Upcoming Seminars / Seminars This Week

Thu 11/16/17 2 pmGoldsmith 317
Everytopic Seminar
Ruth Charney (Brandeis)
Searching for Hyperbolicity
While groups are defined as algebraic objects, they can also be viewed as symmetries of geometric objects. This viewpoint gives rise to powerful tools for studying infinite groups. The work of Max Dehn in the early 20th century on groups acting on the hyperbolic plane was an early indication of this phenomenon. In the 1980's, Dehn's ideas were vastly generalized by Mikhail Gromov to a large class of groups, now known as hyperbolic groups. In recent years there has been an effort to push these ideas even further. If a group fails to be hyperbolic, might it still display some hyperbolic behavior? Might some of the techniques used in hyperbolic geometry still apply? The talk will begin with an introduction to some basic ideas in geometric group theory and Gromov's notion of hyperbolicity, and conclude with a discussion of recent work on finding and encoding hyperbolic behavior in more general groups.
Hosted by Profs. Corey Bregman and Konstantin Matveev

Thu 11/16/17 4 pmAbelson 229
MRSEC Seminar
Ibrahim Cissé (MIT)
Super-resolution imaging of transcription in living mammalian cells
Hosted by John Berezney

Thu 11/16/17 5 pmRosenstiel 118
Special Seminar
Dr. James Haber (Brandeis University)
How Scientists Can Influence Policy
Hosted by Brandeis Science Policy Initiative

Fri 11/17/17 11:15 amRosenstiel 118
Biochemistry-Biophysics Friday Lunchtime Pizza Talks
Lana Saleh (New England Biolabs)
Insight into the biochemistry of oxidation of 5-methylcytosine on DNA by the ten-eleven translocation (TET) enzymes
Hosted by Maria-Eirini Pandelia

Fri 11/17/17 12:30 pmGerstenzang 123
Molecular and Cell Biology & Neuroscience Student Seminars
David Waterman (Haber Lab)
Stephen Alkins (Griffith)

Mon 11/20/17 10:30 amSchwartz 103
Thesis Seminar
Sujala Maharjan (Ph.D. candidate, Vision Lab)
The Effects of Repetition and Spatial Arrangement on the Extraction of Ensemble Statistics

Abstract: People exhibit remarkable accuracy when they try to extract the gist from a stream or a display of multiple items. That ability holds for crowds of faces, collections of objects of varying sizes, to take just two examples. For a comprehensive understanding of this important ability, I devised visual displays whose elements varied in a basic property, brightness. These displays allowed me to systematically explore the obligatory nature of gist extraction and the variable that affect the extraction process. I present three studies. The first evaluated people's propensity to summarize the displays despite having received no instructions to do so. Summary computation from temporal and spatial visual displays tend to be an automatic shortcut response, especially under conditions where relying on the instructions is impossible. Next, I present a study that investigated the influence of repeating items and how such items are arranged within a visual array on summary extraction. I show that the presence of identical items within a display enhances summary extraction causing it to be more accurate. I also demonstrate, when repeated items are closely grouped within a spatial array, they tend to significantly influence summary extraction. Finally, I present an experiment that assessed how changing the number of repeated items and their spatial arrangement affected the accuracy of summary extraction. I show that an increase in repetition within an array results in a more accurate summary. Consistent with previous result, when repeated items are adjacent to each other, they exert greater influence compared to when those items are spread out within an array. Together, these studies elucidate how the visual system extracts relevant information from a visual display, and how this process is affected by the composition of the array itself.

Hosted by Bob Sekuler

Mon 11/20/17 12 noonRosenstiel 118
Molecular Genetics Journal Club
Dr. Moshe Biton (Laboratory of Aviv Regev at the Broad Institute & Xavier lab at CCBI-MGH)
Exploring the gut epithelium in a single cell resolution
Hosted by Sebastian Kadener

Fri 11/24/17 12:30 pm
Molecular and Cell Biology & Neuroscience Student Seminars

Mon 11/27/17 11 amVolen 201
Computational Neuroscience Journal Club
Stephen Van Hooser (Brandeis University)
What does the LGN tell the visual cortex? Knowns and Unknowns

Mon 11/27/17 12 noonRosenstiel 118
Molecular Genetics Journal Club
Tom Rands
Drew Sawyer

Mon 11/27/17 4 pmGerstenzang 121
Eisenbud Lecture Series in Mathematics and Physics
James Sethna (Cornell University)
Sloppy Models, Differential Geometry, and How Science Works
Models of systems biology, climate change, ecosystems, and macroeconomics have parameters that are hard or impossible to measure directly. If we fit these unknown parameters, fiddling with them until they agree with past experiments, how much can we trust their predictions? We have found that predictions can be made despite huge uncertainties in the parameters -- many parameter combinations are mostly unimportant to the collective behavior. We will use ideas and methods from differential geometry to explain what sloppiness is and why it happens so often. We show that physics theories are also sloppy -- that sloppiness may be the underlying reason why the world is comprehensible.
Hosted by Bulbul Chakraborty

Mon 11/27/17 4 pmGerstenzang 122
Chemistry Department Colloquium
Pengyu Hong (Brandeis University )
De novo Glycan Sequencing by Machine Learning from Tandem Mass Spectra
Glycosylation is a common modification by which a glycan (or oligosaccharide) is covalently attached to a target macromolecule (such as, proteins and lipids). This modification serves various important functions (such as, protein folding, protein stability, cell-cell/matrix/environment interaction, immunity, and so on) and is one of the essential factors in optimizing many glycoprotein-based drugs. Hence it is important to profile the changes of glycans under different conditions. Glycan structure analysis is a challenging and essential task in biological and biomedical research. We have developed an advanced algorithm, named GlucoDeNovo, for reconstructing glycans from tandem mass data. We proofed that this problem can be solved with polynomial complexity rather than NP in conventional thinking. GlycoDeNovo features a Machine Learning based IonClassifier, which can effectively rank the reconstructed topology candidates. Experimental results showed that IonClassifier is effective and essential.
Hosted by Li Deng

Tue 11/28/17 12:30 pmGerstenzang 121
Joint Biology/Neuroscience Colloquium
Norbert Perrimon (Harvard Medical School)
Inter organ communication
Hosted by Joyce Rigal

Tue 11/28/17 4 pmAbelson 131
Eisenbud Lecture Series in Mathematics and Physics
James Sethna (Cornell University)
Crackling Noise
A piece of paper or candy wrapper crackles when it is crumpled. A magnet crackles when you change its magnetization slowly. The earth crackles as the continents slowly drift apart, forming earthquakes. Crackling noise happens when a material, when put under a slowly increasing strain, slips through a series of short, sharp events with an enormous range of sizes. There are many thousands of tiny earthquakes each year, but only a few huge ones. The sizes and shapes of earthquakes show regular patterns that they share with magnets, plastically deformed metals, granular materials, and other systems. This suggests that there must be a shared scientific explanation. We shall hear about crackling noise and that it is a symptom of a surprising truth: the system has emergent scale invariance -- it behaves the same on small, medium, and large lengths.
Reception to follow the lecture in Abelson 333.
Hosted by Bulbul Chakraborty

Wed 11/29/17 10 amAbelson 333
Eisenbud Lecture Series in Mathematics and Physics
James Sethna (Cornell University)
Normal form for renormalization groups: The framework for the logs
Ken Wilson's renormalization group solved for the behavior of phase transitions by mapping statistical mechanics into a differential equation in the space of all Hamiltonians, as we examine them on different length scales. This mapping from complex physical systems to simple differential equations has allowed us to explain scale invariance that emerges in everything from crackling noise to the onset of chaos. The results of the renormalization group are commonly advertised as the existence of power law singularities near critical points. This classic prediction is often violated, with logarithms and exponentials that pop up in the most interesting cases. Mathematicians have developed normal form theory to describe the likely behaviors of differential equations. We use normal form theory to systematically group these seeming violations into universality families. We recover and explain the existing literature, predict the nonlinear generalization for universal homogeneous functions, and show that the procedure leads to a better handling of the singularity even for the classic 4-d Ising model.
Hosted by Bulbul Chakraborty

Wed 11/29/17 12 noonRosenstiel 118
Neurobiology Journal Club
Chang Liu (Griffith Lab)
Reciprocal synapses between mushroom body and dopamine neurons form a positive feedback loop required for learning
Ref: Cervantes-Sandoval, I., Phan, A., Chakraborty, M., and Davis, R.L. (2017). Elife.
Alejandro Torrado Pacheco (Turrigiano Lab)
Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring
Ref: Buffington, S. A., Di Prisco, G. V., Auchtung, T. A., Ajami, N. J., Petrosino, J. F., & Costa-Mattioli, M. (2016). Cell, 165(7), 1762-1775.

Wed 11/29/17 5 pmVolen 119
Special Seminar
Mari Fitzduff (Heller School)
Why do people vote irrationally? Insights from Neuroscience
Refreshments Provided
Hosted by Brandeis Science Policy Initiative

Thu 11/30/17 4 pmAbelson 229
MRSEC: Biological Active Materials (IRG2)
Danny Goldstein (Chakraborty Lab)
Hosted by Greg Hoeprich

Fri 12/1/17 12:30 pmGerstenzang 123
Molecular and Cell Biology & Neuroscience Student Seminars
Lauren Tereshko (Sengupta Lab)
Claire Symanski (Jadhav Lab)

Fri 12/1/17 3 pmVolen 201
Cognitive Neuroscience Journal Club
Angela Gutchess (Gutchess Lab)

Tue 12/5/17 12:30 pmGerstenzang 121
Joint Biology/Neuroscience Colloquium
Karen Adelman (Harvard Medical School)
Probing transcription and function at enhancers
Hosted by Mike Marr

Tue 12/5/17 4 pmAbelson 131
Physics Department Colloquium
Roxanne Guenette (Harvard University)
Neutrinos: from zeros to heroes?
The Standard Model, that describes extremely well the particles and their interactions, predicts that neutrinos are massless and only interacts via weak interaction. These properties made neutrinos some of the least interesting particles of the model... until the discovery that they oscillate. This groundbreaking result implies that neutrinos are massive particles and opens the door to physics beyond the Standard Model- the holy grail of particle physicists. In addition, it seems that neutrinos could hold the key to many great mysteries of physics, such as the imbalance in the Universe between matter and anti-matter, and these are now within the reach of the next generation of neutrino experiments. After reviewing the intriguing properties of neutrinos, I will present the open questions in neutrino physics and describe how current and future neutrino experiments, focusing on Liquid Argon experiments, can bring new answers.
Hosted by Bjoern Penning

Wed 12/6/17 12 noonRosenstiel 118
Neurobiology Journal Club
Derek Wise (Nelson/Van Hooser Labs)
Selective inhibitory control of pyramidal neuron ensembles and cortical subnetworks by chandelier cells
Ref: Lu, J., Tucciarone, J., Padilla-Coreano, N., He, M., Gordon, J.A. & Huang, J. (2017). Nature Neuroscience 20, 1377-1383.
Linnea Herzog (Jadhav/Katz Labs)
Reactivations of emotional memory in the hippocampus–amygdala system during sleep
Ref: Girardeau G, Inema I & Buzsaki G (2017). Nature Neuroscience, doi:10.1038/nn.4637.

Thu 12/7/17 4 pmAbelson 229
MRSEC Seminar
Paul Whitford (Northeastern University)
Quantifying the Energy Landscapes of Ribosome Function
Hosted by Baptiste Blanc

Fri 12/8/17 12:30 pmGerstenzang 123
Molecular and Cell Biology & Neuroscience Student Seminars
Josiah Herzog (Paradis Lab)
Linnea Herzog (Katz/Jadhav Labs)

Mon 12/11/17 12 noonRosenstiel 118
Molecular Genetics Journal Club
Prof. Erez Levanon (BarIlan University, Ramat Gan, Israel)
Hosted by Sebastian Kadener

Thu 12/14/17 4 pmAbelson 229
MRSEC Seminar
Anastasios Matzavinos (Brown)
Hosted by Baptiste Blanc

Fri 12/15/17 12:30 pmGerstenzang 123
Molecular and Cell Biology & Neuroscience Student Seminars

Fri 12/22/17 12:30 pm
Molecular and Cell Biology & Neuroscience Student Seminars

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