Dr. Seungchan Kim will co-chair 2019 IEEE BIBM Workshop Single Cell -Omics: Challenges and Opportunities (BIBM-SCOMICS) with Dr. Harshil Dhruv (Tolero Pharmaceuticals, Inc.) and Dr. Anoop Sood (GEGR). The workshop will be a part of IEEE BIBM 2019 (San Diego, CA, Nov. 18-21). The workshop will bring various expertise, including enabling technologies and computational methods utilizing such technologies to empowering biomedical studies. We will place special emphasis on multi-model data acquisition, image analytics, particularly spatial analyses and computational challenges with this large-scale data. The Program Committee includes experts from both academic and industries. More detailed information can be found here, including our own Dr. Xishuang Dong.

Speaker: Mohamed F. Chouikha, Ph.D.

Time & Date: 12:00pm, Wed., November 13, 2019

Room: ELEN 231

Abstract

In 2003 President Bush declared “The way business is transacted, government operates, and national defense is conducted have changed. These activities now rely on an interdependent network of information technology infrastructures called cyberspace.” That same year a national strategic plan to secure cyberspace was published. In this talk, the presenter will discuss the relevance and the impact of cybersecurity since then. Illustrative examples will be given to describe the landscape and to emphasis the importance of the creation of a unified view of cybersecurity based on existing and new tools. The presenter will also describe how PVAMU can be involved in this endeavor. The talk will be kept to a minimum of technical details, but those technical terms needed will be defined in the context of their use.

Speaker Bio

Dr. Mohamed F. Chouikha received his Ph.D. in EE from the University of Colorado in Boulder. In 1988 he joined, the Department of Electrical and Computer Engineering at Howard University, where he was the Department Chair of the ECE Department. He was the Director of the IC-Center of Academic Excellence, the founding and first Director of the Center of Applied High Performance Computing and one of the founding Directors of the Washington Academy of Biomedical Engineering. His research interest covers many subjects including but not limited to Hardware cybersecurity, Statistical Machine Learning, Signal Processing and automatic test pattern generation and verification of complex digital systems. Dr. Chouikha has been actively involved in undergraduate and graduate training for more than 30 years. He has supervised many Masters, PhDs, and Post doctorial students and introduced significant changes in the graduate and undergraduate curricula to reflect modern trends. Another important focus of Dr. Chouikha work has been on enhancing the recruitment and retention of underrepresented minorities in engineering.

Dr. Seungchan Kim is looking for a post-doctoral fellow for Computational Biology and Bioinformatics. Ph.D. in bioinformatics, computational biology, computer science, electrical engineering, or related field with research experience in computational biology and bioinformatics are required to apply. Strong programming skills in R/Bioconductor and/or Python are also required. The post-doctoral fellow is expected to work on Development of Classifiers for Novel Bladder Cancer Subtypes and Noncoding RNA Biomarkers for Noninvasive and Early Detection of Pancreatic Cancer. The projects are highly collaborative, working with cancer biologists, oncologists, and other computational scientists. In addition, it is also expected for the post-doctoral fellow to establish his/her own research portfolio to help her/his career development. The CCSB@PVAMU provides highly collaborative research environment to support the post-doc's research development. The interested applicant should submit their application here (R-002904), or contact Dr. Seungchan Kim for any further inquiry.

Speaker: Yang Shen, Ph.D.

Time & Date: 12:00pm, Thur., November 7, 2019

Room: ELEN 231

Abstract

A major barrier to effective therapeutics for cancers and infectious diseases is that these systems are highly adaptive. Under selective pressures of therapeutics, tumors and bacteria will inevitably evolve therapeutic resistance often through mutating therapeutic targets. Current drug discovery and development processes often react to therapeutic resistance post hoc. In this talk, I will first present a computational scheme that, when interacting with experimental approaches, can help address this challenge a priori. Specifically, we have designed an inverse approach to recast the problem of anticipating resistance mutations into combinatorial protein design; and we have developed an exact algorithm iCFN (interconnected cost function networks) that guarantees the optimal and sub-optimal solutions for multistate protein design. When applied to model ESR1 mutations in metastatic breast cancer, iCFN correctly predicts clinically-validated resistance mutations and provides further mechanistic insights.

Another barrier to therapeutic discovery is the enormous chemical and proteomic spaces, which demands rapid quantification of compound-protein interactions (CPI). There was a lack of computational CPI prediction methods with wide applicability, high accuracy, and mechanistic interpretability. In the second part of the talk, I will present DeepAffinity, our recent AI-empowered method that integrates knowledge- and learning-based approaches to address the challenge using chemical identities and protein sequences alone. Specifically, the semi-supervised deep learning model jointly encodes molecular representations and predicts CPI, with attention mechanisms for model interpretability. Case studies include predicting selective drug-target interactions as well as explaining them in binding sites or selectivity origins.

Speaker Bio

Dr. Yang Shen is an Assistant Professor in the Department of Electrical and Computer Engineering at Texas A&M University. He received his B.E. from the University of Science and Technology of China, Ph.D. in Systems Engineering from Boston University, and postdoctoral training in Biological Engineering and Computer Science at the Massachusetts Institute of Technology. Prior to joining TAMU, he had been a research assistant professor at Toyota Technological Institute at Chicago. Dr. Shen’s research interests are in optimization and learning algorithms for modeling biological molecules, systems, and data. In particular, ongoing projects include prediction and design of protein interactions, mechanistic prediction of protein mutational effects, and resistance-overcoming drug design.

Speaker: Woonyoung Choi, Ph.D.

Time & Date: 12:00pm, Wed., October 23, 2019

Room: ELEN 231

Abstract

Objective of Study: Advances in genomics technologies allow us to investigate molecular heterogeneity in cancer. Recent studies have identified muscle invasive bladder cancer (MIBC) molecular subtypes that are enriched with clinically actionable features such as specific mutations, copy number aberrations (CNAs), or molecular markers. Here, we provide an overview and clinical implications of the molecular subtypes.

Recent Findings: Early studies using unsupervised clustering analyses in bladder cancer revealed that non-muscle invasive bladder cancer (NMIBC) is easily distinguished from MIBC, implying that there are at least two major molecular subtypes in bladder cancer that conform closely with the stage. Recent studies identified MIBC subtypes that resembled the basal and luminal intrinsic subtypes in breast cancer. Basal tumors are associated with advanced stage at presentation and shorter survival in the absence of neoadjuvant chemotherapy. They are enriched with the mutations of TP53 and RB1 and squamous feature. Basal tumors are subdivided into ‘immune infiltrated’ and ‘immune suppressed’ subsets. Immune infiltrated basal tumors are significantly enriched with the characteristics of CD8+ T cells and active IFN-gamma signaling. Luminal tumors are enriched with papillary histology and they also can be subdivided by the signature of fibroblast infiltration, genomic unitability and activating FGFR3 mutations. Importantly, these subtypes have different prognosis and various response to systemic chemotherapy and immunotherapy. If the clinical implication of the molecular subtypes is validated prospectively, this information will be incorporated into the decision making for the management of bladder cancer patients.

Speaker Bio

Dr. Woonyoung Choi is an Assistant Professor of Urology and Director of Genomics for the Greenberg Bladder Cancer Institute at Johns Hopkins University. Dr. Choi was trained as a postdoctoral fellow in the Cancer Genomics Core Laboratory at the University of Texas MD Anderson Cancer Center, then joined at the department of Urology at Johns Hopkins School of medicine to have played a leadership role in the management of the expression profiling facility. Her research is focused on defining the biological mechanisms underlying the molecular subtypes that are observed in bladder cancer, with the goal of developing new therapeutic interventions. Dr. Choi’s research on molecular subtypes has been published in high impact factor journals (Cancer Cell, Nature Review Urology, European Urology) and highly regarded in the bladder cancer research fields.

Speaker: Dumitru A. Iacobas, Ph.D.

Time & Date: 12:00pm, Wed., October 9, 2019

Room: ELEN 231

Abstract

Brain is the most complex organ of the human body, containing almost 100 billion neurons and a roughly equal number of non-neuronal nervous cells: astrocytes, oligodendrocytes and microglia. Brain is organized in a very sophisticated way, well-defined anatomical regions coordinating all major physiological processes in the body. Thus, the hypothalamus is responsible for the regulation of metabolism, body temperature, hunger, parenting and attachment behaviors, thirst, fatigue, sleep, and circadian rhythms. Hippocampus controls anxiety and social fearfulness, spatial learning, memory and novel object recognition. The prefrontal cortex controls the social behavior, including aggression and emotional reactivity. Despite gender equality with respect to the law, male and female behaviors are not identical even for twins, males performing better than females for certain tasks but worse for others. Most likely, the behavior and cognitive differences are related to the ways the brain circuits are formed in each sex and remodel during cerebral activities, progression of a neurological disease or in response to a treatment. Every neuron is connected by synapses with up to ten thousands other neurons. Glutamatergic is the major excitatory and GABAergic the major inhibitory synapse, both of them associated with major mental functions. The cholinergic synapse facilitates learning, memory and attention, the dopaminergic synapse controls learning, memory, motivation and reward, and the serotonergic synapse is involved in learning and memory, emotion, and abnormal mood and cognition. However, the molecular mechanisms specializing each brain area for a particular mental function are still to be understood. Still far from completely known are how the genomic alterations result in cognition and other brain functions decline. The seminar will present speaker’s results from profiling the cortex, forebrain, hypothalamus arcuate and paraventricular nuclei, hippocampal C1, C2 and dentate gyrus, as well cultured astrocytes, oligodendrocytes and neurons from mouse, rat and rabbit models of epilepsy, infantile spasms, autism, gliosis and other neurological disorders.

Speaker Bio

Dr. Iacobas, Research Professor and Director of the CCSB Personalized Genomics Laboratory from 2018, is an expert of both experimental and computational genomics. Trained as a biophysicist (PhD of the University of Bucharest, Romania), he was on faculty positions at medical schools from Romania (1981-2001) and NY (Albert Einstein College of Medicine-Neuroscience 2001-2013, New York Medical College-Pathology 2013-2017). At NYMC he founded and directed the Systems Biology Core and at Einstein he was the Associate Director of the Neurogenomics Core.

Out of the 236 Iacobas’ publications, 53 are as single author, 114 as first author and 31 as last author. The neuroscience-related publications include 3 patents in neuromicroelectrophsyiology, 3 books, 3 book chapters and 40 papers in: Biochem Biopys Res Comm, Biochim Biofis Acta, Biol Theory, Biophys J, Brain Res, Cell Commun Adhes, EMBO J, Eur J Neurosci, Exp Brain Res, Exp Neurol, Front Int Neurosci, Front Neurosci, Genes, Genomics, J Biomol Tech, J Membr Biol, J Neuroend, J Neuroparasitol, J Neurosci Res, Mol Genet Genomics, Nature Sci Rep, Neural Regen Res, Neurochem Intl, Neuron Glia Biol, Physiol Genomics, Prog Biophys Mol Biol. He has also 3 bioprojects, 5 nucleotides, 11 proteins and 56 neuroscience-related genomic datasets included in the database of the National Library of Medicine.

Most recent neuroscience publication is: Iacobas DA, Iacobas S, Lee PR, Cohen JE, Fields RD (2019). Coordinated Activity of Transcriptional Networks Responding to the Pattern of Action Potential Firing in Neurons. Genes 10(10), 754. doi: 10.3390/genes10100754.

Speaker: Bisrat Debeb, DVM, Ph.D.

Time & Date: 12:00pm, Wed., September 25, 2019

Room: ELEN 231

Abstract

Brain metastasis occurs in 15-30% of patients with inflammatory breast cancer (IBC), a very aggressive and highly metastatic variant of breast cancer. Brain metastasis disproportionately affects those patients with HER2+ and basal-like/triple-negative breast cancer (TNBC) subtypes. Despite significant advances in the systemic treatments of breast cancer, only minimally active drugs are currently available for patients with breast cancer brain metastasis. The prognosis for patients with breast cancer brain metastasis is dismal with a survival time ranging from 5 weeks for untreated patients to 6 months for patients given multimodality treatment. Therefore, novel and effective therapeutic approaches are urgently needed for such patients. Understanding the biology and mechanisms underlying metastatic dissemination to the brain are crucial for developing new therapies to treat breast cancer brain metastases. We have developed unique preclinical mouse models of brain metastasis from TNBC and HER2+ IBC cells and used these models to identify key regulators of metastatic dissemination to brain. In this seminar, I will present a brief background on brain metastasis and IBC, discuss the novel models of brain metastasis that we developed in our lab, and provide insights into the molecular mechanisms of some of the top candidate proteins, that we identified through proteomic and transcriptomic approaches, that are associated with aggressiveness and metastasis in IBC.

Speaker Bio

Dr. Bisrat Debeb is an Assistant Professor in the Department of Breast Medical Oncology at The University of Texas MD Anderson Cancer Center in Houston, Texas. Dr. Debeb received his Doctor of Veterinary Medicine (DVM) degree from Addis Ababa University, his Masters from Tuskegee University, and his Ph.D. from Texas A&M University. He completed his postdoctoral training at MD Anderson Cancer Center. The major research interests of Dr. Debeb’s lab are understanding molecular and cellular mechanisms underlying the unique pathobiology of inflammatory breast cancer (IBC), a rare but highly metastatic lethal form of primary breast cancer, and identification of molecular determinants of breast cancer brain metastasis. His lab conducts both basic and translational breast cancer research with an overarching goal of developing novel and effective therapeutic strategies to improve survival of patients with aggressive breast cancer and brain metastasis. Current efforts in his lab include developing mouse models of brain metastasis, identification of novel drivers of IBC tumorigenesis and brain metastasis, and evaluation of serum from IBC patients to identify biomarkers of aggressiveness, brain metastasis and therapy resistance.

On Tuesday, Sept. 10, 2019, Dr. Tesfamichael Kebrom was awarded a Faculty Innovation and Enhancement (FIE) funding for a collaborative research project to “Acquire Plant Growth Facility to Establish Plant Genomics Research at PVAMU”, for the amount of $19,110.00. This collaborative research project is also supported by the College of Agriculture and Human Sciences (CAHS) with $20,000.00, and the Center for Computational Systems Biology with an additional $20,000.00. This collaboration was made possible by enthusiastic support from Dean D'Souza (College of Agriculture and Human Sciences) and Dean Obiomon (Roy G. Perry College of Engineering). For this project, Dr. Kebrom will collaborate with Dr. Xishuang Dong who will provide computational support for the data generated from this collaboration.

Dr. Kebrom was hired as a Research Scientist for Plant Systems Biology at the Center for Computational Systems Biology (Roy G. Perry College of Engineering) and the Cooperative Agricultural Research Center (College of Agriculture and Human Sciences) in April 2019. His current research interest focus on identifying gene regulatory networks and molecular pathways controlling plant growth and development in response to environmental and endogenous factors using plant systems biology approaches, and developing strategies for improving crop yield and tolerance to abiotic stress such as reduced light, water, and plant nutrients.

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