Recommended Readings: Shixin Liu Ph.D. Monday November 14 2016

Monday Lectures

Monday November 14, 2016   3:45 p.m.

Caspary Auditorium

Shixin Liu   Ph.D.

Assistance Professor, The Rockefeller University

Laboratory of Nanoscale Biophysics and Biochemistry

Watching Biological Machines in Action

Recommended Readings:

 Liu, Shixin; Chistol, Gheorghe; Hetherington, Craig L.; et al.  A Viral Packaging Motor Varies Its DNA Rotation and Step Size to Preserve Subunit Coordination as the Capsid Fills.  CELL    157 (3):702-713     APR 24 2014

Chemla, Yann R.  High-Resolution, Hybrid Optical Trapping Methods, and Their Application to Nucleic Acid Processing Proteins.  BIOPOLYMERS   105(10): 704-714    OCT 2016

Ha, Taekjip.  Single-molecule methods leap aheadNATURE METHODS    11(10)1015-1018    OCT 2014

Guo, Peixuan; Grainge, Ian; Zhao, Zhengyi; et al.  Two classes of nucleic acid translocation motors: rotation and revolution without rotation. CELL AND BIOSCIENCE  4:54     SEP 16 2014

Casjens, Sherwood R.  The DNA-packaging nanomotor of tailed bacteriophages.  NATURE REVIEWS MICROBIOLOGY   9(9):647-657   SEP 2011

Chemla, YR; Aathavan, K; Michaelis, J; et al.  Mechanism of force generation of a viral DNA packaging motor. CELL   122(5 ): 683-692   : SEP 9 2005 

Recommended Readings: Marcello Magnasco Ph.D. Monday October 31, 2016

Monday Lectures

Monday October 31, 2016   3:45 p.m.

Caspary Auditorium

Marcello Magnasco, Ph.D.

Professor, Mathematical Physics

The Rockefeller University

Recommended Readings:

Janik VM, and Slater PJB.  Vocal Learning in Mammals.  Advances in the Study of Behavior,   26:59-99     1997    Request through Markus Library at

Reiss D, and McCowan B.  Spontaneous Vocal Mimicry and Production by Bottle-nosed Dolphins (Tursiops truncatus) – evidence for vocal learning.   Journal of Comparative Psychology   107(3):301-312    Sept  1997

McCowan B, Hanser SF, and Doyle LR.  Quantitative Tools for Comparing Animal Communication Systems: information theory applied to bottlenose dolphin whistle repertoires.  Animal Behavior.  57:409-419    Feb 1999

Janik VM.  Cetacean Vocal Learning and Communication.  Current Opinion in Neurobiology.  28:60-65    Oct 2014

Luis AR, Couchinho MN, and dos Santos ME.   Quantitative Analysis of Pulsed Signals Emitted by Wild Bottlenose Dolphins.  PLoS One   11(7):e0157781      July 2016

Gruden P, White PR, Oswald JN, Barkley Y, Cerchio S, Lammers M,and  Baumann-Pickering S.   Differences in Oscillatory Whistles Produced by Spinner (Stenella longirostris) and Pantropical Spotted (Stenella attenuata) Dolphins.   Marine Mammal Science  32:520-534    April 2016

Recommended Readings: Elaine Fuchs PhD October 24, 2016

Monday Lecture Series

Monday October 24, 2016   3:45 p.m.

Caspary Auditorium

Elaine Fuchs, Ph.D.

Rebecca Lancefield Professor

Laboratory of Mammalian Cell Biology and Development

Skin Stem Cells in Silence, Action and Cancer

Recommended Readings:

Quist, S. R.; Eckardt, M.; Kriesche, A.; et al.  Expression of epidermal stem cell markers in skin and adnexal malignancies. BRITISH JOURNAL OF DERMATOLOGY   175(3):520-530     SEP 2016

 Holland, Jane D.; Klaus, Alexandra; Garratt, Alistair N.; et al.  Wnt signaling in stem and cancer stem cells.  CURRENT OPINION IN CELL BIOLOGY    25(2):254-264  APR 2013

Arwert, Esther N.; Hoste, Esther; Watt, Fiona M.    Epithelial stem cells, wound healing and cancer.  NATURE REVIEWS CANCER   12(3):170-180   MAR 2012

Blanpain, Cedric; Fuchs, Elaine  STEM CELL PLASTICITY Plasticity of epithelial stem cells in tissue regeneration.  SCIENCE   344(6189):1243-+  ( Article Number: 1242281)  JUN 13 2014

Hsu, Ya-Chieh; Li, Lishi; Fuchs, Elaine  Transit-Amplifying Cells Orchestrate Stem Cell Activity and Tissue Regeneration. CELL   157(4):935-949     MAY 8 2014

Fuchs, Elaine; Chen, Ting  A matter of life and death: self-renewal in stem cells.  EMBO REPORTS   14 (1): 39-48   JAN 2013 

Oshimori, Naoki; Fuchs, Elaine   The Harmonies Played by TGF-beta in Stem Cell Biology.    CELL STEM CELL   11(6):751-764    DEC 7 2012

Recommended Readings: Joel E. Cohen Ph.D. Monday November 7 2016

Monday Lectures

Monday October 31, 2016   3:45 p.m.

Caspary Auditorium

Joel E. Cohen   Ph.D.

Abby Rockefeller Mauzé Professor of Populations

The Rockefeller University


Departments of International and Public Affairs;
Earth and Environmental Sciences; Ecology, Evolution and Environmental Biology; and Statistics of Columbia University

The Variation is the Theme:

Taylor’s law from Chagas Disease Vector Control to Tornado Outbreaks

Recommended Readings:

Taylor, L. R. Aggregation, variance and the mean.  Nature.  178:732-735    1961

Anderson, Sean C.; Cooper, Andrew B.; Dulvy, Nicholas K.   Ecological prophets: quantifying metapopulation portfolio effects. METHODS IN ECOLOGY AND EVOLUTION  4(10): 971-981      OCT 2013

Meng, Xu. Taylor’s power law: Before and after 50 years of scientific scrutiny.  ArXiv.      2011

Taylor, L. R. and I. P. Woiwod  Temporal Stability as a Density-Dependent Species Characteristic.  Journal of Animal Ecology.   49(1): 209-224   February 1980

Kalyuzhny, Michael; Schreiber, Yishai; Chocron, Rachel; et al.  Temporal fluctuation scaling in populations and communities. ECOLOGY.   95(6):1701-1709   JUN 2014

Recommended Readings: Nicole King Ph.D. October 7 2016

Friday Lecture Series

Friday October 7, 2016   3:45 p.m.

The Fairfield Osborn Memorial Lecture

Caspary Auditorium

Nicole King

Professor, and HHMI Investigator

Dept.of Molecular and Cell Biology, Division of Genetics, Genomics and Development

University of California Berkeley

Bacteria as Master Regulators and Aphrodisiacs

Recommended Readings:

Anderson, Douglas P.; Whitney, Dustin S.; Hanson-Smith, Victor; et al.  Evolution of an ancient protein function involved in organized multicellularity in animals. ELIFE                   5: e10147    JAN 7 2016

Alegado, Rosanna A.; King, Nicole  Bacterial Influences on Animal OriginsCOLD SPRING HARBOR PERSPECTIVES IN BIOLOGY    6(11): a016162  NOV 2014

King, Nicole.  Evolutionary Transitions to Multicellular Life Principles and Mechanisms Forrward.  EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE: PRINCIPLES AND MECHANISMS   Book Series:Advances in Marine Genomics   Volume: 2   Pages: V-VI    2015

King, Nicole; Mueller, Susann.  Environmental microbiology: Revisiting the physiology of microorganisms on the single cell scale. CURRENT OPINION IN MICROBIOLOGY     Volume: 25   Pages: V-VI   Published: JUN 2015

Recommended Readings: Uri Alon Ph.D. October 28 2016

Friday Lecture Series

Friday  October 28  2016    3:45  p.m.

Caspary Auditorium

Uri Alon

Professor, Department of Molecular Cell Biology

Weizmann Institute of Science

Evolutionary Trade Offs and the Geometry of Phenotype Space

Recommended Readings:

Keren, Leeat; Hausser, Jean; Lotan-Pompan, Maya; et al. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness. CELL    166(5):1282-+  AUG 25 2016

Korem, Yael; Szekely, Pablo; Hart, Yuval; et al. Geometry of the Gene Expression Space of Individual Cells. PLOS COMPUTATIONAL BIOLOGY    11(7):e1004224   JUL 2015

Tendler, Avichai; Mayo, Avraham; Alon, Uri  Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells. BMC SYSTEMS BIOLOGY  V 9: article number: 12   MAR 7 2015

Szekely, Pablo; Sheftel, Hila; Mayo, Avi; et al. Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems.  PLOS COMPUTATIONAL BIOLOGY.   9(8): e1003163    AUG 2013

Sheftel, Hila; Shoval, Oren; Mayo, Avi; et al. The geometry of the Pareto front in biological phenotype space. ECOLOGY AND EVOLUTION.   3(6):1471-1483    JUN 2013

Recommended Readings: Rebecca Saxe Ph.D. October 21, 2016

Friday Lecture Series

Friday October 21, 2016   3:45 p.m.

Caspary Auditorium

Rebecca Saxe, Ph.D.

Professor, MIT, Brain and Cognitive Sciences

It’s the Thought that counts: Progress in understanding the 

Neural basis of Theory of Mind

Recommended Readings:

 Chakroff, Alek; Dungan, James; Koster-Hale, Jorie; et al.  When minds matter for moral judgment: intent information is neurally encoded for harmful but not impure acts. SOCIAL COGNITIVE AND AFFECTIVE NEUROSCIENCE   11(3):476-484    MARCH 2016

Jacoby, Nir; Bruneau, Emile; Koster-Hale, Jorie; et al.  Localizing Pain Matrix and Theory of Mind networks with both verbal and non-verbal stimuli. NEUROIMAGE  126:39-48     FEB 1 2016

Deen, Ben; Koldewyn, Kami; Kanwisher, Nancy; et al.  Functional Organization of Social Perception and Cognition in the Superior Temporal Sulcus. CEREBRAL CORTEX    25(11):4596-4609     NOV 2015

Bruneau, Emile G.; Cikara, Mina; Saxe, Rebecca.  Minding the Gap: Narrative Descriptions about Mental States Attenuate Parochial Empathy.  PLOS ONE                 10:e0140838     OCT 27 2015

Andrews-Hanna, Jessica R.; Saxe, Rebecca; Yarkoni, Tal   Contributions of episodic retrieval and mentalizing to autobiographical thought: Evidence from functional neuroimaging, resting-state connectivity, and fMRI meta-analyses. NEUROIMAGE   91:324-335   MAY 1 2014

Koster-Hale, Jorie; Saxe, Rebecca; Dungan, James; et al.  Decoding moral judgments from neural representations of intentions. PNAS   110(14): 5648-5653   APRIL 2 2013

Recommended Readings: Ole Kiehn Ph.D. October 14, 2016

Friday Lecture Series

Friday October 14, 2016   3:45 p.m.

Caspary Auditorium

Ole Kiehn, Ph.D.

Professor, Mammalian Locomotor Laboratory,

Dept. of Neuroscience, Karolinska Institut

Deciphering the Functional Organization of Neuronal Circuits

Controlling Locomotion

Recommended Readings:

Kiehn, Ole.  Decoding the organization of spinal circuits that control locomotion. NATURE REVIEWS NEUROSCIENCE    17(4): 224-238    APR 2016

Bouvier, Julien; Caggiano, Vittorio; Leiras, Roberto; et al. Descending Command Neurons in the Brainstem that Halt Locomotion. CELL   163(5): 1191-1203    NOV 19 2015

Patrick, Susan K.; Noah, J. Adam; Yang, Jaynie F.   Interlimb Coordination in Human Crawling Reveals Similarities in Development and Neural Control With Quadrupeds.JOURNAL OF NEUROPHYSIOLOGY   101(2): 603-613   FEB 2009

Stuart, Douglas G.; Hultborn, Hans. Thomas Graham Brown (1882-1965), Anders Lundberg (1920-), and the neural control of stepping. BRAIN RESEARCH REVIEWS  59(1) : 74-95   NOV 2008

Recommended Readings: Jesse Ausubel M.A. October 10, 2016

Monday Lecture Series

Monday October 10, 2016   4 p.m.

Carson Family Auditorium

Jesse Ausubel, M.A.

Director and Senior Research Associate

Program for the Human Environment, The Rockefeller University

Nature Rebounds

Recommended Readings:

Donlan, J; Berger, J; Bock, CE; et al.  Re-wilding North America. NATURE   436 (7053):913-914    AUG 18 2005

Ausubel, Jesse H. and Paul E. Waggoner.  Dematerialization: Variety, caution, and persistence.  PNAS.   105(35):12774-12779.   June 2008.

Pearce, F and J. Ausubel.  Be green, think big. NEW SCIENTIST   189( 2536): 44-46 JAN 28 2006

Ausubel, Jesse H. and Paul E. Waggoner.  Assessing environmental changes in grasslandsSCIENCE  299(5614): 1844-1844      MAR 21 2003

Kauppi, Pekka E.; Ausubel, Jesse H.; Fang, Jingyun; et al.  Returning forests analyzed with the forest identity.  PNAS.  103(46): 17574-17579     NOV 14 2006

Recommended Readings: Michael Levine Ph.D. Sept 30, 2016

Friday Lecture Series

Norton Zinder Lecture

Michael Levine, Ph.D.

Director, Lewis-Sigler Institute for Integrative Genomics, Princeton Univ.

Anthony B. Evnin Professor, Dept Molecular Biology, Princeton Univ.

Visualization and evolution of transcriptional enhancers

Recommended Readings:

Bothma, J.P., Garcia, H.G., Ng, S., Perry, M.W., Gregor, T., and Levine, M. (2015). Enhancer additivity and nonadditivity are determined by enhancer strength in the Drosophila embryo. eLife 4, 07956.

Farley, E.K., Olson, K.M., Zhang, W., Brandt, A.J., Rokhsar, D.S., and Levine, M. (2015). Suboptimization of developmental enhancers. Science 350, 325-328.

Fukaya, T., Lim, B., and Levine, M. 2016. Enhancer control of transcriptional bursting. Cell 166, 358-368.

Bothma, J., Garcia, H., Gavin, S., Esposito, E., Gregor, T., and Levine, M. (2014). Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS 111, 10598-10603.

Evans, Nicole C.; Swanson, Christina I.; Barolo, Scott.  Sparkling Insights into Enhancer Structure, Function, and Evolution.  TRANSCRIPTIONAL SWITCHES DURING DEVELOPMENT   Book Series: Current Topics in Developmental Biology .  98: 97-120   2012

Gordon, Kacy L.; Ruvinsky, Ilya.  Tempo and Mode in Evolution of Transcriptional Regulation.  PLOS GENETICS.   8(1): e1002432    2012