Genomic fabric remodeling in neurological disorders - a Special Issue of the MDPI Journal Genes will be guest-edited by Drs. Dumitru A Iacobas (CCSB-PVAMU) and David C Spray (Albert Einstein College of Medicine). Details in https://www.mdpi.com/journal/genes/special_issues/Genomic_Fabric

Speaker: Seungchan Kim, Ph.D.

Time & Date: 12:00pm, Wed., February 19, 2020

Room: ELEN 231

Abstract

Single-cell-based sequencing has emerged as an enabling technology to explore molecular patterns of cells at “single cell” level, by dissociating individual cells and sequencing them individually at -omcs level. The technology provides a uniquely detailed view of individual cells, but also poses a significant technical and computational challenges in analyzing such a large-scale data resulting from it. The challenges include sheer scale of data, both in the number of features and the number of samples, and more critically sparsity of data. Various computational models and analysis techniques have been developed to cope with those issues. Biological questions of significance include identifying cell types, discovering subsets of cells based on molecular patterns, and defining molecular signatures of those cell types and subsets. Even though computational challenges exist, single-cell-based RNA sequencing (scRNAseq) data also provide a unique opportunity to study cellular and molecular heterogeneity of individual patient or sample as well as inquire them with systems view, which was not possible previously as all of these approaches require significantly large number of samples. This talk will introduce some of these computational tools, mostly publicly available, and some of tools that we developed, using scRNAseq data from glioblastoma, pancreatic cancer, and pulmonary hypertension.

Speaker Bio

Dr. Seungchan Kim is a Chief Scientist and Executive Professor in the Department of Electrical and Computer Engineering and Director of the CRI Center for Computational Systems Biology at the Prairie View A&M University (PVAMU). Prior to joining PVAMU in December 2016, he was the Head of Biocomputing Unit and an Associate Professor at Integrated Cancer Genomics Division of Translational Genomics Research Institute (TGen). He was one of the founding faculty members of TGen, founded in 2002, by Dr. Trent, then-Scientific Director of the National Human Genome Research Institute at the National Institutes of Health. He was also an Assistant Professor in the School of Computing, Informatics, Decision Systems Engineering (CIDSE) at the Arizona State University from 2004 till 2011. Dr. Kim received his Ph.D. in Electrical Engineering from the Texas A&M University. He was also trained as a post-doctoral fellow at the Cancer Genetics Branch of National Human Genome Research Institute. Dr. Kim is well recognized in the field of Bioinformatics and Computational Systems Biology research, both nationally and internationally. His research interests include: 1) mathematical modeling of genetic regulatory networks, 2) development of computational methods to analyze multitude of high throughput multi-omics data to identify disease biomarkers, and 3) computational models to diagnose patients or predict patient outcomes, for example, disease subtypes or drug response. His studies have had a large influence on the development of computational tools to study underlying mechanisms for cancer development and better understand the molecular mechanisms behind cancer biology and biological systems.

Speaker: Mathew Sadiku, Ph.D.

Time & Date: 12:00pm, Wed., February 05, 2020

Room: ELEN 231

Abstract

The industrial revolution changed the dynamics of our society through rapid urbanization, rise of cities, diversity of the workforce, rise of the middle class, and creation of job opportunities. The Internet revolution brought with it changes that were not only technological but societal and pervasive in scope. The Internet today is a widespread information infrastructure, which is often called the Information Superhighway. It is regarded by many as the greatest technological disruption of all time. The speaker has identified seven key emerging Internet-related technologies: Internet of things, big data, cloud computing, cybersecurity, smart anything (smart home, smart cities, smart transportation, etc.), software-defined networking, and online education. Together these technologies are transformational. This seminar presents a brief introduction, applications, and challenges for each technology.

Speaker Bio

Dr. Matthew Sadiku is presently a professor of electrical and computer engineering at Prairie View A&M University, Prairie View, Texas. He is the author of over 720 professional papers and over 80 books including “Elements of Electromagnetics” (Oxford University Press, 7th ed., 2018), “Fundamentals of Electric Circuits” (McGraw-Hill, 6th ed., 2017, with C. Alexander), “Computational Electromagnetics with MATLAB” (CRC, 4th ed., 2018), “Metropolitan Area Networks” (CRC Press, 1995), and “Principles of Modern Communication Systems” (Cambridge University Press, 2017, with S. O. Agbo). Some of his books have been translated into French, Korean, Chinese (and Chinese Long Form in Taiwan), Italian, Portuguese, and Spanish. He is an IEEE fellow and the recipient of many awards.

Speaker: Megumi Hada, Ph.D.

Time & Date: 12:00pm, Wed., January 22, 2020

Room: ELEN 231

Abstract

Long duration space flight in deep space is becoming a closer reality. Radiation in deep space is the most significant health concern. The space environment consists of varying field of radiation particles including high-energy protons, high charge and energy (HZE) nuclei, as well as secondary particles that are generated when the primary particles penetrate the spacecraft shielding. High-LET heavy ions are particularly effective in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, which can be utilized as a biomarker for radiation insults. Over the years, we have studied chromosomal damage in human fibroblast, epithelial, and lymphocyte cells exposed in vitro to energetic charged particles generated at several international accelerator facilities. We have also studied chromosome aberrations in astronaut’s peripheral blood lymphocytes before and after space flight. Various fluorescence in situ hybridization techniques have been used to identify chromosome regions ranging from the telomere region to whole chromosome painting of all chromosomes simultaneously in one cell. I will summarize the results of the investigations and discuss the unique radiation signatures and biomarkers for space radiation exposure.

Speaker Bio

Dr. Megumi Hada is a Senior Research Scientist in the CRI / Radiation Institute for Science & Engineering. She has been worked Human Health Program at NASA before she moved to PVAMU 3 years ago. Her research interest is in effects of space radiation environment modeling and studying biological consequences on humans. Main focus of her research is how to protect astronauts from space radiation exposure by developing counter measures and risk assessment. Recently she has started study combined effects of microgravity and space radiation on human cells.

Speaker: Anna Joy, Ph.D.

Time & Date: 12:00pm, Wed., December 11, 2019

Room: ELEN 231

Abstract

Variations in the tumor immune microenvironment between Glioblastoma (GBM) patients complicates development and testing of immunotherapies. We used publicly available single cell RNA sequencing data of GBM patients to extract pan immune-specific genes in GBM. Interrogating bulk GBM sequencing or microarray data with pan immune-specific genes should allow examination of the immune component. We used pan immune-specific genes to investigate subtypes of GBM immune microenvironments. Consensus clustering using these genes on GBM TCGA RNAseq data gave 4 distinct subtypes while 12% of tumors were not assigned to any of those subtypes. Immune subtypes had distinct clinical outcomes. Differences in median survival (16.6 vs 5.8 months; longest vs. shortest survival; p < 1e-05 Logrank, Wald and Likelihood ratio tests) suggests the immune microenvironment significantly impacts clinical course. Cox univariate analysis indicates age had no contribution to risk (HR = 1.034; 95% confidence interval 1.017-1.052). We propose that immune-subtyping of GBM with pan immune-specific genes will lead to biomarkers that predict immunotherapeutic response. It will also help to identify molecular pathways and targets that suppress the immune anti-tumor response.

Speaker Bio

Dr. Anna Joy is a Research Associate Professor in the Center for Computational Systems Biology. Her research focus is to understand mechanisms of tumorigenesis, progression and therapy resistance in Glioblastoma brain tumors for discovery of novel drug targets and treatment biomarkers. She has elucidated an unexpected role for a member of the PI3K/AKT tumor driver pathway that has consequences for pathway inhibitors. She is currently developing a biomarker that shows promise in identifying the immune microenvironment of Glioblastoma patients and may be used for immunotherapy selection.

Speaker: Richard Wilkins, Ph.D.

Time & Date: 12:00pm, Wed., December 4, 2019

Room: ELEN 231

Abstract

Operations in the earth’s upper atmosphere and in outer space must contend with an increased level of ionizing radiation that can be harmful to both humans and instrumentation. This ionizing radiation comes from the sun and from outside the solar system via violent cosmic activities such as star supernovae. The earth’s atmosphere and inherent magnetic field provide shielding at the earth’s surface. Forms of artificial shielding can help reduce or at least mitigate radiation exposure in aerospace applications. PVAMU has performed numerous experiments using ground-based ionizing radiation sources relevant to components of the aerospace radiation environment. These experiments are designed to evaluate the shielding effectiveness of novel, multifunctional materials with respect to “standard” aerospace materials. This talk will discuss these experiments and their implication for aerospace safety and reliability.

Speaker Bio

Dr. Richard Wilkins received a B.S. in physics from the University of Pittsburgh and a Ph.D. in condensed matter physics from the University of Michigan – Ann Arbor in 1991. He studied semiconductor surfaces during as a post-doctoral researcher in the Department of Physics at Texas A&M University. In 1993, he join the NASA funded Laboratory for Radiation Studies at Prairie View A&M University (PVAMU) as a research scientist. In 1997, Dr. Wilkins joined the faculty in the Department of Electrical and Computer Engineering at PVAMU as an assistant professor and professor in 2010. In 2000, he became the director of the NASA Center for Applied Radiation Research (CARR). Following CARR in 2008, NASA established the Center for Radiation Engineering and Research for Space Exploration (CRESSE) at PVAMU with Dr. Wilkins as director. During the funding cycle, CARR and CRESSE had an annual budget of $1 million or more, three staff, more than five faculty investigators and associated graduate and undergraduate researchers. His research interests focus on radiation effects and dosimetry, and he has co-authored papers on radiation effects on novel electronic materials and devices, radiation dosimetry and radiation shielding. In collaboration with Rice University, he led an effort to perform the first radiation experiments on carbon nanotube materials for which he was awarded a Group Achievement Award (GAA) from NASA in 2001. More recently (2014), he was part of a GAA for the “ISS UR-1” project where minority universities sent a biochemical payload to the International Space Station, and in 2019 a GAA for the RaD-X Science Team for aviation radiation studies.

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.

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