Student Seminar

The BME Student Seminar launched in the summer of 2015 with the goal of creating a laid-back environment where BME graduate students can share their research and get feedback from their peers. The Student Seminar runs monthly and is a great venue to practice for a conference or prospectus presentation, work on your presentation skills, or simply bounce ideas off of your peers.

If you are interested in presenting, please email!

To view past speakers, check out the archive here.

Spring 2020 Presenters

Date Speaker Talk Title
02/21/2020 Jack Giblin (BOAS Lab) Quantifying hypoxic effects of capillary flow disruptions

Fall 2019 Presenters

Date Speaker Talk Title
10/25/2019 Matti Groll (Stepp Lab) How does the target selection method affect accelerometer-based AAC devices?
10/25/2019 Michael Sheets (Dunlop Lab) Light-inducible recombinases for bacterial optogenetics
11/22/2019 ~~ ~~
12/12/2019 ~~ ~~

Talks will be held from 12pm – 1pm in ERB 203 with lunch provided.


[Student Seminar] 12/18/18 Israel Desta + Christos Michas

December 14th, 2018in Grad Seminar
Our last student seminar of the semester will be on Tuesday 12/18 in ERB 203 from 12-1 pm. Israel Desta from the Vajda lab and Christos Michas from the Chen/White labs will be presenting on their work. Come out to hear about the research your peers are doing across the department, and, as always, enjoy lunch with your colleagues. Information on each talk can be found below.
We hope to see you there! And for those of you who are already travelling, have a great break!
Israel Desta
Improving prediction of antibody-antigen complexes
     Accurate determination of antibody-antigen interactions is an important step in several academic and pharmaceutical endeavors. Experimental structure determination has not been able to catch up with identifying biological protein complexes for drug discovery, as it is too costly and time consuming. With computational methods such as protein docking, this gap can be potentially bridged. One of the most widely used protein-docking servers is ClusPro developed in our lab in 2004. On the latest benchmark set of proteins, ClusPro was able to predict 48% of antibody-antigen complexes accurately. The goal of my PhD is to improve on ClusPro's prediction accuracy of antibody-antigen complexes. I will be using a two-pronged approach in order to achieve this. Firstly, I will be improving the contact-based potential called Decoys as a Reference (DARS) that is currently in use in ClusPro. The antibody specific DARS (aADARS), currently utilizes only 4 of the known 18 atom types and also uses 1 distance bin as a measure of contact. I am working on expanding both the number of atom types considered and also the number of distance bins. Secondly, I am planning to use ClusPro's capabilities in predicting true epitope as an additional screening of predicted poses. Preliminary results show that ClusPro predicts true epitopes the majority of the time despite getting the actual structure of the complex wrong. The latter approach will need to utilize conventional machine learning and/or deep learning to enhance accuracy.
Christos Michas
3D-printed microfluidic valves for simulating the cardiac cycle in vitro 
     The cardiac cycle is divided into four distinct phases, during which the myocardium is exposed to different patterns of blood pressure and tissue elongation. The pressure-sensitive cardiac valves give rise to these four phases, and changes in the differential pressure and elongation of each phase impacts cardiac tissue structure and function. The absence of a valvular mechanism in current in vitro cardiac micromodels limits the ability of these models to simulate the in vivo ventricular function and to translate their findings to cardiac output metrics traditionally used in the clinic. Using two-photon direct laser writing, we fabricate a passive microfluidic check valve that can impose unidirectional, pulsatile flow when exposed to oscillatory fluid pressure. We demonstrate opening and closing pressures below 1Pa, rendering our construct suitable as a miniaturized valve replica in an in vitro cardiac system. Future work aims to use this technology to mimic all phases of the cardiac cycle and study the cardiac remodeling that occurs when each phase is altered.

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[Student Seminar] 11/13/18 The Art of Scientific Illustration – Bell Varongchayakul

November 9th, 2018in Grad Seminar
Our November Student Seminar will be held on Tuesday Nov 13th from 12-1 pm in ERB 203. Dr. Bell Varongchayakul will be giving a talk entitled "The Art of Scientific Illustration." This talk will focus on how to make and design scientific figures and some fundamentals of graphic illustration. It should be a very interesting and practical talk, as this is a skill that all grad students will use at some point in their academic career. As always, lunch will be served.

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[Student Seminar] Speaker Solicitations for October Lightning talks 10/16/18

October 4th, 2018in Grad Seminar

Hi Everyone,

The October edition of the GSC student seminar series is our annual Lightning Talks seminar, in which we have a larger number of presenters give one slide, five minute presentations on their research. This is to 1.) mix up presentations styles and keep the seminar series fresh and 2.) give our first-years a chance to see work from a number of labs across the department in one go.

This year's lightning talks will take place at our regular Tuesday lunch seminar time (12-1pm) on October 16th in ERB 203.

Of course, we won't be able to do this without speakers to present and that's where you all come in. If you would like to give a lightning talk please fill out this form.

Otherwise, keep your calendar open for lunch on Tuesday 10/16, and we will see you there!

Your GSC

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[Student Seminar] 9/25/18 Smrithi Sunil and Shawn Javdan

September 24th, 2018in Grad Seminar

The GSC Student Seminar Series kicks off this upcoming Tuesday, 9/25, @ 12 pm in ERB 203. This installment will highlight work from students in the Neurophotonics Center and the Biological Design Center. 

  • Smrithi Sunil (David Boas Lab): "A macroscopic to microscopic view of hemodynamics and neurovascular coupling during stroke recovery"
  • Shwan Javdan (Allyson Sgro Lab): "Visualizing Extracellular Signaling Dynamics"

The Student Seminar series are student organized talks that allow grad students in the department to present on their research and practice their communication skills. This year, we would like to move the focus more towards highlighting students' research across different fields, and we will be exploring new formats. September will feature two 20 min talks, October will feature Lightening Talks, and November will feature a skills workshop focused on Scientific Illustration. As always, lunch will be served. We hope to see you there!


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[Student Seminar] Introduction to LaTeX

June 8th, 2018in Grad Seminar

Hi BME's,

LaTeX is an elegant tool to help create beautiful, professional documents. Come to our June Student Seminar on Thursday (6/7) to learn about:
-  What LaTeX is
-  Why use it instead of MS Word
-  How to use it to create professional looking documents.
Our very own Hannah Peterson will be giving the seminar at noon in ERB 203. Lunch will be served. See you all there!

GSC Student Seminars is created to enable BME grad students to share their research with their peers in a low-stress environment. We welcome all types of presentations and discussions - it can be practice for a conference talk or defense, general talk about research ideas or best practices, or just rant about lab frustrations. If you're interested in presenting or leading a discussion, email us at We'll buy lunch!

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[Student Seminar] 12/12/17 Lia Bonacci

December 10th, 2017in Grad Seminar
Please join us on Tuesday, December 12th at 1:00pm in ERB 203 for our next BME Student Seminar. Our goal is to create a laid-back environment where BME grad students can share their research and get feedback from their peers. Lia Bonacci will be presenting her research on the Cocktail Party Problem. Come by to learn about his work, provide feedback, and (of course) enjoy lunch with your peers!

When: Tuesday, December 12th 1:00pm - 2:00pm
Where: ERB 203

Title: Neural Correlates of Selective Attention: Enhancing Communication at the Cocktail Party

Abstract: Interaction with the outside world is guided by the ability to direct and maintain attention, selecting objects of interest while simultaneously suppressing distractors. However, many individuals struggle to communicate in noisy environmentssettings in which a multitude of stimuli constantly compete for attention. In these settings, it would be useful to monitor where an individual is directing their attention. This ability would make it possible to assist in object selection, enhancing how well a listener understands surrounding stimuli. Selective attention has been shown to modulate the neural response to both auditory and visual stimuli. Yet the neural mechanisms underlying selective attention are still not well understood. Electroencephalography (EEG) is often used to examine these mechanisms, namely through measurement of event-related potentials and oscillatory power.  Using EEG, we will identify neural correlates of selective attention to dynamic auditory and visual stimuli. By doing so, we hope to gain insight into the neural mechanisms that underlie selective attention in both sensory modalities. In addition, these correlates will form the feature space for a classifier that can reliably determine where an individual has directed attention in a complex scene. The goal of this work is to assess the degree to which EEG can be used in real time to monitor direction of attention and assist communication in noisy environments.

GSC Grad Student Seminars is a laid-back way to share research with your peers. We welcome practices for talks, prospectus, thesis defense, research rants, science discussions, and anything in between. Interested in presenting or leading a discussion? Sign up here, or nominate a peer whose research you're curious about.

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Special Student Seminar 12/5/17

December 10th, 2017in Grad Seminar
Please join us on December 5th at 1:00pm in ERB 203 for our next BME Student Seminar. This month, we'll be having a special seminar regarding graduate student life, led by our executive co-chair, Andrew Acevedo. Come discuss the PhD Experience, and enjoy lunch with your peers!
When: Tuesday, December 5th , 1 - 2 PM
Where: ERB 203
Andrew Acevedo, GSC Executive Co-Chair
Some Thoughts on the Modern PhD Experience
In a special edition of the student seminar series, we will be talking about the graduate student experience and being in a PhD program in 2017. The discussion will be centered around the National Graduate Survey conducted by Nature which explored career development and PhD program satisfaction of grad students internationally. The discussion will also touch on some current events in the news pertaining to graduate students. Relevant initiatives being pursued at the GSC, Department, and University level will be highlighted. We hope for this to open up to a conversation about people's experiences and views.

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Student Seminar Speed Presentations

September 26th, 2017in Grad Seminar
When: Tuesday, September 26th, 4:00 - 5:30pm
Where: LSEB 103

Please join us on Tuesday, September 26th at 4:00pm in LSEB 103 for our next BME Graduate Student Seminar. Our goal for this seminar is to expose you to a range of research going on in the BME department, and help set expectations for your rotation projects. Several current students will share their current or past research with you. Due to the speakers' scheduling restrictions, we'll start the talks at ~4:30. Feel free to show up early to mingle and enjoy Otto's Pizza with your peers!

Anup Tank Robyler Lab
Christine Nykyforchyn Waxman Lab
Joshua Kays Dennis Lab
Raeef Istfan Robyler Lab
Sam Ghilardi Dennis Lab
Sanaya Shroff Han Lab
Shwan Javadan Sgro Lab

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