Elif Tekin is a postdoc in the Yeh and Savage groups through the departments of Biomathematics and Ecology and Eovlutionary Biology. Elif is working on mathematical theory along with data and image analysis to elucidate optimal branching angles and asymmetric branching in vessel lengths in real vascular networks. She is also conducting research on how to measure emergent interactions that occur when more than two components (pairwise interactions) are involved. These theoretical questions are being applied both to consumer-resource interactions in food webs and combinations of antibiotics used to treat bacteria and slow antibiotic resistance.
Alex Brummer is a postdoc in the Savage group through the Depts. of Biomathematics and of Ecology and Evolutionary Biology. Alex is working to develop new models for asymmetric branching in vascular netowrks and how the degree or pattern of asymmetry could affect values of allomatetric scaling exponents that encapsulate, for instance, how metabolic rate, heart rate, lifespan, and sleep change with body size across species. These models invovle both detailed modeling of the fluid dynamics of blood or water through these networks as well as models for how these networks fill space and branch in a fractal-like manner to satsify both these spatial and fluid-mechanical constraints. Concurrent with this, Alex is using our group's software to analyze images of vaculature from various tissue and taxa that range from plants to animals, from lung to brain, and from roots to leaves. This helps both to identify patterns of vascular branching that are prevalent in nature and to test models. Current work is trying to classify networks based on their branhcing, including applications to tumor growth and stroke recovery.
Bjørn Østman is a postdoc in the Yeh and Savage groups through the Dept. of Ecology and Evolutionary Biology. Bjørn is working to understand interactions among multiple drugs and how this affects fitness landscapes such that evolution could be exploited to slow the pace at which antibiotic resistance develops. He accomplishes this through the analysis and visualization of large datasets based on newly developed models and concepts that are compared with existing ideas in the literature.
Daniel Wieczynski is a postdoc in the Savage group through the Dept. of Ecology and Evolutionary Biology. Dan is working to analyze large datasets and to test and developed models related to Trait Driver Theory to better understand and predict how the distribution of organismal traits (e.g., optimal temperature for growth, thermal breadth, Specific Leaf Area (SLA), etc.) changes with environmental drivers (e.g., temperature and water availablity across latitude, altitude, and other gradients.
Mauricio Cruz Loya is a doctoral student in the department of Biomathematics at UCLA. Previously, he received a bachelor's degree in Basic Biomedical Research from the National Autonomous University of Mexico. He is currently doing theoretical and computational work to try to understand the effects on bacterial antibiotic resistance when multiple antibiotics are combined.
Panagiotis Lymperopoulos is an undergraduate majoring in Computational and Systems Biology. He is devising genetic algorithms to explore optimal geometric structures in vascular networks that need to fill space and efficicently deliver resources via fluid flow (e.g., blood).
Jocelyn Shen is a high school student who is working with the Savage lab to test new code for analyzing vascular networks. She is currently working to implement machine-learning methods to classify branching nodes and vacular networks (e.g., different tissues and taxa).
Caroline Choi is a high school student who is working with the Savage lab to test new code for analyzing vascular networks and write code to calculate scaling exponents based on these data.
Inthat Boonpongmanee is a high school student who works in the Savage lab to test the new C++ code for analyzing vascular networks with less hierarchical and more grid like structures such as those found in stroke recovery and leaves.
Matthew Burke is a high school student who works in the Savage lab to test the new C++ code for analyzing vascular networks with less hierarchical and more grid like structures such as those found in stroke recovery and leaves.
Mitchell Newberry successfully defended his masters degree at UCLA in September. He is currently a graduate student at the University of Pennsylvania with Joshua Plotkin. For his project he wrote software in OCaml to read angiographic data (e.g., MRI, CT scans, X-rays, etc.) and use image processing to extract the structure of the vascular system, including a skeletonized network version and measures of vessel raddi, length, volumes, and more. He also wrote software for visualizing and analyzing the extracted data to determing the fractal exponents and types of distributions that characterize the vessel geometry across branching junctions.
Lewis Lee is a doctoral student in the Department of Biomathematics and the System & Integrative Biology Training Program. Current research in collaboration with Dr. Pamela Yeh’s laboratory aims to uncover structural dynamics of phenotypic variation in fluctuating environments using an experimental microbial system. This investigation may generate new theoretical constructs for use in the study and mathematical modeling of bacterial and tumor heterogeneity.
Kevin Leu is an MSTP student in the School of Medicine at UCLA. He is working to help connect models and data for tumor growth, and specifically how the structure and flow of tumor vasculature can be used to predict rates of growth, fractions of proliferative, quiescent, and necrotic cells, and regrowth after treatment.
Janice Chan is currently a graduate student in Organismic and Evolutionary Biology at Harvard University. While an undergraduate at UCLA, she learned Matlab and begain analyzing key traits, such as consumption and population growth rate, from our comprehensive database to test the hypothesis of "Hotter is Better"--higher temperatures result in higher absolute values for fitness and other traits.
Kina Winoto graduated with a computer science degree from the UCLA School of Engineering and Applied Science. After leaving UCLA, she earned a Masters in Computer Science Columbia University and now works at Sandia National Laboratories. As part of and NSF funded REU project, she worked on a comprehensive database for the temperature responses of traits and migrated it from Access to MySql. She also streamlined the database as part of this process and helpied to develop a web interface for other researchers to upload, download, and analyze data as part of this evolving trait database.
Preeti Chayapathi graduated from UCLA in 2015 as a Computational and Systems Biology major. She conducted research to explore space filling geometries and how they connect with self similarity, asymmetry, and scaling in vascular networks. She alsoworked to developin code that would allow the Angicart software to be run from Matlab and be fully coordinated with the data analysis.
Tang-wei (William) King graduated from UCLA and is now a graduate student in the Department of Biology and University of Washington. He has in interests in marine biology and thermal responses. He helped to manage the Biotraits database and website, and he analyzed data from Biotraits to test for latitudinal patterns in thermal responses within and across species.
Kathryn Burch graduated from UCLA as an Computational and Systems Biology major and will soon start as a graduate student in Bioinformatics at UCLA. She is involved in research to explore self similarity, asymmetry, and scaling in vascular networks. She is running the OCaml code, Angicart, on angiographic images and analyzing the large volumes of data extracted from those images. She is interested in how results vary across species and between healthy and diseased states.
Benjamin Demaree graduated from Santa Clara University and is now a graduate student in Bioengineering at UC Berkeley. He was an AmGen scholar in my lab during the Summer of 2013. He researched self similarity, asymmetry, and scaling in vascular networks. He wrote code to analyze vascular data and simulated vascular networks with asymmetric branching to discover simple models that best match real data.
Dalit Yadegaran graduated from UCLA. Her work involved a research project to explored mechanisms that control species interactions. The project uses high-speed video and automated tracking software to understand how environmental drivers (e.g., light, temperature, humidity, etc) affect the components and dynamics of predator-prey relationships. She was primarily responsible for running predator-prey trials with a variety of insects as well as analysis of video using Matlab.
Agafe Saguros graduated from UCLA and used video and automated tracking software to understand how temperature affects predator-prey interactions in insects via its effects on components such as body velocity, detection distance, turning angle, handling time, and other factors. She is currently a pharmacy intern at the University Medical Center of Southern Nevada.
Sania Pouyanard graduated from UCLA and worked with video and automated tracking software to study how temperature and dimensionality of the seach space/habitat can affect consumption rates in predator-prey interactions for insects.
Angelicia Thomas graduated from Alabama A&M University as a physics major. She worked in the Savage lab to stitchtogether images of zerbrafish vasculature across the entire body of the fish and that could be tracked across development. She also used angicart to analyze the data and search for patterns in the vasculature.
Junyu Cao graduated from Xi'an Jiatong University and will be attending graduate school at UC Berkeley in Operations Research and Management. Junyu worked to developed new theory for the function of sleep by analyzing developmental data for sleep times, brain size, and brain metabolic rate, and then comparing results for how sleep changes with size across species. By investigating prominent hypotheses for the function of sleep, such as repair and reorgnization, this research could help disentangle the relative roles and timing of various functions.
Shanice Seawright is an undergraduate biology major at Alabama A&M who is working in the Savage Lab for the summer. She is applying the angicart software to new images systems, which will involve image processing, application of softwar, and data analysis.
Nandini Chitale is an undergraduate major in Computational and System Biology at UCLA. She analyzed the biotraits database to look for shifts in thermal repsonses across habitats. She also helped maintain and improve the functionality of the biotraits database.
Maya Josyula graduated from high school from Cupertino, CA and will begin CalTech in Fall 2015. She helped to perform a sensitivity analysis for algorithms used in the OCaml code, Angicart, as applied to available angiographic images. She also helped to analyze data for branching angles and for asymmetric length distributions as well as understanding and helping to develop models to understand these data. She is now enrolled as an undergraduate at Cal Tech.
Matthew Aquilina helped the lab edit and improve its MySQL databases and webpages for searching and downloading data.
Edward Hu analyzed empirical data for vascular networks and helped to conduct rigorous tests of theories for optimal branching angles and length distributions. He is now enrolled as an undergraduate at USC.
Aditya Athota worked on computational models of how vascular networks efficiently fill the three-dimensional space of the body.
Quentin Lepak worked in the Savage lab to analyze empirical data for vascular networks in order to test models for optimal branching angles and distributions of vessel lengths. He is now an undergraduate here at UCLA.
Seth Talyansky is a high school student who worked with the Savage lab to test new code for analysying vascular networks with less hierarchical and more grid like structures such as those found in stroke recovery and levaes.