditorium

Jon Clardy, Ph.D.

Hsien Wu and Daisy Yen Wu Professor,

Department of Biological Chemistry and Molecular Pharmacology

The Rockefeller University

Small Molecule Modulators of Multilateral Symbioses

Recommended Readings:

Pupo, Monica T.; Currie, Cameron R.; Clardy, Jon (2017). Microbial Symbionts of Insects are the Focus of the First International Cooperative Biodiversity Group (ICBG) in Brazil. JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY. 28 (3): 393-401

Ruzzini, Antonio C.; Clardy, Jon (2016). Gene Flow and Molecular Innovation in Bacteria. CURRENT BIOLOGY. 26(18)R859-R864

Cantley, Alexandra M.; Clardy, Jon (2015). Animals in a bacterial world: opportunities for chemical ecology.  NATURAL PRODUCT REPORTS. 32(7): 888-892

Sit, Clarissa S.; Ruzzini, Antonio C.; Van Arnam, Ethan B.; et al. (2015). Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112(43)13150-13154

Ramadhar, Timothy R.; Beemelmanns, Christine; Currie, Cameron R.; et al. (2014). Bacterial symbionts in agricultural systems provide a strategic source for antibiotic discover. JOURNAL OF ANTIBIOTICS. 67(1): 53-58

Crawford, Jason M.; Clardy, Jon (2011). Bacterial symbionts and natural products. CHEMICAL COMMUNICATIONS. 47(27): 7559-7566

Oh, Dong-Chan; Poulsen, Michael; Currie, Cameron R.; et al. (2009). Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis.  NATURE CHEMICAL BIOLOGY. 5(6) 391-393