Publications

1. †Ashraf Yaseen, Stacia M. DeSantis, Rachit Sabharwal, Yashar Talebi, Michael D. Swartz, Shiming Zhang, Luis Leon Novelo, Cesar L Pinzon-Gomez, Sarah E. Messiah, Melissa Valerio-Shewmaker, Harold W. Kohl, Jessica Ross, David Lakey, Jennifer A. Shuford, Stephen J. Pont and Eric Boerwinkle. Baseline characteristics of SARS-CoV-2 vaccine non-responders in a large population-based sample. PLoS One. 2024. (accepted)

2. †Ashraf Yaseen, Claudia Robertson, Jovany Cruz Navarro, Jingxiao Chen, Brian Heckler, Stacia DeSantis, Nancy Temkin, Jason Barber, Brandon Foreman, Ramon Diaz-Arrastia, Randall Chesnut, Geoff Manley, David Wright, Mary Vassar, Adam Ferguson, Amy Markowitz, Jose-Miguel Yamal. Integrating, Harmonizing, and Curating Studies with High-Frequency and Hourly Physiological Data: Proof of Concept from Seven Traumatic Brain Injury Datasets. Journal of Neurotrauma. 2023 Aug 16. doi: 10.1089/neu.2023.0023. PMID: 37341031.

3. *Zitong Zhang, *Rachit Sabharwal, Miryoung Lee, Kehe Zhang, Paul McGaha, Michelle Crum, Cici Bauer, Susan P. Fisher-Hoch, Joseph B. McCormick, Belinda M Reininger, Samantha Thomas, Esmeralda Guajardo, Daniel Pinon, §Ashraf Yaseen. An Interactive Online Dashboard with Covid-19 Trends and Data Analysis in Northeast and South Texas. The Texas Public Health Journal (TPHJ). Volume 76 Issue 2. 2023.

4. *Zitong Zhang, §Ashraf Yaseen. A Content-Based Dataset Recommendation System for Biomedical Datasets. 2023 6th International Conference on Information and Computer Technologies (ICICT), Raleigh, NC, USA, 2023 pp. 198-202. doi: 10.1109/ICICT58900.2023.00040

5. *Jie Zhu, §Ashraf Yaseen, Luis Leon-Novelo. Incorporating uncertainty quantification for actionable insights and performance improvement of academic recommenders. Knowledge 2023, 3, 293-306. https://doi.org/10.3390/knowledge3030020

6. *Zitong Zhang, Braja Gopal Patra, §Ashraf Yaseen, *Jie Zhu, *Rachit Sabharwal, Kirk Roberts, Tru Cao, and Hulin Wu. Scholarly Recommendation Systems: A Literature Survey. Knowledge and Information Systems (2023), https://doi.org/10.1007/s10115-023-01901-x

7. Stacia DeSantis, †Ashraf Yaseen, Tianyao Hao, Luis León-Novelo, Yashar Talebi, Melissa Valerio-Shewmaker, Cesar Pinzon Gomez, Sarah Messiah, Harold Koh, Steven Kelder, Jessica Ross, Lindsay Padilla, Mark Silberman, Samantha Tuzo, David Lakey, Jennifer Shuford, Stephen Pont, Eric Boerwinkle, Michael Swartz. Incidence and predictors of breakthrough and severe breakthrough infections of SARSCoV-2 after primary series vaccination in adults: A population-based survey of 90,000 participants. Journal of Infectious Diseases. 2023 May 12;227(10):1164-1172. doi: 10.1093/infdis/jiad020. PMID: 36729177

8. *Jie Zhu, Braja Patra, Hulin Wu, §Ashraf Yaseen. A novel NIH research grant recommender using BERT. PLoS One. 2023 Jan 17;18(1):e0278636. doi: 10.1371/journal.pone.0278636

9. *Jie Zhu, §Ashraf Yaseen. A Recommender for Research Collaborators Using Graph Neural Networks. Frontiers in Artificial Intelligence. 2022 Aug 1;5:881704. doi: 10.3389/frai.2022.881704. PMID: 35978654; PMCID: PMC9376356.

10. *Jie Zhu, Hulin Wu, §Ashraf Yaseen. Sensitivity Analysis of a BERT-based scholarly recommendation system, FLAIRS Conference Proceedings, 35. 2022. https://doi.org/10.32473/flairs.v35i.130595.

11. Stacia DeSantis, Luis Leon-Novelo, Michael Swartz, Ashraf Yaseen, Melissa Valerio, Yashar Talebi, Frances Brito, Jessica Ross, Harold Kohl III, Sarah Messiah, Steve Kelder, Leqing Wu, Shiming Zhang, Kimberly Aguillard, Michael Gonzalez, Onyinye Omega-Njemnob, David Lakey, Jennifer Shuford, Stephen Pont, Eric Boerwinkle. Methodology to estimate natural- and vaccine-induced antibodies to SARS-CoV-2 in a large geographic region. PLOS ONE, 2022 Sep 9. PMID: 36084125 PMCID: PMC9462720 DOI: 10.1371/journal.pone.0273694

12. Sarah Messiah, Tianyao Hao, Stacia DeSantis, Michael Swartz, Yashar Talebi, Harold Kohl, Shiming Zhang, Melissa Valerio-Shewmaker, Ashraf Yaseen, Steven Kelder, Jessica Ross, Michael Gonzalez, Leqing Wu, Lindsay Padilla, Kourtney Lopez, David Lakey, Jennifer Shuford, Stephen Pont, Eric Boerwinkle. Comparison of Persistent Symptoms Following SARS-CoV-2 Infection by Antibody Status in Nonhospitalized Children and Adolescents. The Pediatric Infectious Disease Journal. 2022;INF.0000000000003653. doi:10.1097/INF.0000000000003653

13. Michael Swartz, Stacia DeSantis, Ashraf Yaseen, Frances Brito, Melissa Valerio-Shewmaker , Sarah E Messiah, Luis G Leon-Novelo, Harold Kohl, Cesar Pinzon-Gomez, Tianyao Hao, Shiming Zhang, Yashar Talebi, Joy Yoo, Jessica Ross, Michael O Gonzalez, Leqing Wu, Steven H Kelder, Mark Silberman, Samantha Tuzo, Stephen J Pont, Jennifer Shuford, David Lakey, Eric Boerwinkle. Antibody duration after infection from SARS-CoV-2 in the Texas Coronavirus Antibody Response Survey. [published online ahead of print, 2022 May 6]. Journal of Infectious Diseases. 2022;jiac167. doi:10.1093/infdis/jiac167

14. Sarah Messiah, Stacia DeSantis, Luis Leon-Novelo, Yashar Talebi, Frances Brito, Harold Kohl, Melissa Valerio-Shewmaker, Jessica Ross, Michael Swartz, Ashraf Yaseen, Steven Kelder, Shiming Zhang, Onyinye Omega-Njemnobi, Michael Gonzalez, Leqing Wu, Eric Boerwinkle, David Lakey, Jennifer Shuford, Stephen Pont; Durability of SARS-CoV-2 Antibodies From Natural Infection in Children and Adolescents. Pediatrics June 2022; 149 (6): e2021055505. 10.1542/peds.2021-055505

15. Melissa Valerio-Shewmaker, Stacia DeSantis, Michael Swartz, Ashraf Yaseen, Michael Gonzalez, Harold Kohl, Steven Kelder, Sarah Messiah, Kimberly Aguillard, Camille Breaux, Leqing Wu, Jennifer Shuford, Stephen Pont, David Lakey, Eric Boerwinkle. Strategies to Estimate Prevalence of SARS-CoV-2 Antibodies in a Texas Vulnerable Population: Results From Phase I of the Texas Coronavirus Antibody Response Survey. Frontiers in Public Health. 2021 Dec 14;9:753487. doi: 10.3389/fpubh.2021.753487. PMID: 34970525; PMCID: PMC8712464.

16. Sarah Messiah, Melissa Valerio-Shewmaker, Stacia DeSantis, Michael Swartz, Ashraf Yaseen, Frances Brito, Harold Kohl, Steven Kelder, Kimberly Aguillard, Onyinye Omega-Njemnobi, Camille Breaux, Jessica Ross, Michael Gonzalez, Shiming Zhang, Leqing Wu, David Lakey, Jennifer Shuford, Stephen Pont, Eric Boerwinkle. Estimated Prevalence of SARS-CoV-2 Antibodies in the Texas Pediatric Population, 2021. The Lancet, available at SSRN: https://ssrn.com/abstract=3868061 or http://dx.doi.org/10.2139/ssrn.3868061

17. Cong Zhu, Radhe Mohan, Steven Hsesheng Lin, Goo Jun, Ashraf Yaseen, Xiaoqian Jiang, Han Chen, Qianxia Wang, Wenhua Cao, Brian Hobbs. Identifying Individualized Risk Profiles for Radiotherapy-Induced Lymphopenia Among Patients With Esophageal Cancer Using Machine Learning. JCO Clinical Cancer Informatics. 2021 Sep;5:1044-1053. doi: 10.1200/CCI.21.00098. PMID: 34665662; PMCID: PMC8812653.

18. *Jie Zhu, Braja Patra, Hulin Wu, §Ashraf Yaseen. Recommender system of scholarly papers using public datasets, AMIA Jt Summits Transl Sci Proc. 2021 May 17;2021:672-679. PMID: 34457183; PMCID: PMC8378599.

19. Braja Patra, Babak Soltanalizadeh, Nan Deng, Leqing Wu, Vahed Maroufy, Wenjin Jim Zheng, Kirk Roberts, Hulin Wu, §Ashraf Yaseen. An Informatics Research Platform to Make Public Gene Expression Time-Course Datasets Reusable for More Scientific Discoveries. Database, Volume 2020, 2020, PMID: 33247935 PMCID: PMC7698665 DOI: 10.1093/database/baaa074.

20. Derek W. Brown, Stacia M. DeSantis, Thomas J. Greene, Vahed Maroufi, Ashraf Yaseen, Hulin Wu, George Williams, Michael D. Swartz. A Novel Approach for Propensity Score Matching and Stratification in the Presence of Multiple Treatments: Application to an EHR-Derived Study of Subarachnoid Hemorrhage. Statistics in Medicine. 39: 2308– 2323. 2020.  doi: 10.1002/sim.8540. Epub 2020 Apr 16. PMID: 32297677; PMCID: PMC7334100.

21. George Williams, Vahed Maroufy, Laila Rasmy, Derek Brown, Duo Yu, Hai Zhu, Yashar Talebi, Xueying Wang, Emy Thomas, Gen Zhu, Ashraf Yaseen, Hongyu Miao, Luis Leon Novelo, Degui Zhi, Stacia DeSantis, Hongjian Zhu, Jose-Miguel Yamal, David Aguilar, and Hulin Wu. Vasopressor Treatment and Mortality Following Non-Traumatic Subarachnoid Hemorrhage: A Nationwide EHR Analysis. Neurosurgical Focus. 2020. doi: 10.3171/2020.2.FOCUS191002. PMID: 32357322

22. Vahed Maroufy,  Pankil Shah, Arvand Asghari, Nan Deng, Rosemarie Le, Juan Camilo Ramírez, Ashraf Yaseen, W. Zheng, Michihisa Umetani, Hulin Wu. Gene expression dynamic analysis reveals co-activation of Sonic Hedgehog and epidermal growth factor followed by dynamic silencing. Oncotarget. 11. 10.18632/oncotarget.27547. 2020.

23. †Ashraf Yaseen, Hao Ji, and Yaohang Li, “A Load-Balancing Workload Distribution Scheme for Three-Body Interaction Computation on Graphics Processing Units (GPU)”. Journal of Parallel and Distributed Computing, 87: 91–101, 2016. https://doi.org/10.1016/j.jpdc.2015.10.003

24. †Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, and Yaohang Li “FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information”. BMC Bioinformatics, vol. 17 Suppl 8, pp. 281, 2016. doi: 10.1186/s12859-016-1117-3. PMCID: PMC5009531PMID: 27587065

25. Mais Nijim and Ashraf Yaseen, “HuBum: Energy Efficient Hybrid Mobile Storage Systems using Solid States and Buffer Disks”. Journal of Computer Communication and Collaboration, 2015. (DOIC: 2292-1036-2015-04-001-59)

26. †Ashraf Yaseen and Yaohang Li, “Context-based Features Enhance Protein Secondary Structure Prediction Accuracy”. Journal of Chemical Information and Modeling, 54 (3), pp 992–1002, 2014. doi: 10.1021/ci400647u. Epub 2014 Mar 12. PMID: 24571803.

27. †Ashraf Yaseen and Yaohang Li, “Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features”, BMC Bioinformatics,15(Suppl 8):S3, 2014. doi: 10.1186/1471-2105-15-S8-S3 | PMCID: PMC4120151PMID: 25080939

28. Zhiqiang Wu, Bin Wang, Chi-Hao Cheng, Dr. Deng Cao, and Ashraf Yaseen. "Software Defined Radio Laboratory Platform for Enhancing Undergraduate Communication and Networking Curricula," 2014 ASEE Conference, 2014.

29. †Ashraf Yaseen and Yaohang Li, “Dinosolve: A Protein Disulfide Bonding Prediction Server using Context-based Features to Enhance Prediction Accuracy”, BMC Bioinformatics, 14(Suppl 13):S9, 2013. doi: 10.1186/1471-2105-14-S13-S9. Epub 2013 Oct 1. PMID: 24267383; PMCID: PMC3849605

30. Yaohang Li and Ashraf Yaseen, "Pareto-based Optimal Sampling Method and Its Applications in Protein Structural Conformation Sampling". AAAI Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, Bellevue, 2013.

31. †Ashraf Yaseen and Yaohang Li “Predicting Protein Solvent Accessibility with Sequence, Evolutionary Information and Context-based Features”. Biotechnology and Bioinformatics Symposium, (BIOT2013) Provo, 2013.

32. †Ashraf Yaseen and Yaohang Li “Template-based Prediction of Protein 8-states Secondary Structures”.3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS2013), New Orleans 2013.

33. †Ashraf Yaseen and Yaohang Li “Enhancing Protein Disulfide Bonding Prediction Accuracy with Context-based Features”, Proceedings of Biotechnology and Bioinformatics Symposium, (BIOT2012), Provo, 2012.

34. †Ashraf Yaseen and Yaohang Li, “Accelerating Knowledge-based Energy Evaluation in Protein Structure Modeling with Graphics Processing Units,” Journal of Parallel and Distributed Computing, 72(2): 297-307, 2012. https://doi.org/10.1016/j.jpdc.2011.10.005

35. Weihang Zhu, Ashraf Yaseen and Yaohang Li “DEMCMC-GPU: An Efficient Multi-Objective Optimization Method with GPU Acceleration on the Fermi Architecture” New Generation Computing, 29(2): 163-184, 2011.

36. †Ashraf Yaseen, Kurt J. Maly, Steven J. Zeil and Mohammad Zubair “Performance Evaluation of Oracle Semantic Technologies with respect to User Defined Rules”.  Proceeding of Database and Expert Systems Applications, DEXA, International Workshops, Toulouse, France, August 29, 2011.

Invited Talks

• Lack of antibody response in those vaccinated or with natural exposure. [Session: Examining SARS-CoV2 Response Over Time Using a Longitudinal Design: Texas CARES Survey]. American Public Health Association (APHA). November 7, 2022. Boston, MA.

• Texas CARES Community Update, Lessons Learned and Next Steps. Healthier Texas Summit. October 21, 2022. Austin TX.

• Epidemiology Special Session: Understanding the Human Antibody Response to Sars-Cov-2 in Diverse Populations: The Texas Coronavirus Antibody Response Survey (CARES). Data Management and Visualization. American Public Health Association (APHA). October 25, 2021, Denver, Colorado.

• Understanding the Human Antibody Response to SARS-CoV-2 in Diverse Populations: The Texas Coronavirus Antibody Response Survey (CARES) - Melissa Valerio, Sarah Messiah and Ashraf Yaseen, University of Texas. World Health Organization (WHO) Solidarity II. August 27, 2021.

• Texas C.A.R.E.S. Coronavirus Antibody REsponse Survey. Texas CARES Portal: An Interactive Platform with Visualizations, Maps, and Summary Statistics to Illustrate and Understand the Human Response to COVID-19. Texas Department of State Health Services (DSHS) Grand Rounds. June 16, 2021.

Posters

• *Jie Zhu, Braja Patra, Hulin Wu and Ashraf Yaseen. Recommender system of scholarly papers using public datasets. ICSA Applied Statistics Symposium. Houston, Texas.  December 13-16, 2020.

• *Praveenraj Uthamarajan and Ashraf Yaseen, “Analysis of Systems using Distributed Consensus Algorithms”. College of Engineering-TAMUK, 2017.

• *Megha Lalluvadia and Ashraf Yaseen, "Applications of Text Classification". College of Engineering-TAMUK, 2017.

• *Varun Agrawal, Gaurav Dokania, and Ashraf Yaseen, “Predicting protein flexibility and disorder”. Texas A&M University System 12th Annual Pathways Student Research Symposium, Corpus Christi, TX, 2015.

• *Anurag Gupta, Hridya Gopalakrishna, and Ashraf Yaseen, “Predicting protein solvent accessibility”. Texas A&M University System 12th Annual Pathways Student Research Symposium, Corpus Christi, TX, 2015.

• †Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, and Yaohang Li “Predicting Protein Flexibility using Context-based Statistics, Predicted Structural Features, and Sequence Information”. 11th International Symposium on Bioinformatics Research and Applications (ISBRA), Norfolk, Virginia, 2015. (Awarded #1 best poster).

• †Ashraf Yaseen, Akeem Edwards and Yaohang Li, “Improving Intermediate Steps in ab initio Protein Molding”,14th Annual Tidewater Student Research Poster Session at Christopher Newport University. Nov, 2012.