Recommended Readings: David Pellman, M.D. Friday June 1, 2018

Friday Lectures

Friday, June 1, 2018  3:45 p.m.

Caspary Auditorium

David Pellman M.D.

Margaret M. Dyson Professor

Department of Cell Biology

Harvard Medical School

Mechanisms of Rapid Genome Evolution

Recommended Readings:

Science News

Dana-Farber Cancer Institute. Researchers identify origin of chromosomal oddity in some cancer cells. May 27, 2015. EurekAlert

Empirical Articles

Marteil, Gaelle; Guerrero, Adan; Vieira, Andre F.; et al. (2018). Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation. NATURE COMMUNICATIONS. 9    

Zhang, Cheng-Zhong; Spektor, Alexander; Cornils, Hauke; et al. (2015). Chromothripsis from DNA damage in micronuclei. NATURE. 522 (7555): 179-+

Selmecki, Anna M.; Maruvka, Yosef E.; Richmond, Phillip A.; et al. (2015). Polyploidy can drive rapid adaptation in yeast. NATURE. 519 (7543): 349-+

Crasta, Karen; Ganem, Neil J.; Dagher, Regina; et al. (2012). DNA breaks and chromosome pulverization from errors in mitosis. NATURE. 482 (7383): 53-U70

Carter, Scott L.; Cibulskis, Kristian; Helman, Elena; et al. (2012). Absolute quantification of somatic DNA alterations in human cancer. NATURE BIOTECHNOLOGY. 30 (5): 413-+

Ganem, Neil J.; Godinho, Susana A.; Pellman, David. (2009). A mechanism linking extra centrosomes to chromosomal instability. NATURE. 460 (7252): 278-U146

Review Paper

Zhang, Cheng-Zhong; Leibowitz, Mitchell L.; Pellman, David. (2013). Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. GENES AND DEVELOPMENT. 27 (23): 2513-2530   

Gordon, David J.; Resio, Benjamin; Pellman, David. (2012). Causes and consequences of aneuploidy in cancer. NATURE REVIEWS GENETICS. 13 (3): 189-203

Book Chapter

Leibowitz, Mitchell L.; Zhang, Cheng-Zhong; Pellman, David. (2015). Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. ANNUAL REVIEW OF GENETICS. 49: 183-211

Recommended Readings: Stephen Elledge, Ph.D. Friday May 18, 2018

Friday Lectures

Friday, May 18, 2018  3:45 p.m.

Caspary Auditorium

Stephen J. Elledge Ph.D.

Gregor Mendel Professor

Department of Genetics

Harvard Medical School

Microgenetics: What We Can Learn About Protein Degradation from Bits of Genes

Recommended Readings:

Science News

Your viral infection history in a single drop of blood. June 4, 2015. ScienceDaily

Empirical Articles

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z.; et al. (2018). Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. CELL. 173 (2): 499-+

Liao, Sida; Davoli, Teresa; Leng, Yumei; et al. (2017). A genetic interaction analysis identifies cancer drivers that modify EGFR dependency. GENES AND DEVELOPMENT. 31 (2): 184-196

Xu, George J.; Kula, Tomasz; Xu, Qikai; et al. (2015). Comprehensive serological profiling of human populations using a synthetic human virome. SCIENCE. 348 (6239)

Emanuele, Michael J.; Elia, Andrew E. H.; Xu, Qikai; et al. (2011). Global Identification of Modular Cullin-RING Ligase Substrates. CELL. 147 (2): 459-474

Larman, H. Benjamin; Zhao, Zhenming; Laserson, Uri; et al. (2011). Autoantigen discovery with a synthetic human peptidome. NATURE BIOTECHNOLOGY. 29 (6): 535-U101

Yen, Hsueh-Chi Sherry; Xu, Qikai; Chou, Danny M.; et al. (2008). Global Protein Stability Profiling in Mammalian Cells. SCIENCE. 322 (5903): 918-923

Yen, Hsueh-Chi Sherry; Elledge, Stephen J. (2008). Identification of SCF Ubiquitin Ligase Substrates by Global Protein Stability Profiling. SCIENCE. 322 (5903): 923-929

Review Paper

Ciccia, Alberto; Elledge, Stephen J. (2010). The DNA Damage Response: Making It Safe to Play with Knives. MOLECULAR CELL. 40 (2): 179-204

Luo, Ji; Solimini, Nicole L.; Elledge, Stephen J. (2009). Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction. CELL. 136 (5): 823-837


Recommended Readings: Stephen Goff, Ph.D. Friday May 11, 2018

Friday Lectures

Friday, May 11, 2018  3:45 p.m.

Caspary Auditorium

Stephen Goff Ph.D.

Higgins Professor

Department of Biochemistry and Molecular Biophysics

Columbia University College of Physicians and Surgeons

Quiet, Please: Silencing Retroviral DNAs

Recommended Readings:

Empirical Articles

Lee, Andreia; CingOz, Oya; Sabo, Yosef; et al. (2018). Characterization of interaction between Trim28 and YY1 in silencing proviral DNA of Moloney murine leukemia virus. VIROLOGY. 516: 165-175

Geis, Franziska K.; Galla, Melanie; Hoffmann, Dirk; et al. (2017). Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells. RETROVIROLOGY. 14

Wang, Gary Z.; Goff, Stephen P. (2017). Transcriptional Silencing of Moloney Murine Leukemia Virus in Human Embryonic Carcinoma Cells. JOURNAL OF VIROLOGY. 91 (1)

Wang, Cheng; Goff, Stephen P. (2017). Differential control of retrovirus silencing in embryonic cells by proteasomal regulation of the ZFP809 retroviral repressor. PNAS. 114 (6): E922-E930

Wang, Gary Z.; Wang, Ying; Goff, Stephen P. (2016). Histones Are Rapidly Loaded onto Unintegrated Retroviral DNAs Soon after Nuclear Entry. CELL HOST MICROBE.  20 (6): 798-809

Griffin, Daniel O.; Goff, Stephen P. (2015). HIV-1 Is Restricted prior to Integration of Viral DNA in Primary Cord-Derived Human CD34(+) Cells. JOURNAL OF VIROLOGY. 89 (15): 8096-8100

Yang, Bin Xia; El Farran, Chadi A.; Guo, Hong Chao; et al. (2015). Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells. CELL. 163 (1): 230-245

Review Paper

Schlesinger, Sharon; Goff, Stephen P. (2015). Retroviral Transcriptional Regulation and Embryonic Stem Cells: War and Peace. MOLECULAR AND CELLULAR BIOLOGY. 35 (5): 770-777

Studamire, Barbara; Goff, Stephen P. (2010). Interactions of Host Proteins with the Murine Leukemia Virus Integrase. VIRUSES. 2 (5): 1110-1145

Recommended Readings: Michael P. Rout, Ph.D. Monday April 2, 2018

Monday Lectures

Monday, April 2, 2018  4:00 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.


Laboratory of Cellular and Structural Biology

The Rockefeller University

A Hole New View: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Science News

March 15, 2018. Scientists map the portal to the cell’s nucleus. Science Daily.

Empirical Articles

Upla, Paula; Kim, Seung Joong; Sampathkumar, Parthasarathy; et al. (2017). Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. STRUCTURE. 25 (3): 434-445

Hayama, Ryo; Rout, Michael P.; Fernandez-Martinez, Javier. (2017). The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. CURRENT OPINION IN CELL BIOLOGY. 46: 110-118

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-+

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PNAS. 113 (18): E2489-E2497

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; et al. (2014). Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. MOLECULAR & CELLULAR PROTEOMICS. 13 (11): 2911-2926

Wente, Susan R.; Rout, Michael P. (2010). The Nuclear Pore Complex and Nuclear Transport. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 2 (10)

Review Papers

Field, Mark C.; Koreny, Ludek; Rout, Michael P. (2014). Enriching the Pore: Splendid Complexity from Humble Origins. TRAFFIC. 15 (2): 141-156

Strambio-De-Castillia, Caterina; Niepel, Mario; Rout, Michael P. (2010). The nuclear pore complex: bridging nuclear transport and gene regulation. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 11 (7): 490-501

Book Chapter

Jovanovic-Talisman, Tijana; Chait, Brian T.; Rout, Michael P. (2014). NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport. METHODS IN CELL BIOLOGY. 122: 379-393  

Recommended Readings: Edward H. Egelman, Ph.D. Friday January 19th, 2018

Friday Lectures

Friday, January 19, 2018  3:45 p.m.

Caspary Auditorium

Edward Egelman, Ph.D.

Harrison Distinguished Professor

Biochemistry and Molecular Genetics

University of Virginia Medical School

Cryo-EM of Protein and Nucleoprotein Polymers at Near-Atomic Resolution

Recommended Readings:

Science News

Kenny Walter. Virus Holds Key to Durable Material. (2017, Jul 20). Virus Holds Key to Durable Material. R&D Magazine

Empirical Articles

Egelman, Edward H. (2017). Cryo-EM of bacterial pili and archaeal flagellar filaments. CURRENT OPINION IN STRUCTURAL BIOLOGY. 46: 31-37

Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra; et al. (2017). A structural model of flagellar filament switching across multiple bacterial species. NATURE COMMUNICATIONS. 8: 960

Wang, Fengbin; Coureuil, Mathieu; Osinski, Tomasz; et al. (2017). Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. STRUCTURE. 25 (9): 1423-+

Kasson, Peter; DiMaio, Frank; Yu, Xiong; et al. (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. ELIFE. 6  

Kolappan, Subramania; Coureuil, Mathieu; Yu, Xiong; et al. (2016). Structure of the Neisseria meningitidis Type IV pilus. NATURE COMMUNICATIONS. 7: 13015

Braun, Tatjana; Vos, Matthijn R.; Kalisman, Nir; et al. (2016). Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. PNAS. 113 (37): 10352-10357

Egelman, Edward H. (2016). The Current Revolution in Cryo-EM. BIOPHYSICAL JOURNAL. 110 (5): 1008-1012

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; et al. (2015). De novo protein structure determination from near-atomic-resolution cryo-EM maps. NATURE METHODS. 12 (4): 335-U84

DiMaio, Frank; Yu, Xiong; Rensen, Elena; et al. (2015). A virus that infects a hyperthermophile encapsidates A-form DNA. SCIENCE. 348 (6237): 914-917

Review Papers

Egelman, Edward H. (2015). Three-dimensional reconstruction of helical polymers. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 581: 54-58

Recommended Readings: Joan A. Steitz, Ph.D. Friday January 5th, 2018

Friday Lectures

Friday, January 5, 2018  3:45 p.m.

Caspary Auditorium

Joan A. Steitz, Ph.D.

Sterling Professor

Molecular Biophysics and Biochemistry

Yale University

RNA Triple Helices in Cellular and Viral Biology


Recommended Readings:

Science News

Michael White. Oct 17, 2017. The Women Who Should Win the Nobel Prize—but Haven’t. PacificStandard

Empirical Articles

Brown, Jessica A.; Kinzig, Charles G.; DeGregorio, Suzanne J.; et al. (2016). Methyltransferase-like protein 16 binds the 3 ‘-terminal triple helix of MALAT1 long noncoding RNA. PNAS. 113 (49): 14013-14018

Brown, Jessica A.; Kinzig, Charles G.; Degregorio, Suzanne J.; et al. (2016). Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA. 22 (5): 743-749

Brown, Jessica A.; Bulkley, David; Wang, Jimin; et al. (2014). Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 21 (7): 633-640

Guo, Yang Eric; Riley, Kasandra J.; Iwasaki, Akiko; et al. (2014). Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. MOLECULAR CELL. 54 (1): 67-79

Brown, Jessica A.; Valenstein, Max L.; Yario, Therese A.; et al. (2012). Formation of triple-helical structures by the 3 ‘-end sequences of MALAT1 and MEN beta noncoding RNAs. PNAS. 109 (47): 19202-19207

Borah, Sumit; Darricarrere, Nicole; Darnell, Alicia; et al. (2011). A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS PATHOGENS. 7 (10)

Mitton-Fry, Rachel M.; DeGregorio, Suzanne J.; Wang, Jimin; et al. (2010). Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. SCIENCE. 330 (6008): 1244-1247

Review Papers

Tycowski, Kazimierz T.; Guo, Yang Eric; Lee, Nara; et al. (2015). Viral noncoding RNAs: more surprises. GENES & DEVELOPMENT. 29 (6): 567-584

Cech, Thomas R.; Steitz, Joan A. (2014). The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones. CELL. 157 (1): 77-94

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: Gregory M. Alushin, Ph.D. Monday November 13th, 2017

Monday Lectures

Monday, November 13, 2017  3:45 p.m.

Carson Family Auditorium

Gregory M. Alushin, Ph.D.

Assistant Professor and Head

Laboratory of Structural Biophysics and Mechanobiology

The Rockefeller University

Cytoskeletal Structural Plasticity in Force Generation and Mechanosensation

Recommended Readings:

Empirical Articles

Omabegho T, Gurel PS, Cheng CY, Kim LY, Ruijgrok PV, Das R, Alushin GM, Bryant Z. (2017). Controllable molecular motors engineered from myosin and RNA. NATURE NANOTECHNOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Swaminathan V, Alushin GM, Waterman CM. (2017). Mechanosensation: A Catch Bond That Only Hooks One Way. CURRENT BIOLOGY. 27 (21):R1158–R1160

Kim, Laura Y.; Thompson, Peter M.; Lee, Hyunna T.; et al. (2016). The Structural Basis of Actin Organization by Vinculin and Metavinculin. JOURNAL OF MOLECULAR BIOLOGY.  428 (1): 10-25

Skau, Colleen T.; Fischer, Robert S.; Gurel, Pinar; et al. (2016). FMN2 Makes Perinuclear Actin to Protect Nuclei during Confined Migration and Promote Metastasis. CELL. 167 (6):1571-+

Review Papers

Thomas DG, Robinson DN. (2017). The fifth sense: Mechanosensory regulation of alpha-actinin-4 and its relevance for cancer metastasis. SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Mishra, Mithilesh; Huang, Junqi; Balasubramanian, Mohan K. (2014). The yeast actin cytoskeleton. FEMS MICROBIOLOGY REVIEWS. 38 (2): 213-227

Book Chapter

Luo, Tianzhi; Robinson, Douglas N. (2011). The Role of the Actin Cytoskeleton in Mechanosensation. MECHANOSENSITIVITY AND MECHANOTRANSDUCTION. Mechanosensitivity in Cells and Tissues. 4: 25-65


Recommended Readings: Sten Linnarsson, Ph.D. Friday November 10th, 2017

Friday Lectures

Friday, November 10, 2017  3:45 p.m.

Caspary Auditorium

Sten Linnarsson, Ph.D.


Department of Medical Biochemistry and Biophysics

Karolinska Institute

Unraveling Brain Development using Single-cell Technologies

Recommended Readings:


Ed Yong. Oct 14, 2016. A Google Maps for the Human Body. The Atlantic

Empirical Articles

Cervo, Pia Rivetti di Val; Romanov, Roman A.; Spigolon, Giada; et al. (2017). Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model. NATURE. 35 (5): 444-+

La Manno, Gioele; Gyllborg, Daniel; Codeluppi, Simone; et al. (2016). Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. CELL. 167 (2): 566-+  

Marques, Sueli; Zeisel, Amit; Codeluppi, Simone; et al. (2016). Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. SCIENCE. 352 (6291): 1326-1329

Zeisel, Amit; Munoz-Manchado, Ana B.; Codeluppi, Simone; et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. SCIENCE. 347 (6226): 1138-1142

Islam, Saiful; Zeisel, Amit; Joost, Simon; et al. (2014). Quantitative single-cell RNA-seq with unique molecular identifiers.  NATURE METHODS. 11 (2): 163-+

Review Paper

Shapiro, Ehud; Biezuner, Tamir; Linnarsson, Sten (2013). Single-cell sequencing-based technologies will revolutionize whole-organism science.  NATURE REVIEWS GENETICS. 14 (9): 618-630




Recommended Readings: Seth Darst, Ph.D. Monday November 6th, 2017

Monday Lectures

Monday, November 6, 2017  3:45 p.m.

Carson Family Auditorium

Seth Darst, Ph.D.

Jack Fishman Professor and Head

Laboratory of Molecular Biophysics

The Rockefeller University

Promoter Melting by Bacterial RNA Polymerase – One Step at a Time

Recommended Readings:

Feklistov, Andrey; Bae, Brian; Hauver, Jesse; et al. (2017). RNA polymerase motions during promoter melting. SCIENCE. 356 (6340): 863-866

Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine; et al. (2017). Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. ELIFE. 6

Chen, James; Wassarman, Karen M.; Feng, Shili; et al. (2017). 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. MOLECULAR CELL. 68 (2): 388-+

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; et al. (2015). Structure of a bacterial RNA polymerase holoenzyme open promoter complex. ELIFE. 4

Davis, Elizabeth; Chen, James; Leon, Katherine; et al. (2015). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD.  NUCLEIC ACIDS RESEARCH. 43 (1): 433-445

Chen, Jie; Darst, Seth A.; Thirumalai, D. (2010). Promoter melting triggered by bacterial RNA polymerase occurs in three steps. PNAS. 107 (28): 12523-12528