WEBINARS | JANUARY 12-APRIL 27, 2020

Bioengineering Colloquia & Open BME Seminar

Bioengineering Colloquia

Tuesdays, 4:30 - 5:15 pm CT

The Rice Bioengineering Colloquia is a seminar series that has a long tradition at the Department of Bioengineering at Rice University. Each week, experts from around the world are brought to Rice to present the latest findings and research in the broadly defined bioengineering field. In Spring 2021, the BIOE Colloquia will be held on Tuesdays.

Attendees must register in advance to receive the Zoom Webinar link. Graduate students enrolled in BIOE 699 must register for each event to count their attendance.

Register with the link below.


Open BME Seminar

Thursdays, 3:00 - 4:30 pm CT

The Open BME Seminar series is a virtual seminar series newly created in 2021 to feature leaders and rising stars in the field of biomedical engineering (BME). It is hosted by seven BME departments from Rice University, Washington University in St. Louis, Case Western Reserve University, University of Virginia, Northwestern University, University of Pittsburgh, and University of Michigan. This special seminar series will be held on selected Thursdays.

Register with the link below.


Upcoming Seminars

Spring 2021


Tuesday, April 20 @ 4:30 pm CT

REGISTER HERE

Tony HuBioengineering Colloquia

Tony Ye Hu, PhD

Professor in Biochemistry & Molecular Biology, Biomedical Engineering, and Microbiology,
Weatherhead Presidential Chair in Biotechnology Innovation,
Founding Director of the Center for Cellular and Molecular Diagnostics
Tulane University

"Written in Blood"

Abstract | Hu’s laboratory develops and validates novel nanomaterial assay platforms designed to utilize serum, or other body fluids, for biomarker discovery and all aspects of disease diagnosis and evaluation, including: 1) early diagnosis; 2) discrimination among specific disease stages (e.g., latent, activating latent, and active infections) or prognoses (e.g., low versus high risk for treatment failure, drug resistance, or metastasis); 3) the evaluation of microbial or malignant disease burden for treatment monitoring; and 4) the early detection of drug resistance. These platforms are being designed as an integrated suite of nanomaterial applications that allows rapid modification for different disease targets, including emerging infectious diseases, through biomarker substitution.

Biography

Dr. Tony Hu is a Professor in Biochemistry and Molecular Biology, Biomedical Engineering, and Microbiology at Tulane University. He is also the Weatherhead Presidential Chair in Biotechnology Innovation and founding Director of the Center for Cellular and Molecular Diagnostics at Tulane School of Medicine. Dr. Hu received his Ph.D. in Biomedical Engineering from the University of Texas at Austin in 2009. He is also a co-founder of two biotech startup companies, Ares Diagnosis Inc. in San Jose, CA and NanoPin Technologies in Phoenix, AZ.

Dr. Hu’s research focuses on the development of nanomaterial platforms and proteomic approaches that are designed to enrich biomarker capture from microbial pathogens, or enhance biomarker signal, to improve the detection sensitivity, specificity, or quantitation of pathogen-derived soluble or extracellular vesicle (EV)-associated factors in complex biological samples. His research differs from conventional biomarker discovery and detection research for clinical microbiology in that it employs the special properties of nanomaterials to improve assay performance and reproducibility. This can have profound impact on the ability to detect and quantitate target low abundance biomarkers in complex mixtures, allowing the analysis of biomarkers that would otherwise be undetectable. Dr. Hu has made significant contributions to microbial diagnostics for critical global health initiatives, including a serum/plasma assay for all forms of tuberculosis and a mass spectrometry-based approach to differentiate closely related mycobacterium and Ebolavirus species. His work has resulted in publications of over 100 high-impact papers and 15 patent applications involving nanomedicine. Five of them have been licensed by US-based companies.


Past Seminars

Spring 2021


Joint - Seminar | Department of Bioengineering & Department of Chemistry

Wednesday, April 14 @ 12:00 pm CST

Jason ChinBioengineering Colloquia

Jason W. Chin, PhD

Joint Head & Programme Leader, Division of Protein & Nucleic Acid Chemistry, Head, Centre for Chemical & Synthetic Biology, MRC Laboratory of Molecular Biology
Professor of Chemistry and Chemical Biology, Department of Chemistry, Cambridge, UK

"Reprogramming the Genetic Code"

Abstract | In terrestrial life, DNA is copied to messenger RNA, and the 64 triplet codons in messenger RNAs are decoded – in the process of translation – to synthesize proteins. Cellular protein translation provides the ultimate paradigm for the synthesis of long polymers of defined sequence and composition, but is commonly limited to polymerizing the 20 canonical amino acids. I will describe our progress towards the encoded synthesis of non-canonical biopolymers. These advances may form a basis for new classes of genetically encoded polymeric materials and medicines. To realize our goals we are re-imagining some of the most conserved features of the cell; we have created new ribosomes, new aminoacyl-tRNA synthetase/tRNA pairs, and organisms with entirely synthetic genomes in which we have rewritten the genetic code.

Host: Han Xiao, PhD & George Lu, PhD


Tuesday, April 13 @ 4:30 pm CT

HarrisWangBioengineering Colloquia

Harris H. Wang, PhD

Associate Professor, Department of Systems Biology, Columbia University

"Interrogating and programming microbiomes with next-generation synthetic biology"

Abstract | Microbes that live in soil are responsible for a variety of key decomposition and remediation activities in the biosphere. Microbes that colonize the gastrointestinal tract play important roles in host metabolism, immunity, and homeostasis. Better tools to study and alter these microbiomes are essential for unlocking their vast potential to improve human health and the environment. This talk will describe our recent efforts to develop next-generation characterization and manipulation tools for microbial communities. Specifically, I will discuss new platforms for automated microbial culturomics, techniques to delineate the spatiotemporal dynamics of microbial ecosystems and methods to genetically engineer complex microbial consortia. These emerging capabilities provide a foundation to accelerate the development of microbiome-based products and therapies.

Biography

Harris Wang is an Associate Professor at Columbia University jointly appointed in the Department of Systems Biology and the Department of Pathology and Cell Biology. Dr. Wang received his B.S. degrees in Mathematics and Physics from MIT and his Ph.D. in Biophysics from Harvard University. His research group mainly develops enabling genomic technologies to characterize the mammalian gut microbiome and to engineer these microbes with the capacity to monitor and improve human health. Dr. Wang is an Investigator of the Burroughs Wellcome Fund and the recipient of numerous awards, including the NIH Director’s Early Independence Award, NSF CAREER, Sloan Research Fellowship, ONR Young Investigator, Schaefer Scholars, and Forbes’ 30 Under 30 in Science. In early 2017, Dr. Wang received the Presidential Early Career Award for Scientists and Engineers (PECASE) from President Obama, which is “the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers.”


Thursday, April 8 @ 3 pm CT

James CollinsOpen BME Seminar

James J. Collins, PhD

Termeer Professor of Medical Engineering & Science, Department of Biological Engineering, Massachusetts Institute of Technology

"Synthetic Biology: Life Redesigned"

Host: Sanjeev Shroff, PhD | University of Pittsburgh


Thursday, April 1 @ 3 pm CT

Timothy DowningOpen BME Seminar

Timothy Downing, PhD

Assistant Professor, Department of Biomedical Engineering, University of California Irvine

"Synthetic genome regulation for cell and tissue engineering"

Host: Sriram Chandrasekaran, PhD | University of Michigan


Tuesday, March 30 @ 4:30 pm CT

Jeff HastyBioengineering Colloquia

Jeff Hasty, PhD

Professor, Department of Bioengineering, University of California - San Diego

"Engineered Gene Circuits: From Clocks to Tumors and Small Ecologies"

Abstract | For synthetic biology applications, intracellular variability is a major obstacle to the fidelity required for "programming" cells. A major theme in our research has been to investigate how determinism can arise from the synchronization of a large number of cells. I will review our basic approach to synchronization within the context of engineered bacteria that can be used to safely produce and deliver therapeutics from within solid tumors. Specifically, we have engineered a clinically relevant bacterium to lyse synchronously at a threshold population density and to release genetically encoded cargo. Following quorum lysis, a small number of surviving bacteria reseed the growing population, thus leading to pulsatile delivery cycles. We have extended this approach to small ecologies, whereby engineered periodic lysis can lead to ecological stability and generate interesting drug delivery schemes. Our current work explores how a small number of interacting species behave when constrained to grow on a surface as opposed to a well-mixed culture. It is known that non-hierarchical competitive dynamics, such as cyclical interactions, can sustain biodiversity. We have rationally designed a minimal microbial community with three strains of E. coli that cyclically interact through (i) the inhibition of protein production, (ii) the digestion of genomic DNA, and (iii) the disruption of the cell membrane. We find that intrinsic differences in these three major mechanisms of bacterial warfare lead to an unbalanced community that is, counterintuitively, dominated by the weakest strain. This work represents early steps towards probing small engineered ecologies in complex environments.

Biography

Jeff Hasty received his Ph.D. in physics from the Georgia Institute of Technology in 1997, where he learned how to do science from his advisor Kurt Wiesenfeld. He was subsequently a postdoctoral fellow at Boston University, where he learned engineering from Jim Collins in the Applied BioDynamics Lab (’98-’01). Somewhere during his postdoctoral stay with Jim he mutated from a theoretical physicist into a hybrid computational/molecular biologist. He is currently at the University of California, San Diego, where he is a Professor in the Departments of Molecular Biology and Bioengineering, Director of the BioCircuits Institute, and Co-Director of the UCSD qBio Ph.D Specialization Program. His major scientific achievements have been in the fields of Synthetic and Systems Biology. In Synthetic Biology, he and his group has established a new paradigm for the design and construction of genetic circuits in living cells. They developed this paradigm by engineering new methods for coupling the dynamics of single cells, such that circuit design is viewed at the level of many interacting colonies of bacteria. In Systems Biology, they have shown how regulatory networks that underly metabolism can mediate the cellular response to a dynamically changing environment. Using computational modeling and microfluidic devices, they have predicted and demonstrated the importance of active degradation of unnecessary transcripts upon diauxie shift. They subsequently showed that this process optimizes growth rate due to a spatially localized competition for translational machinery between metabolic transcripts and transcripts that drive cell cycle progression. Technical achievements have focused on the development of microfluidic technology. Their devices are applicable to many cell types and contain traps that are designed to facilitate healthy cell growth in a monolayer, which ensures the same focal plane for high resolution microscopy. They have designed a system that subjects the cells to a periodic or randomly modulated environmental input signals. Cells, constructs, and microfluidic devices from their lab are in use for research and teaching around the world and they are known for sharing genetic circuits and microfluidic technology that “just work”.


Thursday, March 25 @ 3 pm CT

Warren GraysonOpen BME Seminar

Warren Grayson, PhD

Professor, Department of Biomedical Engineering, Johns Hopkins University

"Making Faces: Regenerating Craniofacial Bone"

Host: Guillermo Ameer, PhD | Northwestern University 


Tuesday, March 23 @ 4:30 pm CT

Shana KelleyBioengineering Colloquia

Shana Kelley, PhD

University Professor, Department of Biomedical Engineering, Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Toronto

"Rare Cell Profiling Platforms for Therapeutic Discovery and Patient Monitoring"

Abstract | The analysis of heterogeneous ensembles of rare cells requires single-cell resolution to allow phenotypic and genotypic information to be collected accurately. We developed a new approach for high-throughput cell sorting and profiling, Magnetic Ranking Cytometry, that uses the loading of individual cells with functionalized magnetic nanoparticles as a means to report on biomarker expression at the single cell level. This approach can be used to profile immune cells and circulating tumor cells in blood and provides a high-information content liquid biopsy in a single measurement. It profiles both protein (Nature Nanotechnology, 2017, Nature Biomedical Engineering, 2021) and nucleic acid (Nature Chemistry, 2018) analytes at the single cell level. Recently, we have used this approach to perform high-throughput, phenotypic CRISPR screens at the whole genome level (Nature Biomedical Engineering, 2019) and are now using this platform as a tool for therapeutic target discovery. This platform also enables the development of high-precision cell-based therapies.

Biography

Dr. Shana Kelley is a University Professor at the University of Toronto and a member of the Departments of Biomedical Engineering, Chemistry, Biochemistry, and Pharmaceutical Sciences. The Kelley research group works in a variety of areas spanning biophysical/bioanalytical chemistry, chemical biology and nanotechnology, and has pioneered new methods for tracking molecular and cellular analytes with unprecedented sensitivity.

Dr. Kelley’s work has been recognized with a variety of distinctions, including being named one of “Canada’s Top 40 under 40”, a NSERC E.W.R. Steacie Fellow, the 2011 Steacie Prize, and the 2016 NSERC Brockhouse Prize. She has also been recognized with the ACS Inorganic Nanoscience Award, the Pittsburgh Conference Achievement Award, an Alfred P. Sloan Research Fellowship, a Camille Dreyfus Teacher-Scholar award, a NSF CAREER Award, a Dreyfus New Faculty Award, and was also named a “Top 100 Innovator” by MIT’s Technology Review.

Kelley is an inventor on over 50 patents issued worldwide. She is a founder of four molecular diagnostics companies, GeneOhm Sciences (acquired by Becton Dickinson in 2005), Xagenic Inc. (acquired by General Atomics in 2017), Cellular Analytics (founded in 2019), and Arma Biosciences (founded in 2020).

Dr. Kelley is the Director of PRiME, an initiative focused on next-generation Precision Medicine that unites physical scientists, engineers, biologists and clinicians developing new therapeutics and diagnostics. Kelley serves as a Board Director for the Fight Against Cancer Innovation Trust (FACIT) and the Canadian Academy of Health Sciences. She is an Associate Editor for ACS Sensors, and an Editorial Advisory Board Member for the Journal of the American Chemical Society, Nano Letters, and ACS Nano.


Thursday, March 18 @ 3 pm CT

Daniel RueckertOpen BME Seminar

Daniel Rueckert, PhD

Professor, Visual Information Processing, Department of Computing, Imperial College London

"Learning clinically useful information from medical images"

Host: Frederick Epstein, PhD | University of Virginia

Thursday, March 4 @ 3 pm CT

Danielle BassettOpen BME Seminar

Danielle Bassett, PhD

J. Peter Skirkanich Professor, Department of Bioengineering, University of Pennsylvania

"Systems Neuroscience"

Host: Robert Kirsch, PhD | Case Western Reserve University


Tuesday, March 2 @ 4:30 pm CT

Enrico OpriBioengineering Colloquia

Enrico Opri, PhD

Postdoctoral Fellow, Emory University

"Advancing Deep Brain Stimulation Therapy in Movement Disorders: from surgical implantation to behavior-based responsive therapeutic stimulation"

Abstract | Deep brain stimulation (DBS) has become standard therapy for medically refractory patients with Parkinson’s disease (PD), essential tremor (ET), and other neurological disorders. The two main challenges for DBS standard-of-care are rooted in the accurate positioning of the DBS leads during intraoperative implantation and the postoperative programming of the implanted DBS device, both needed to achieve the sought optimal therapeutic benefit. However, both processes rely on subjective patient exams, on expert neurophysiologists to optimize implant trajectory and programming, and on time-consuming trial-and-error approaches. Furthermore, existing commercially available stimulation approaches (continuous stimulation, also known as open-loop stimulation) lack integration with patient behavior and environmental factors. We sought to address these shortcomings in the ET population, by demonstrating the feasibility of on-demand responsive stimulation using only thalamocortical neuromarkers that modulate movement related-behavior. This led to the design and implementation of the first fully embedded closed-loop algorithm for chronic neurostimulators (CL-DBS) in humans affected by ET, which achieved an equally effective treatment compared to current DBS approaches while having a more efficient stimulation energy profile. Furthermore, CL-DBS demonstrated potential in decreasing DBS-related side effects (e.g. speech impairments). Additionally, the unique window provided by intraoperative acute recordings, allowed us to further our understanding of the thalamocortical network. We showed that there is significant cross-rhythm communication between thalamocortical regions and that changes in motor behavior correspond to changes in thalamocortical phase-amplitude coupling (PAC) profiles, demonstrating it is a crucial mechanism for gating motor behavior. We then sought to improve intraoperative DBS implantation for the PD population by leveraging a novel biomarker, DBS local evoked potential (DLEP), which strongly correlates with the location of the typical target-subregions of the nuclei of interest, the subthalamic nucleus (STN) and globus pallidus internus (GPi). Most importantly, the proposed methodology requires no patient interaction and could be leveraged for implementing an objective, real-time guided placement of the DBS lead, with a less time-consuming process and subjectivity compared to traditional mapping procedures.

Biography

Dr. Enrico Opri is currently a T32 NIH-funded postdoctoral fellow at Emory University, School of Medicine. Dr. Opri completed his BS and MS degrees in Biomedical Engineering at Politecnico di Milano, and his MS and PhD degrees in Biomedical Engineering at the University of Florida. His doctoral work focused on closed-loop deep brain stimulation (DBS) for the improved treatment of patients affected by essential tremor and mechanism of thalamocortical communication in motor behavior in humans. As a postdoctoral fellow, his research interest focuses on engineering guided and objective electrophysiology-based methodologies for the improvement and enhancement of the current standard-of-care in DBS programming and surgical implantation. He spearheads open-source and community effort initiatives for neuroscience, and he is currently part of the core development team of Lead-DBS, an open and widely used toolbox to process patient brain imaging, especially for DBS studies. Outside the lab, Enrico enjoys baking and upcycling old electronics.


Thursday, February 25 @ 4:30 pm CT

Catera WilderBioengineering Colloquia

Catera Wilder, PhD

Postdoctoral Fellow, Alexander Hoffmann Lab, Department of Microbiology, Immunology & Molecular Genetics, UCLA

"Dynamic control of interferon signaling and gene regulation and its role in regulating the immune response"

Abstract | Interferons (IFNs) are cytokines that coordinate the innate immune response to prevent the spread of viral infections. The importance of the IFN response has been recently highlighted, as misregulated IFN expression has been correlated with COVID19 disease severity. Two IFN families (i.e. type I and III IFNs) are responsible for suppressing viral replication, but only type I IFNs induce an inflammatory response, which can be tissue destructive if not properly regulated. As both type I and III IFNs activate the same transcription factor, IFN-stimulated gene factor (ISGF3), it remains unclear how they elicit differential gene expression programs. We found that in lung epithelial cells IFN-β and IFN-λ3 induced multi-phasic ISGF3 responses that differ in prominent dynamic features. In order to determine the underlying mechanisms of this IFN-type-specific response, we pursued a mechanistic systems biology approach – involving iterative mathematical modeling and quantitative experimentation – that revealed several nested positive and negative feedback and feedforward loops whose precise timing and strength determine ISGF3 dynamics. Gene expression analysis revealed IFN-type specific gene induction. These results suggest that IFN-induced gene expression programs in lung epithelial cells may be regulated by the dynamics of ISGF3 activity, which are IFN type-specific and determined by coordinated feedback and feedforward loops. Understanding the control of the JAK-STAT signaling pathway between type I and type III IFNs and identifying key IFN type-specific control mechanisms may enable novel therapeutic strategies to address type I IFN misregulation in a variety of inflammatory and autoimmune diseases.

Biography

Catera is a UCLA Chancellor’s Postdoctoral Fellow in the lab of Alexander Hoffmann. She received her Ph.D. in Biomedical Engineering under the direction of Manu Platt. She is currently focused on understanding innate immune and inflammatory responses by studying ISGF3 transcription factor dynamic regulation using a systems biology approach in order to develop predictive, quantitative tools of immune responses. Her work investigating the interferon signaling and transcriptional regulation has uncovered stimulus specific responses determined by coordinated feedback and feedforward loops. She plans on using this research as the foundation of her own research program investigating the spatiotemporal control of intra- and inter-cellular IFN signaling networks.


Thursday, February 25 @ 3 pm CT

Adriana VelazquezOpen BME Seminar

Adriana Velazquez

Group Lead Medical Devices and In-Vitro Diagnostics, World Health Organization

"As the world gets smaller, how can we expand the biomedical engineering impact to global health?"

Host: Horst von Recum, PhD | Case Western Reserve University


Thursday, February 18 @ 3 pm CT

Matthew PorteusOpen BME Seminar

Matthew Porteus, MD, PhD

Sutardja Clark Professor of Definitive and Curative Medicine, Department of Pediatrics, Stanford School of Medicine

"Genome Editing to Create Curative Cellular Therapies"

Host: Gang Bao, PhD | Rice University

Abstract | Genome editing is a powerful approach to genetically engineer cells with single nucleotide precision. The precision can be used in a wide variety of ways to generate cells that could cure patients of disease. In this talk, I will discuss how we have developed a CRISPR/Cas9 based system that can not only correct single nucleotide disease causing mutations, but can also integrate gene cassettes at specific locations. We have applied this system to a variety of stem cells, including pluripotent and somatic, to leverage the biologic properties of stem cells to regenerate organ systems, including the blood and immune systems. In addition, genome editing can also be combined with the principles of synthetic biology to engineer cells with new therapeutic functions, including for both improved safety and efficacy. Finally, I will end by discussing the biologic and engineering challenges to applying targeted integration genome editing in vivo.

Biography

Matthew Porteus MD, PhD is a Professor in the Department of Pediatrics and Institute of Stem Cell Biology and Regenerative Medicine and Maternal-Child Health Research Institute at Stanford. He is the co-Director for the Stanford Center for Definitive and Curative Medicine (CDCM). His primary research focus is on developing genome editing as an approach to cure disease, particularly those of the blood and immune system (such as sickle cell disease) but also of other organ systems as well. His goal is to combine his research and clinical interests to develop innovative curative therapies. And his dream is to one day develop gene editing so that patients are cured of their disease before they or their parents even knew they had it. He served on the 2017 National Academy Study Committee of Human Genome Editing and currently serves on the Scientific Advisory Board for WADA on Cell and Gene Doping and the NIH NExTRAC advisory committee evaluating the emergence of new technologies.


Tuesday, February 9 @ 4:30 pm CT

Erez Lieberman AidenBioengineering Colloquia

Erez Lieberman Aiden, PhD

Associate Professor, Molecular and Human Genetics, Department of Genetics, Baylor College of Medicine

"A 3D Code in the Human Genome"

Abstract | Stretched out from end-to-end, the human genome – a sequence of 3 billion chemical letters inscribed in a molecule called DNA – is over 2 meters long. Famously, short stretches of DNA fold into a double helix, which wind around histone proteins to form the 10nm fiber. But what about longer pieces? Does the genome’s fold influence function? How does the information contained in such an ultra-dense packing even remain accessible? In this talk, I describe our work developing ‘Hi-C’ (Lieberman-Aiden et al., Science, 2009; Aiden, Science, 2011) and more recently ‘in-situ Hi-C’ (Rao & Huntley et al., Cell, 2014), which use proximity ligation to transform pairs of physically adjacent DNA loci into chimeric DNA sequences. Sequencing a library of such chimeras makes it possible to create genome-wide maps of physical contacts between pairs of loci, revealing features of genome folding in 3D. Next, I will describe recent work using in situ Hi-C to construct haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind the protein CTCF. The CTCF motifs at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs “facing” one another. Next, I will discuss the biophysical mechanism that underlies chromatin looping. Specifically, our data is consistent with the formation of loops by extrusion (Sanborn & Rao et al., PNAS, 2015). In fact, in many cases, the local structure of Hi-C maps may be predicted in silico based on patterns of CTCF binding and an extrusion-based model. Finally, I will show that by modifying CTCF motifs using CRISPR, we can reliably add, move, and delete loops and domains. Thus, it possible not only to “read” the genome’s 3D architecture, but also to write it.

Biography

Erez Lieberman Aiden received his PhD from Harvard and MIT in 2010. After several years at Harvard's Society of Fellows and at Google as Visiting Faculty, he became Assistant Professor of Genetics at Baylor College of Medicine and of Computer Science and Applied Mathematics at Rice University.

Dr. Aiden's inventions include the Hi-C method for three-dimensional DNA sequencing, which enables scientists to examine how the two-meter long human genome folds up inside the tiny space of the cell nucleus (Lieberman-Aiden & Van Berkum et al., Science, 2009). In 2014, his laboratory reported the first comprehensive map of loops across the human genome, mapping their anchors with single-base-pair resolution (Rao & Huntley et al., Cell, 2014). In 2015, his lab showed that these loops form by extrusion, and that it is possible to add and remove loops and domains in a predictable fashion using targeted mutations as short as a single base pair (Sanborn & Rao et al., PNAS, 2014). In 2017, his lab showed that it is possible to use 3D maps, generated using Hi-C, to assemble mammalian genomes, entirely from scratch, from short reads alone, at a total cost of under $10,000 (Dudchenko et al., Cell, 2014). Using this methodology, the Aiden lab reported the first end-to-end genome of the Aedes aegypti genome, which carries the Zika virus. Assembling the Aedes aegypti genome from end-to-end had been highlighted as essential to the worldwide Zika response by a front page article in the New York Times.

In addition, together with Jean-Baptiste Michel, Dr. Aiden also developed the Google Ngram Viewer, a tool for probing cultural change by exploring the frequency of words and phrases in books over the centuries. Now a product at Google, the Ngram Viewer is used every day by millions of people worldwide.

Dr. Aiden's research has won numerous awards, including recognition for one of the top 20 "Biotech Breakthroughs that will Change Medicine", by Popular Mechanics, membership in Technology Review's 2009 TR35, recognizing the top 35 innovators under 35; and in Cell's 2014 40 Under 40. His work has been featured on the front page of the New York Times, the Boston Globe, the Wall Street Journal, and the Houston Chronicle. One of his talks has been viewed over 1 million times at TED.com. Three of his research papers have appeared on the cover of Nature and Science. In 2012, he received the President's Early Career Award in Science and Engineering, the highest government honor for young scientists, from Barack Obama. In 2014, Fast Company called him "America's brightest young academic." In 2015, his laboratory was recognized on the floor of the US House of Representatives for its discoveries about the structure of DNA.


Thursday, February 4 @ 3 pm CT

Bruce TrombergOpen BME Seminar

Bruce J. Tromberg, PhD

Director, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH)

"Bioengineering for COVID-19: Rapid Acceleration of Diagnostics (RADx) at Unprecedented Speed and Scale"

Host: Lori Setton, PhD | Washington University in St. Louis


JANUARY 26 @ 4:30 pm CT

YoshidaBioengineering Colloquia

Kyoko Yoshida, PhD

Senior Scientist, Cardiac Biomechanics Group, Department of Biomedical Engineering, University of Virginia

"The mechanics behind the miracle of life: Maternal soft tissue growth and remodeling"

Abstract | Pregnancy stands at the interface of mechanics and biology. The growing fetus continuously loads the maternal organs while circulating hormones surge. In response to these dynamic mechanical and biological cues, virtually all maternal soft tissues grow and remodel. For example, a mother’s uterus will increase its cavity volume by 1000-fold, and her heart will pump 50% more blood over nine months of pregnancy. Precise mechanical function of the maternal reproductive tract and heart is critical for supporting a healthy pregnancy. If a mother’s uterus contracts or her cervix dilates too early, the pregnancy can result in preterm birth. If her heart fails to remodel correctly, she can develop heart failure towards the end of the pregnancy or immediately after giving birth. Alarmingly, rates of preterm birth and heart problems during pregnancy continue to rise. My research aims to uncover how mechanical and biological cues interact to drive pregnancy-induced soft tissue growth, remodeling, and mechanical function. I propose to achieve this goal by combining two emerging computational modeling approaches from the fields of biomechanics and systems biology: an organ-level mechanical model of how growth modifies stretch and contractility and a network model of the many intracellular signaling pathways that lead to growth.

This seminar will outline my Ph.D. work, which focused on experimental and computational pregnancy biomechanics, and my motivations to focus on heart growth mechanics for my postdoctoral research. Finally, I will outline how I will combine the skills I learned during my Ph.D. and postdoc to pursue my independent work, where I seek to answer the question: How does the uterus grow and stretch by 1000-fold but not contract until labor?

Biography

Dr. Kyoko Yoshida, Ph.D., is a Senior Scientist in the Department of Biomedical Engineering at the University of Virginia. She previously obtained her Ph.D. in Mechanical Engineering from Columbia University as an NSF Graduate Research Fellow and her B.S. in Mechanical Engineering from the University of Notre Dame. Her research focuses on the biomechanics of soft tissue growth and remodeling, including the cervix, uterus, and heart. Specifically, she is interested in using computational and experimental approaches to understand how mechanical and hormonal signaling interact to control maternal soft tissue adaptations during pregnancy to support both mother and baby for a healthy pregnancy.


JANUARY 19 @ 4 pm CT

Farid Alisafaei, PhDBioengineering Colloquia

Farid Alisafaei, PhD

NIH-T32 Postdoctoral Fellow, University of Pennsylvania

"Cell-Matrix Interactions in Cancer and Fibrosis"

Abstract | Although cross-disciplinary efforts in mechanobiology have elucidated a wealth of mechanical pathways and biomolecules relating mechanics to physiology and pathophysiology, identification of basic governing principles and development of predictive frameworks has lagged. In this seminar, I will present a theoretical framework that I developed to elucidate how different components of a cell work in concert to sense mechanical signals from the extracellular environment and transform these into biochemical responses and mechanical actions that, in turn, alter the extracellular environment. When combined with tightly integrated experiments, the model reveals roles of the cytoskeleton, nucleus, focal adhesions, and ion channels in sensing and responding to mechanical signals, in both healthy tissue and disease progression. The talk will conclude with examples of how the model enables us to understand and harness the role of force and mechanics in physiological processes such as wound healing, and pathological processes such as fibrocontractile diseases and tumor progression.

Biography

Farid Alisafaei, Ph.D., studies computational models of evolving biological and tissue-engineered systems. He is an NIH-T32 postdoctoral fellow at the University of Pennsylvania and a member of the NSF Science and Technology Center for Engineering Mechanobiology (CEMB). Dr. Alisafaei's current research focuses on how cells sense and respond to the mechanical properties of their microenvironment. His models have been applied to understand the mechanobiology of cancer progression, stem cell migration, and fibrocontractile diseases.


JANUARY 12 @ 4 pm CT

María CoronelBioengineering Colloquia

María Coronel, PhD

Postdoctoral Fellow, George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology

"Engineering Synthetic Biomaterials for Islet Transplantation"

Abstract | Two major challenges to the translation of cellular-based tissue-engineered therapies are the lack of adequate oxygen support post-implantation and the need for systemic immunosuppression to halt the strong inflammatory and immunological response of the host. As such, strategies that aim at addressing oxygen demand, and local immunological responses can be highly beneficial in the translation of these therapies. In this seminar, I will focus on two biomaterial strategies to create a more favorable transplant niche for pancreatic islet transplantation. The first half will describe an in-situ oxygen-releasing biomaterial fabricated through the incorporation of solid peroxides in a silicone polymer. The implementation of this localized, controlled and sustained oxygen-generator mitigates the activation of detrimental hypoxia-induced pathways in islets and enhances the potency of extrahepatic 3D islet-loaded devices in a diabetic animal model. In the second part, I will focus on engineering synthetic biomaterials for the delivery of immunomodulatory signals for transplant acceptance. Biomaterial carriers fabricated with polyethylene glycol microgels are used to deliver immunomodulatory signals to regulate the local microenvironment and prevent allograft rejection in a clinically relevant pre-clinical transplant model. The use of synthetic materials as an off-the-shelf platform, without the need for manipulating the biological cell product, improves the clinical translatability of this engineered approach. Designing safer, responsive biomaterials to boost the delivery of targeted therapeutics will significantly reinvigorate interventional cell-based tissue-engineered therapies.

Biography

Dr. María M. Coronel is currently a Juvenile Diabetes Research Foundation postdoctoral fellow at the Georgia Institute of Technology. Dr. Coronel completed her BS degree in Biomedical Engineering from the University of Miami, and her Ph.D. degree in Biomedical Engineering from the University of Florida as a National Institute of Health predoctoral fellow. Her doctoral work focused on engineering oxygen-generating materials for addressing the universal challenge of hypoxia within three-dimensional tissue-engineered implants. As a postdoctoral fellow, her research interest focus on engineering tools and principles to understand, stimulate, and modulate the immune system to develop controlled targeted interventional therapies. In addition to research, Dr. Coronel aims to be an advocate for diversity and inclusion in STEM as the co-president of the postdoctoral group and a founding member of the diversity, equity, and inclusion committee in bioengineering at Georgia Tech. Outside of the lab María enjoys cooking, baking, and traveling.


Past Seminars

Fall 2020

August 25, 2020 at 4 pm CST

Speaker 1
Arjun Raj, PhD
Professor, Bioengineering
University of Pennsylvania

"Emergent cellular ecosystems in melanoma revealed by single cell analysis"

Speaker 2
M.N.V. Ravi Kumar, PhD
Professor, Pharmaceutical Sciences
Texas A&M University - College Station

"Engineering the next generation of nanomedicines"

September 1, 2020 at 4 pm CST

Speaker 1
Jennifer Wargo, MD, MMSc
Professor, Department of Genomic Medicine, Division of Cancer Medicine
The University of Texas MD Anderson Cancer Center

"The role of the gut and tumor microbiome in cancer"

Speaker 2
Wei Gao, PhD
Assistant Professor of Medical Engineering, Division of Engineering and Applied Science
California Institute of Technology

"Skin-Interfaced Wearable Sweat Biosensors"

September 8, 2020 at 4 pm CST

Speaker 1
Arnab Mukherjee, PhD
Assistant Professor, Chemical Engineering
University of California Santa Barbara

"Molecular imaging with protein-based magnetic resonance reporters"

Speaker 2
Kristy Ainslie, PhD
Vice Chair, Division of Pharmacoengineering and Molecular Pharmaceutics
Professor, UNC Department of Biomedical Engineering

"Acetalated dextran: A spoonful of sugar helps the medicine (and vaccines) go down!"

September 15, 2020 at 4 pm CST

Speaker 1
Daniel Heller, PhD
Associate Professor, Molecular Pharmacology & Chemistry and Biomedical Sciences
Memorial Sloan-Kettering Cancer Center

Speaker 2
Neha Kamat, PhD
Assistant Professor of Biomedical Engineering
Northwestern

September 22, 2020 at 4 pm CST

Speaker 1
Mary Dunlop, PhD
Associate Professor, Department of Biomedical Engineering
Boston University

"Dynamics, Feedback, and Transient Stress Tolerance in Single Cells"

Speaker 2
Seung-Schik Yoo, PhD
Associate Professor, Department of Radiology
Harvard Medical School

"Acoustic disruption of drug-plasma protein binding as a new mode of neuromodulation"

October 6, 2020 at 4 pm CST

Speaker 1
Markita Landry, PhD
Assistant Professor of Chemical and Biomolecular Engineering
UC Berkeley

"Nanomaterials Enable Delivery of Genetic Material Without Transgene Integration in Mature Plants"

Speaker 2
Chang Liu, PhD
Associate Professor of Biomedical Engineering, Chemistry and Molecular Biology & Biochemistry
UC Irvine

"Synthetic Genetic Systems for Rapid Mutation and Continuous Evolution in vivo"

October 13, 2020 at 4 pm CST

Tara Deans, PhD
Assistant Professor of Biomedical Engineering
University of Utah

"Using synthetic biology to engineer therapeutic devices"

October 20, 2020 at 4 pm CST

John Ngo, PhD
Assistant Professor of Biomedical Engineering
Boston University

“Synthetic Mechanobiology: Engineering how cells sense and interpret mechanical cues”

October 27, 2020 at 4 pm CST

Speaker 1
Elisa Franco, PhD
Associate Professor of Mechanical & Aerospace Engineering and Bioengineering
UCLA

"Programming dynamic behaviors in molecular systems and materials"

Speaker 2
Elebeoba May, PhD
Associate Professor of Biomedical Engineering
University of Houston

"Investigating the Impact of the Proinflammatory Microenvironment on the Dynamics of Host Response to Infection"

November 10, 2020 at 4 pm CST

Speaker 1
Karmella Haynes, PhD
Associate Professor of Biomedical Engineering
Georgia Institute of Technology and Emory University

"Epigenetic co-regulation of genes with engineered sensor-actuator proteins"

Speaker 2
Timothy Downing, PhD
Assistant Professor of Biomedical Engineering
UC Irvine

"Synthetic Genome Regulation for Cell and Tissue Engineering"

November 17, 2020 at 4 pm CST

Susan N. Thomas, PhD
Associate Professor, George W. Woodruff School of Mechanical Engineering
Georgia Tech

"Engineered biomaterials and microfluidic systems that augment cancer immunotherapy and to analyze disease mechanisms"

December 8, 2020 at 4 pm CST

Julea Vlassakis, PhD
Postdoctoral Scholar, Department of Bioengineering
UC Berkeley

"Probing protein interactions from molecular to cellular scales with microscale technologies"