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Texas Biomed Announces New Faculty Member for Quantitative Biology

Texas Biomedical Research Institute has recruited a new faculty member to San Antonio. Diako Ebrahimi, Ph.D., begins his new position today as Assistant Professor at Texas Biomed. He will establish his own research program in quantitative biology related to the fields of viral and cancer immunology and also collaborate on research projects with Texas Biomed Faculty. Dr. Ebrahimi’s recruitment is part of the Institute’s 10-year strategic plan to recruit nearly 20 new faculty members and double the size of the Institute.

“My goal is to develop a collaborative and cross-disciplinary research program that combines multi-omic quantitative analysis with targeted experimental strategies to identify and answer key questions in the fields of viral and cancer immunity,” Ebrahimi shared. “Currently, large amounts of data are being generated across disciplines to study complex biological processes. However, cross-disciplinary quantitative skills are urgently needed to analyze and interpret these massive datasets and direct future targeted experiments.”

Dr. Ebrahimi joins Texas Biomed from the University of Minnesota where he was an Assistant Professor in the Department of Biochemistry, Molecular Biology and Biophysics. He is currently the principal investigator on a National Institutes of Health grant focused on Molecular Determinants of HIV Hypermutation that runs through 2020 and another study that concludes this year. For nearly 10 years, Dr. Ebrahimi has focused his research efforts on combining data and information from a variety of scientific disciplines, from chemistry and virology to cancer, genomics, evolution and bioinformatics to develop new research initiatives in viral and cancer genomics using quantitative biology.

“My previous studies led to discoveries about the roles of methylation, a biochemical process necessary for normal function of biological processes in the body, and APOBEC-induced mutationin the inhibition and evolution of viruses,” Dr. Ebrahimi said. “My current studies focus on population-specific virus-host interaction mechanisms and dysregulated processes in cancer.” This information provides critical knowledge required to develop precision medicine strategies for prevention and/or treatment.

Prior to his appointment at the University of Minnesota, he was a research fellow and lecturer at the School of Medical Sciences and School of Chemistry at the University of New South Wales in Sydney, Australia from 2007-2014.

“Dr. Ebrahimi is a critical hire for Texas Biomed as he strengthens our institutional expertise in quantitative biology, complements our ongoing research in HIV and other infectious diseases, and expands our focus to the study of the interface between immunology and cancer,” said Texas Biomed Vice President for Research Joanne Turner, Ph.D. “Dr. Ebrahimi will certainly enhance our collaborative culture, in line with our institutional values. I anticipate that Diako will quickly form several collaborations inside and outside of Texas Biomed that will enhance his own science and the science of others.”

Dr. Ebrahimi has published more than 30 journal articles and holds numerous awards and honors. Most recently, he was selected as the 2018 Reviewers’ Choice award recipient from the American Society for Human Genetics and received a New Investigator Scholarship in 2018 from the Conference on Retroviruses and Opportunistic Infections. He is a member of the American Society for Human Genetics and American Society for Microbiology among several others.

“Texas Biomed has a very strong, visionary and committed leadership team with amazing resources, great scientists with diverse backgrounds and faculty who acknowledge the importance of cross-disciplinary quantitative biology research,” Dr. Ebrahimi said. “It is a very collaborative environment, and San Antonio is a beautiful city!”

Dr. Ebrahimi received his Bachelor of Science in Chemistry from Chamran University in Ahvaz, Iran and his Master of Science in Analytical Chemistry from Razi University in Kermanshah, Iran. He obtained his Ph.D. in Quantitative Chemistry in 2007 from the University of New South Wales in Sydney, Australia.

He is married to Dr. Leila Hejazi, who is a Senior Chemist at Medtronic. They have two daughters – Jino, who is 14 and looks forward to joining a new swim team in San Antonio and Rojin who is 5 and enjoys dance. As a family, they enjoy road trips, touring much of the U.S., including trips from San Francisco to Los Angeles to San Diego, as well as Minneapolis, Chicago, Toronto and Niagara Falls among several others. They have already toured the “Texas Triangle” with a road trip through Dallas, Austin, San Antonio, Houston and Galveston.

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Recharging of Flying Base Stations using Airborne RF Energy Sources

Recharging of Flying Base Stations using Airborne RF Energy Sources

Dr. Ayub Bokani’s team presented a new method at WCNC2019 conference for recharging flying base stations, carried by Unmanned Aerial Vehicles (UAVs), using wireless power transfer from dedicated, airborne, Radio Frequency (RF) energy sources.

Image result for uav

In particular, they studied a system in which UAVs receive wireless power without being disrupted from their regular trajectory. The optimal placement of the energy sources are studied so as to maximize received power from the energy sources by the receiver UAVs flying with a linear trajectory over a square area. They found that for their studied scenario of two UAVs, if an even number of energy sources are used, placing them in the optimal locations maximizes the total received power while achieving fairness among the UAVs. However, in the case of using an odd number of energy sources, it is possible to either maximize the total received power, or achieve fairness, but not both at the same time. Numerical results show that placing the energy sources at the suggested optimal locations results in significant power gain compared to nonoptimal placements.

Introduction to AdliLab

Our ultimate research goals are to understand key drivers of cancer and identify novel therapeutic drug combinations to prevent cancer development and chemotherapy resistance. To achieve these goals, our lab is using and developing genomic and epigenomic mapping, editing and imaging approaches to understand genome regulation in normal and malignant settings. We integrate experimental approaches with large-scale computational data analysis to verify our experimental observations and come up with new testable hypotheses.

Our laboratory is utilizing and also developing cutting-edge functional genomics strategies and developing novel CRISPR based manipulation tools to understand dynamic gene regulation and 3D genome organization in normal and malignant settings. These efforts are based on our previous expertise in genome-wide approaches, and development of novel technologies for cancer research. Our lab has developed particular experitse in utilizing and developing CRISPR based technologies.

Our lab is located on the 6th floor of Jordan Hall (Room 6228) and we are part of University of Virginia, School of Medicine, Department of Biochemistry and Molecular Genetics.

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Conference: March 4–7, 2018 | Boston, Massachusetts

Conference: March 4–7, 2018 | Boston, Massachusetts

Dr. Diako Ebrahimi presneted a talk about the molecular determinants of HIV hypermutation at CROI 2019, Boston.

Abstract Body: 

The human genome encodes seven APOBEC3 (A3) enzymes, at least four of which (A3D, A3F, A3G, and A3H) can induce G-to-A mutations in HIV-1 genomes. These enzymes leave two distinct hypermutation signatures: GG-to-AG and GA-to-AA. The former signature is dominant in viral sequences hypermutated in vitro by A3G, whereas the latter is prevalent in sequences hypermutated in vitro by A3D, A3F, or A3H. Current, in vitro based models posit that all HIV-restrictive A3 enzymes are ubiquitously active and cooperate to hypermutate HIV. However we have discovered that an in vivo hypermutated virus typically bears a dominant GG-to-AG signature or a dominant GA-to-AA signature, which would be expected from independent encounters with A3G or A3D/F/H, but not from both enzyme classes simultaneously. This hypermutation bias towards GG-to-AG or GA-to-AA suggests the existence of a mechanism that prevents A3 proteins from simultaneously targeting HIV-1.

We performed four independent analyses: 1) We analyzed all reported in vivo hypermutated HIV-1 sequences (1164 sequences from 988 patients) using two independent methods (non-alignment-based and alignment-based); 2) We analyzed all of the 564 SNPs of the A3 locus in 2504 individuals from 26 populations (1000 Genomes Project). 3) We quantified, using RNAseq data, all of the reported A3 transcripts in 461 donors from the 1000 Genome Project ; 4) We quantified, the linkage disequilibrium in 120 kb A3 locus.

By analyzing A3 SNPs, RNAseq, and hypermutated viral sequences from thousands of HIV-1 patients and healthy donors, we have generated three independent datasets that indicate the source of skewed hypermutation patterns is natural genetic variations in A3G and A3H. First, only one hypermutation signature predominates in most clinical HIV-1 isolates. Second, A3G and A3H form two continuous haplotype blocks as a result of strong genetic linkage. Block 1 is prevalent outside Africa (particularly Asia) and contains the hypo-functional A3H HapI (GKE). Block 2 is prevalent in Africa and contains the hyper-functional A3H HapII (RDD). Third, A3H HapI and HapII and their respective A3G haplotypes a-g-t-t-t and g-c-c-c-c are expressed differentially.

Overall, these results indicate that A3G and A3H are expressed differentially in different human populations and that these enzymes are the main sources HIV-1 hypermutation. The mutually exclusive function of A3G and A3H may be a source of weakness in our immunity to HIV-1.

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Dr. Diako Ebrahimi presented a talk about the hidden molecular signatures of viral and cancer immunity at UCSF, March 21, 2019.

The QBI Seminar Series is presenting Diako Ebrahimi on March 21  at 11 am in room BH-215. Dr. Ebrahimi will talk about the quantitative biology approaches he uses to discover important hidden patterns in the fields of virus-host interactions and cancer. His recent quantitative biology studies have unveiled hidden dysregulated processes in cancer and have also helped reveal novel host-pathogen interaction mechanisms. The purpose of Ebrahmimi’s visit is to share these new findings with the Krogan Lab and discuss collaboration opportunities. 

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CyberCRC PhD Scholarship on Adversarial Machine Learning @ UNSW Sydney & CSIRO’s Data61

CyberCRC PhD Scholarship on Adversarial Machine Learning @ UNSW Sydney & CSIRO’s Data61

The use of machine learning models has become ubiquitous. Their predictions are used to make decisions about healthcare, security, investments and many other critical applications. These models are widely used in many cyber defense systems for network security operations, malware analysis, etc. But despite the many successes, the very property that makes machine learning desirable: adaptability, is a vulnerability that may be exploited by an attacker that could potentially result in the severe degradation of the integrity, security, and performance of cyber defense systems. All machine learning systems are trained using datasets that are assumed to be representative and valid for the subject matter in question. However, malicious actors can impact how the artificial intelligence system functions by poisoning the training data. This threat is exacerbated when the machine learning pipeline that includes data collection, curation, labeling, and training is not controlled completely by the model owner. This project will focus on understanding, evaluating, and improving the effectiveness of machine learning methods in the presence of motivated and sophisticated adversaries.

The scholarship is funded through the Cyber Security Cooperative Research Centre (CSCRC), which is focused on delivering industry-driven cybersecurity research outcomes that have an impact and address real-world cybersecurity problems with innovative solutions. The CSCRC has been granted $50m of funding over 7 years from the Australian Government’s Cooperative Research Centres Program.

The student will be supervised by a capable team including academics from UNSW and researchers from CSIRO’s Data61. There will be an opportunity to engage with industry partners.

The scholarship is open to both domestic and international students. International applicants should be able to secure a Tuition Fee Scholarship from UNSW. This entails an academic record that is equivalent to an Australian First Class Honours degree in Computer Science from a reputed institute. A publication track record in machine learning and/or security is highly desirable.

The scholarship includes:

  • $37K per annum (tax-free) for a period of 3 years; extendable up to 1 year
  • Option to secure an additional $13k per annum top-up if certain additional criteria are met
  • Access to operational budget for research support and conference travel
  • Mentoring and training opportunities through the CSCRC

Interested candidates should send their CV and academic transcripts to Professor Salil Kanhere (

Zeelamo Logo

Zeelamo Logo

Dear Zeelamo members,

We are still working on our platform’s logo and what you currently see is a temporary design. We encourage all our graphic designer members to participate in this logo design competition and get a reward.

ئه‌ندامانی هێژای زیلامۆ،
ئه‌و لۆگۆیه‌ كه‌ ئێستا ده‌یبینن دیزانینێكی كاتیه‌ و به‌ زوویی ده‌گۆڕدرێت. داوا له‌ هه‌مووی ئه‌و ئه‌ندامانه‌ ده‌كه‌ین كه‌ ته‌جروبه‌ی گرافیك دیزاینیان هه‌یه‌ كه‌ له‌ دیزاینی لۆگۆی زیلامۆ دا یارمه‌تیمان بده‌ن و خه‌ڵاتیش وه‌رگرن.

زیلامۆ له‌ وشه‌ی كوردی زیله‌مۆ یان هه‌مان ژیله‌مۆ وه‌رگیراوه‌.

Science and Technology Academy

لۆگۆی زیلامۆ

لۆگۆی زیلامۆ

سڵاو به‌ڕێزان،

پاش ماوه‌یه‌كی زۆر لێكۆڵینه‌وه‌ و هه‌ڵسه‌نگاندن، له‌ سه‌ر ڕای گشتی كۆمیته‌ی به‌ڕێوه‌ به‌رایه‌تی گرووپی به‌ره‌و باشترین زانكۆكانی جیهان و ده‌سته‌ی تازه‌ پێك هاتووی پلاتفۆرمی كوردیش سكاڵر، بڕیار درا كه‌ نێوی پلاتفۆرمه‌كه‌مان بگۆڕین به‌ زیلامۆ. ئه‌و وشه‌یه‌ له‌ زیله‌مۆ وه‌رگیراوه‌ كه‌ له‌ كتێبی هه‌نبانه‌ بۆرینه‌ی مامۆستا هه‌ژ‌ار دا هه‌ر مانای ژیله‌مۆ ی هه‌یه‌.

له‌ ماوه‌ی چه‌ند ڕۆژی داهاتوو دا هه‌وڵ ده‌ده‌ین ئه‌و ئاڵ و گۆڕیه‌ له‌ سه‌ر به‌شه‌ جیاكانی ماڵپه‌ڕه‌كه‌مان دا ئه‌نجام بده‌ین و هیوادارین له‌ ماوه‌یه‌كی كورت دا ده‌ست بكه‌ین به‌ ساز كردنی ئه‌پڵیلیكه‌یشنی مۆبایل، هه‌م بۆ ئه‌ندرۆید و هه‌م بۆ ئایفۆن.

له‌و قۆناغه‌ دا پێویستمان به‌ لۆگۆیه‌كی پرۆفشناڵه‌ بۆ پلاتفۆرمه‌كه‌مان. ئه‌و كۆگۆیه‌ ده‌بێ ئامانجی گشتیمان نیشان بدات. هه‌ر كه‌س ده‌توانێ لۆگۆ دیزاین بكات، تكایه‌ راسته‌و خۆ بۆ منی بنێرن. له‌ ده‌سته‌ی به‌ڕێوه‌ به‌رایه‌تی دا هه‌موویان به‌ وردی هه‌ڵده‌سه‌نگێنین و له‌ ئه‌نجام دا باشترین لۆگۆ هه‌ڵده‌بژێرین.

وه‌ك خه‌ڵات، ئه‌و كه‌سه‌ی كه‌ لۆگۆكه‌ی به‌ره‌نده‌ ده‌بێت ده‌عوه‌ت ده‌كرێ كه‌ له‌ ده‌سته‌ی به‌ڕێوه‌به‌رایه‌تی دا له‌ به‌شی گرافیك دا لگه‌ڵمان بێ.

زۆر سوپاس

Science & Technology Academy