Constantine Dovrolis

Constantine Dovrolis
constantine@gatech.edu
For more than a decade, Constantine Dovrolis has been exploring the evolution of our interconnected world. Dovrolis serves as a Professor in the School of Computer Science, College of Computing at the Georgia Institute of Technology and is an affiliate of the Institute for Information Security & Privacy. He received his Bachelor's of Computer Engineering from the Technical University of Crete in 1995; Master’s degree from the University of Rochester in 1996, and his Doctoral degree from the University of Wisconsin-Madison in 2000.  Prior to joining Georgia Tech in August 2002, Dovrolis held visiting positions at Thomson Research in Paris, Simula Research in Oslo, and FORTH in Crete. His current research focuses on the evolution of the Internet, Internet economics, and on applications of network measurement.  He also is interested in cross-disciplinary applications of network science as it relates to biology, clIMaTe science and neuroscience. Dovrolis has served as an editor for the IEEE/ACM’s Transactions on Networking, the ACM Communications Review, and he served as the program co-chair for PAM'05, IMC'07, CoNEXT'11, and as the general chair for HotNets'07.  He was honored with the National Science Foundation CAREER Award in 2003.                                                   
Professor
Phone
404-385-4205
Office
Klaus 3346
Additional Research
Data Mining & Analytics; IT Economics; Internet Infrastructure & Operating Systems Network science is an emerging discipline focusing on the analysis and design of complex systems that can be modeled as networks. During the last decade or so network science has attracted physicists, mathematicians, biologists, neuroscientists, engineers, and of course computer scientists. I believe that this area has the potential to create major scientific breakthroughs, especially because it is highly interdisciplinary. We have applied network science methods to investigate the "hourglass effect" in developmental biology. The developmental hourglass' describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage''). Recent studies have found evidence in support of the hourglass effect at the genomic level. For instance, the phylotypic stage expresses the oldest and most conserved transcriptomes. However, the regulatory mechanism that causes the hourglass pattern remains an open question. We have used an evolutionary model of regulatory gene interactions during development to identify the conditions under which the hourglass effect can emerge in a general setting. The model focuses on the hierarchical gene regulatory network that controls the developmental process, and on the evolution of a population under random perturbations in the structure of that network. The model predicts, under fairly general assumptions, the emergence of an hourglass pattern in the structure of a temporal representation of the underlying gene regulatory network. The evolutionary age of the corresponding genes also follows an hourglass pattern, with the oldest genes concentrated at the hourglass waist. The key behind the hourglass effect is that developmental regulators should have an increasingly specific function as development progresses. Analysis of developmental gene expression profiles from Drosophila melanogaster and Arabidopsis thaliana provide consistent results with our theoretical predictions. We are currently working on the inference and analysis of functional and brain networks. More information about this project will be posted soon.
IRI and Role
Bioengineering and Bioscience > Faculty
Data Engineering and Science > Affiliated Faculty
Data Engineering and Science
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Computing > School of Computer Science

Shaheen Dewji, Ph.D.

Shaheen Dewji, Ph.D.
shaheen.dewji@gatech.edu

Shaheen Azim Dewji, Ph.D., (she/her/hers) is an Assistant Professor in the Nuclear & Radiological Engineering and Medical Physics Programs at the Georgia Institute of Technology, where she leads the Radiological Engineering, Detection, and Dosimetry (RED²) research group. Dewji joined Georgia Tech following three years as faculty at Texas A&M University in the Department of Nuclear Engineering, and as a Faculty Fellow of the Center for Nuclear Security Science and Policy Initiatives (NSSPI). In her prior role at Oak Ridge National Laboratory, where she remained for almost 9 years, Dewji was Radiological Scientist in the Center for Radiation Protection Knowledge. Her research interests include development of dose coefficients, shielding design, and nuclear material detection assay using gamma-ray spectroscopy. Her recent work has focused on associated challenges in uncertainty quantification in dose estimation/reconstruction associated with the external exposure and internal uptake of radionuclides associated with applications of emergency response, defense, nuclear medicine, and occupational/public safety using Monte Carlo radiation transport codes and internal dose modeling. Dewji completed her Masters and Ph.D. degrees in Nuclear and Radiological Engineering at the Georgia Institute of Technology in Atlanta, GA and was a fellow of the Sam Nunn Security Program. She received her Bachelor of Science in Physics from the University of British Columbia. Dewji currently serves on the National Academies of Science, Engineering, and Medicine – Nuclear and Radiation Studies Board and is a member of the Board of Directors for both the American Nuclear Society and Health Physics Society.
   

Assistant Professor
Phone
404.894.5800
Office
Boggs 3-15
IRI and Role
Bioengineering and Bioscience > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Engineering > Woodruff School of Mechanical Engineering

Zachary Danziger

Zachary Danziger
zachary.danziger@emory.edu

The effortlessness of moving your body belies the lurking complexity driving it. We are trying to understand how the nervous system makes something so complicated as controlling a human body feel so natural. We use human subjects studies, animal experiments, mathematical biology, and artificial intelligence to understand neural control of movement. New theories and insight promise advances in physical therapy, human-machine collaboration, brain-computer interfaces, neural modulation of peripheral reflexes, and more.

Associate Professor Division of Physical Therapy, Department of Rehabilitation Medicine
Associate Professor, W.H. Coulter Department of Biomedical Engineering
Phone
404-712-4801
IRI and Role
Bioengineering and Bioscience > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Emory University

Aditi Das

Aditi Das
aditi.das@chemistry.gatech.edu

Aditi Das did her BSc. (Hons.) Chemistry from St. Stephen's College Delhi, followed by M.S. (Chemistry) from I.I.T (Kanpur). She received her Ph.D. in Chemistry from Princeton University. She did post-doctoral work with Prof. Steve Sligar. She joined University of Illinois, Urbana-Champaign (UIUC) as a tenure track assistant professor in 2012. In 2019, she was promoted to associate professor with tenure. In 2022, she joined School of Chemistry and Biochemistry at Georgia Institute of Technology as an associate professor with tenure. Her research is in the area of enzymology of oxygenases that are involved lipid metabolism and cannabinoid metabolism.

Das is recipient of an American Heart Associate (AHA) career award and has been funded by National Institute of Health (NIH - NIGMS, NIDA and NCCIH), USDA, and National Multiple Sclerosis Society (NMSS). Her research was recognized by several National awards: Young Investigator award From Eicosanoid Research Foundation, Mary Swartz Rose Young Investigator Award and E.L.R. Stokstad award from American Society for Nutrition (ASN) for outstanding research on bioactive compounds for human health. She is also the recipient of Zoetis Research Excellence Award from her college. She was a co-organizer of the International Conference on Cytochrome P450. Recently her laboratory contributed several papers on cannabinoid metabolism by p450s. In recognition of this work, she was awarded El Sohly award from the ACS-Cannabis division for excellence in Cannabis research and is invited to give plenary lecture at ISSX meeting.  Das is also a standing study section member of BBM NIH study section. 

Associate Professor
Phone
609-203-6924
Office
3306 IBB
IRI and Role
Bioengineering and Bioscience > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Sciences > School of Chemistry & Biochemistry

James Dahlman

James Dahlman
james.dahlman@bme.gatech.edu

James Dahlman is a bioengineer / molecular engineer whose work lies at the interface of chemistry, nanotechnology, genomics, and gene editing. His lab focuses on targeted drug delivery, in vivo gene editing, Cas9 therapies, siRNA therapies, and developing new technologies to improve biomaterial design. 

The DahlmanLab is known for applying 'big data' technologies to nanomedicine. The lab is pioneering DNA barcoded nanoparticles; using DNA barcodes, >200 nanoparticles can be analyzed simultaneously in vivo. These nanoparticles are studied directly in vivo, and used to deliver targeted therapies like siRNA, mRNA, or Cas9. As a result of this work, James was named 1 of the 35 most innovative people under the age of 35 by MIT Technnology Review in 2018. James has won many national / international awards, and has published in Science, Nature Nanotechnology, Nature Biotechnology, Nature Cell Biology, Cell, Science Translational Medicine, PNAS, JACS, ACS Nano, Nano Letters, and other journals. James has also designed nanoparticles that efficiently deliver RNAs to the lung and heart. These nanoparticles can deliver 5 siRNAs at once in vivo, and are under consideration for clinical development. As a result, the lab has an interest in immunology and vascular biology. 

James supports entirely new research students come up with independently. To this end, DahlmanLab students learn how to (i) generate new ideas, (ii) select the good ones, and (iii) efficiently test whether the good ideas will actually work. 

Dahlman Lab students learn how to design/characterize/administer nanoparticles, how to isolate different cell types in vivo, how to rationally design DNA to record information, Cas9 therapies, and deep sequencing. As a result, the lab is an interdisciplinary group with students that have backgrounds in medicinal chemistry, BME, bioinformatics, biochemistry, and other fields. The lab welcomes students with all types of scientific backgrounds. The lab firmly stands by students, independent of their personal beliefs, preferences, or backgrounds.

Associate Professor
Phone
404-385-5262
Office
UAW 2101
Additional Research
In the Dahlman Lab, we focus on the interface between nanotechology, molecular biology, and genomics. We design drug delivery vehicles that target RNA and other nucleic acids to cells in the body. We have delivered RNAs to endothelial cells, and have treated heart disease, cancer, inflammation, pulmonary hypertension, emphysema, and even vein graft disease. Because we can deliver RNAs to blood vessels at low doses, sometimes we decide to deliver multiple therapeutic RNAs to the same cell at once. These 'multigene therapies' have been used to treat heart disease and cancer. Why is this important? Most diseases are caused by combinations of genes, not a single gene. We also rationally design the nucleic acids we want to deliver. For example, we re-engineered the Cas9 sgRNA to turn on genes, instead of turning them off. This enabled us to easily turn on gene A and turn off gene B in the same cell.
IRI and Role
Bioengineering and Bioscience > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Engineering > Coulter Department of Biomedical Engineering

Ahmet Coskun

Ahmet Coskun
acoskun7@gatech.edu

Ahmet Coskun is a systems biotechnologist and bioengineer, working at the nexus of multiplex imaging and quantitative cell biology.

Single Cell Biotechnology Lab is strategically positioned for imaging one cell at a time for spatial context. We are multi-disciplinary researchers interested in photons, ions, and electrons and their interactions with cells and tissues.  Using large-scale experiments and computational analysis, we address fundamental challenges in cancers, immunology, and pediatric diseases. Variability of single cell profiles can be used to understand differences in therapeutic response, as well as satisfy our curiosity on understanding how cells are spatially organized in nature.

Our lab aims to deliver biotechnologies for spatial multi-omics profiling vision at the single cell level.

1) Spatial genomics: Our lab was part of an early efforts to demonstrate spatially resolved RNA profiling in single cells using a sequential FISH method. We will continue leveraging seqFISH and correlation FISH (another computational RNA imaging method) for exploring spatial dynamics of cellular societies.

2) Spatial proteomics: Our lab develops expertise on antibody-oligonucleotide based barcoding for multiplex protein imaging using CODEX technology. We combine CODEX with super-resolution and 3D imaging to visualize and quantify subcellular epigenetic states of immune and cancer cells.

3) Spatial metabolomics: Our lab works on computational and isotope barcoding approaches for small molecule profiling using MIBI (Multiplexed ion beam imaging). 3D and subcellular metabolic state of individual cells are used to model functional modes of cellular decision making in health and disease.

We also develop machine learning and deep learning algorithms to make sense of imaging based single cell big data.

In a nutshell, we create image-based ‘omic technologies to reveal spatial nature of biological systems. We benefit from enabler tools:  Super-resolution bioimaging, barcoded biochemical reagents, advanced algorithms and automated microfludics. Topical interests include Spatial Biology, Liquid Biopsy, and Global Oncology.

Ahmet Coskun trained at Stanford (Postdoc/Instructor with Garry Nolan), Caltech (Postdoc with Long Cai) and UCLA (PhD with Aydogan Ozcan). His lab is currently funded by NIH K25, BWF CASI, Georgia Tech & Emory.

Assistant Professor of Biomedical Engineering
Phone
404-894-3866
Office
Petit Biotechnology Building, Office 1311
Additional Research
The Single Cell Biotechnology Lab aims to study spatial biology in health and disease. Our research lies at the nexus of multiplex bioimaging, microfluidic biodynamics, and big data biocomputation. Using high-dimensional nanoscale imaging datasets, we address fundamental challenges in immuno-engineering, cancers, and pediatric diseases. Our lab pursues a transformative multi-omics technology to integrate spatially resolved epigenetics and spatial genomics, proteomics, and metabolomics, all in the same platform. We uniquely benefit from super-resolution microscopy, imaging mass spectrometry, combinatorial molecular barcoding, and machine learning to enhance the information capacity of our cellular data. Variability of single cell images can be used to understand differences in therapeutic responses, as well as satisfy our curiosity on understanding how cells are spatially organized in nature.
IRI and Role
Bioengineering and Bioscience > Faculty
Data Engineering and Science > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology

Lily Cheung

Lily Cheung
lily.cheung@gatech.edu

Lily Cheung got her research start as a sophomore at Rutgers University, where she graduated Summa Cum Laude with a B.S. in Chemical Engineering in 2008. She then earned her Ph.D. in Chemical Engineering from Princeton University in 2013. Under the supervision of Stanislav Shvartsman, she characterized gene regulatory networks controlling the development of the model organism Drosophila melanogaster, using a combination of molecular biology, genetics, and reaction-diffusion modeling.

During her postdoctoral training with Wolf Frommer at the Carnegie Institution for Science, she designed biomolecular sensors to quantify sugar transport in plants. Her current interests include the use of high-throughput quantitative techniques and mathematical modeling to advance our understanding of how metabolic and gene regulatory networks interact to control plant growth.

Lily is the recipient of a NSF NPGI Postdoctoral Fellowship in Biology, a NSF CAREER Award, and a Human Frontier Science Program Early Career Award.

Assistant Professor
Phone
404-894-2826
Office
ES&T L1230
Additional Research
Engineering of genetically encoded biosensors Quantitative fluorescence microscopy and image analysis Computational models of gene regulatory networks Transcriptional regulation and developmental biology of plants The past fifteen years has seen dramatic advancements in genome sequencing and editing. The cost of sequencing a genome has decreased by two orders of magnitude, giving rise to new systems-level approaches to biology research that aim to understand life as an emerging property of all the molecular interactions in an organism. At the same time, technologies that allow site-specific modifications of the genome are enabling researchers to manipulate multicellular organisms in unprecedented ways. From reductionist approaches to systems biology, and from conventional plant breeding to synthetic biology, the future of plant biology research relies on the adoption of computational methods to analyze experimental data and develop predictive models. In biomedicine, mathematical models are already revolutionizing drug discovery; in agriculture, they have the potential to generate more efficient, faster growing crop varieties. The goal of the Cheung lab is to bring quantitative techniques and mathematical modeling to plants in order to gain systems-level insight into their physiology and development - particularly to understanding how metabolic and gene regulatory networks interact to control homeostasis and growth.
IRI and Role
Bioengineering and Bioscience > Faculty
Renewable Bioproducts > Faculty
Bioengineering and Bioscience
Renewable Bioproducts
University, College, and School/Department
Georgia Institute of Technology > College of Engineering > School of Chemical and Biomolecular Engineering

Sam Brown

Sam Brown
sam.brown@biology.gatech.edu

Sam Brown's lab studies the multi-scale dynamics of infectious disease. Their goal is to improve the treatment and control of infectious diseases through a multi-scale understanding of microbial interactions. Their approach is highly interdisciplinary, combining theory and experiment, evolution, ecology and molecular microbiology in order to understand and control the multi-scale dynamics of bacteria pathogens.

Professor
Office
ES&T 2244
Additional Research
Evolutionary microbiology, bacterial social life, virulence and drug resistance
IRI and Role
Bioengineering and Bioscience > Faculty
Data Engineering and Science > Research Community
Data Engineering and Science
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Sciences > School of Biological Sciences

Mark Borodovsky

Mark Borodovsky
borodovsky@gatech.edu

Dr. Borodovsky and his group develop machine learning algorithms for computational analysis of biological sequences: DNA, RNA and proteins. Our primary focus is on prediction of protein-coding genes and regulatory sites in genomic DNA. Probabilistic models play an important role in the algorithm framework, given the probabilistic nature of biological sequence evolution.

Regents' Professor
Director, Center for Bioinformatics and Computational Genomics
Senior Advisor in Bioinformatics, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention in Atlanta
Phone
404-894-8432
Office
EBB 2105
Additional Research

Development and applicaton of new machine learning and pattern recognition methods in bioinformatics and biological systems. Development and applicaton of new machine learning and pattern recognition methods in bioinformatics and biological systems. Chromatin; Epigenetics; Bioinformatics

IRI and Role
Bioengineering and Bioscience > Faculty
Data Engineering and Science > Affiliated Faculty
Data Engineering and Science
Bioengineering and Bioscience
University, College, and School/Department
Georgia Institute of Technology > College of Engineering > Coulter Department of Biomedical Engineering

Guy Benian

Guy Benian
pathgb@emory.edu

Guy Benian is a professor of cell biology and pathology in the Department of Pathology and Laboratory Medicine at Emory University School of Medicine. His research focus is on myofibril assembly and maintenance in the model genetic system, Caenorhabditis elegans; focus on the functions and structures of giant multi-domain proteins, and the mechanism by which myofibrils are attached to the muscle cell membrane and transmit force.

Department of Pathology and Laboratory Medicine Professor
Professor of Cell Biology, Emory University School of Medicine
Professor of Pathology, Emory University School of Medicine
Phone
404-727-5953
Office
Biomedical Research Building 105E
Additional Research
We use the powerful model genetic organism, C. elegans, to discover new conserved aspects about muscle assembly, maintenance and regulation. Although our work is basic science, it has relevance to human diseases of muscle including cardiomyopathies and muscular dystrophies. Our main projects are: (1) The structures and functions of giant polypeptides in muscle, >700,000 Da, that consist of multiple Ig and Fn domains and one or two protein kinase domains. One focus is to determine the substrates for these kinases, and how they are activated (normally autoinhibited). The problem of activation is being studied in collaboration with structural biologist Olga Mayans (Univ. of Konstanz) and biomedical engineer Hang Lu (Georgia Tech). Recently, we have discovered that UNC-89 (human "obscurin") kinase activity is required for proper mitochondrial organization and function. This has initiated a collaboration with Jennifer Kwong in Emory's Pediatrics Dept. (2) The molecular mechanism by which the muscle contractile units (sarcomeres) are attached to the muscle cell membrane and transmit force. This involves "integrin adhesion complexes" (IACs) consisting of the trans-membrane protein integrin and many other proteins. C. elegans muscle has 3 such IACs, and through a mutant screen, we discovered a conserved protein (a GEF for Rac) that directs assembly specifically at one of these sites. (3) In collaboration with biophysicist Andres Oberhauser (UTMB), we are studying the mechanisms by which the conserved myosin head chaperone, UNC-45 folds or re-folds myosin heads, and we have recently discovered a role for UNC-45 in muscle aging (sarcopenia). This project has also branched into a screen for small compounds that increase the expression of UNC-45 and reduce sarcopenia. (4) We have a long-term collaboration with Dan Kalman in Emory's Pathology Dept. to study the beneficial effects of small molecules produced by the gut microbiome that promote healthspan, especially the attenuation of sarcopenia.
IRI and Role
Bioengineering and Bioscience > Faculty
Bioengineering and Bioscience
University, College, and School/Department
Emory University > Department of Pathology