May 13th 2024
Congratulations to undergraduate Aarti Darji, Ph.D. candidate Amir Hajighasemi, and Ph.D. candidate Jillur Rahman Saurav on the acceptance of their poster for multimodal pathology search at the ISMB conference, within the MLCSB track. Your hard work and dedication have truly paid off!
May 7th 2024
Congratulations to Amir Hajighasemi on passing his comprehensive examination and officially becoming a PhD candidate! This marks an important milestone in his academic career. Well done, Amir!
April 30th 2024
Congratulations to Visiting Assistant Professor Helen Shang and PhD. Candidate Parisa Boodaghi Malidarreh for the publication of their paper titled Generalizability of PGS313 for breast cancer risk in a Los Angeles biobank in Cell Press Human Genetics and Genomics. This significant contribution advances our understanding of breast cancer risk assessment and highlights the potential of polygenic risk scores in diverse populations.
April 26th 2024
Congratulations to Aarushi Jain on successfully defending her masters thesis! With this significant milestone achieved, she is now set to begin her exciting journey at AMD as an ML Inference Acceleration Software Development Engineer. Best of luck, Aarushi, in your new role!
April 25th 2024
Congratulations to Visiting Assistant Professor Helen H. Shang and Postdoctoral Fellow Mohammad Sadegh Nasr for the publication of their paper titled Histopathology Slide Indexing and Search — Are We There Yet? as a New England Journal of Medicine AI Case Report. This insightful work contributes to the ongoing discussion surrounding histopathology slide indexing and search, shedding light on the current progress and potential future directions in this important area of research.
April 24th 2024
Congratulations to Jillur Rahman Saurav on successfully passing his comprehensive exam and advancing to the status of PhD candidate! This marks a significant milestone in his academic journey.
April 23rd 2024
Congratulations to Parisa Boodaghimalidarreh, who has passed her comprehensive exam and is now officially a PhD candidate! This milestone marks a significant achievement in her academic career.
March 21st 2024
Congratulations to Michael Robben, Balan Ramesh, Shana Pau, Demetra Meletis, Jacob Luber, and Jeffery Demuth for their co-authored paper titled scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis. This groundbreaking research utilizes single-cell RNA sequencing to uncover novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis. The paper was published in Genome Biology and Evolution, highlighting its significant contribution to evolutionary biology and genetic research.
March 20th 2024
Congratulations to Parisa Boodaghimalidarreh, Biraaj Rout, Mohammad Sadegh Nasr, Md Jillur Rahman Saurav, Jai Prakash Yadav Veerla, Partha Sai Guttikonda, Amir Hajighasemi, Aarti Darji, Cody Tyler Reynolds, and Helen Shang on our three IEEE ISBI 2024 poster acceptances this year!
March 15th 2024
Congratulations to Anne M. Alsup, Kelli Fowlds, Michael Cho, and Jacob M. Luber for their co-authored paper titled BetaBuddy - An automated end-to-end computer vision pipeline for analysis of calcium fluorescence dynamics in β-cells. This innovative work presents an automated solution for analyzing calcium fluorescence dynamics in β-cells, offering valuable insights into cellular function. The paper was published in the Plos One journal, showcasing its contribution to the scientific community.
March 4th 2024
Congrats to Mohammad Sadegh Nasr and Helen Shang on having their AI case report accepted by the New England Journal of Medicine! This prestigious acceptance highlights their significant contributions to the application of artificial intelligence in medical research.
March 4th 2024
Congrats to Jai Prakash Yadav Veerla on passing his comprehensive exam! This accomplishment is a crucial step in his academic journey, bringing him closer to achieving his doctoral goals.
February 26th 2024
Congratulations to Aarti Darji on being selected for the HuBMAP Consortium undergraduate summer research program! This summer, she will work in the laboratory of Dr. Nils Gehlenborg in the Department of Biomedical Informatics at Harvard Medical School, enhancing her experience and contributing to cutting-edge research.
February 13th 2024
Congrats to Kelli Fowlds and Anne Marie Alsup on having their paper BetaBuddy - An Automated End-to-End Computer Vision Pipeline for Analysis of Calcium Fluorescence Dynamics in β-cells accepted in PLOS ONE! This publication is a testament to their innovative research in the field of computational biology.
February 9th 2024
Massive congratulations to Jai Prakash Yadav Veerla, whose paper Demonstration of an Adversarial Attack Against a Multimodal Vision Language Model for Pathology Imaging has been accepted at the IEEE International Symposium on Biomedical Imaging (ISBI)! This significant achievement highlights his contributions to the field of computational pathology.
January 16th 2024
Congratulations to Michael Robben, Md ZOhorul Islam, Sam Zimmerman, Jon Weidanz, Jose Ordovas-Montanes, Aleksandar Kostic, and Jacob Luber for their co-authored paper titled Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice . This groundbreaking research utilizes single-cell RNA sequencing to uncover T cell receptor clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice. The paper was published at “Research Square”, showcasing its importance in the field of immunology and autoimmune disease research.
January 8th 2024
Congratulations to Jai Prakash Veerla, Poojitha Thota, Partha Sai Guttikonda, Shirin Nilizadeh, and Jacob M. Luber for their co-authored paper titled Vulnerabilities Unveiled - Adversarially Attacking a Multimodal Vision Language Model for Pathology Imaging. This insightful research sheds light on vulnerabilities in multimodal vision language models for pathology imaging, particularly through adversarial attacks.
January 4th 2024
Congratulations to Parisa Boodaghi Malidarreh, Biraaj Rout, Mohammad Sadegh Nasr, Priyanshi Borad, Jillur Rahman Saurav, Jai Prakash Veerla, Kelli Fenelon, Theodora Koromila, and Jacob M. Luber for their co-authored paper titled Predicting Future States with Spatial Point Processes in Single Molecule Resolution Spatial Transcriptomics. This pioneering research utilizes spatial point processes to predict future states in single molecule resolution spatial transcriptomics.
December 19th 2023
Congratulations to Neel R Vora and Amir Hajighasemi on their publication titled Real-Time Diagnostic Integrity Meets Efficiency - A Novel Platform-Agnostic Architecture for Physiological Signal Compression. This paper introduces an innovative approach to data compression that maintains the integrity of real-time diagnostics across various platforms.
December 15th 2023
Congrats to Mohammad Sadegh Nasr on his doctoral hooding! This ceremony marks a momentous occasion, celebrating his successful completion of the doctoral program.
December 8th 2023
Congrats to Biraaj Rout, who has successfully passed his CSE masters thesis defense! This achievement marks a significant milestone in his academic journey.
December 6th 2023
Mohammad Sadegh Nasr defended his thesis today. This pivotal moment in his academic career marks the culmination of years of dedicated research and study.
December 4th 2023
Congrats to Parisa Boodaghimalidarreh for passing her PhD diagnostic exam! This achievement marks a significant milestone in her doctoral journey.
November 29th 2023
Congrats to Helen Shang for matching into the hematology & oncology fellowship at UCLA! As she prepares to complete her residency this year, this fellowship is a pivotal step towards her training to become a specialist cancer doctor.
November 6th 2023
Congratulations to Michael Robben on the publication of his paper titled The State of Applying Artificial Intelligence to Tissue Imaging for Cancer Research and Early Detection in F1000Research. This important work discusses the advancements and implications of AI in improving cancer diagnostics through enhanced imaging techniques.
October 24th 2023
Congrats to Hajighasemi, Amir who has passed his PhD Diagnostic Exam!
October 24th 2023
Congrats to Veerla, Jai Prakash Yadav on paper submission to ACM TEI for his VR CODEX viewer today and getting his VR CODEX viewer accepted to the the Apple early preview developer program for Apple vision pro.
September 19th 2023
Congrats to Darji, Aarti on winning the TexBioMed 1st place undergraduate prize and on her poster presentation at THIA 2023.
August 31st 2023
Congratulations to Saurav for talk picture of A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels at 2023 IEEE 20th Conference on Computational Intelligence in Bioinformatics and Computational Biology
August 29th 2023
Congratulations to Jillur Rahman Saurav and Mohammad Sadegh Nasr on the acceptance of their paper titled A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels at the 2023 IEEE 20th Conference on Computational Intelligence in Bioinformatics and Computational Biology. This innovative work leverages cutting-edge generative models to enhance image synthesis in biomedical research.
August 21st 2023
Congratulations to Nasr, Mohammad Sadegh who has been offered postdoctoral positions at both MIT and MD Anderson.
August 8th 2023
Congratulations to Aarushi Jain on presenting a poster “Speeding up the CERFIT analysis code, part of the D3-D, Superficiality Real Time Workflow
August 4th 2023
Congrats to Boodaghimalidarreh, Parisa, who gave a talk in The Department of Bioengineering at Johns Hopkins University.
July 24th 2023
Congrats to Jain, Aarushi, who has landed a Fall Internship at AMD Research!
July 22nd 2023
Congrats to Shang, Helen whose abstract has been accepted at the European Society for Medical Oncology Congress 2023, the leading solid tumor conference.
July 5th 2023
Congrats to Veerla, Jai Prakash Yadav whose short paper has been accepted for oral presentation at IEEE CIBCB!
July 2nd 2023
Congratulations to Jai Prakash Veerla, Jillur Rahman Saurav, Michael Robben, and Jacob M. Luber on their collaborative publication titled Analyzing Lack of Concordance Between the Proteome and Transcriptome in Paired scRNA-Seq and Multiplexed Spatial Proteomics at the 2023 IEEE 20th Conference on Computational Intelligence in Bioinformatics and Computational Biology. This groundbreaking research explores crucial disparities in cellular processes, advancing our understanding of cellular biology.
July 1st 2023
Congratulations to Michael Robben on the publication of his paper titled Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology in the Journal of Computational Biology. This study offers valuable insights into the optimization of machine learning techniques for complex genetic analysis.
June 11th 2023
Congratulations to Amir Hajighasemi and Md Jillur Rahman Saurav on their publication titled Multimodal Pathology Image Search Between H&E Slides and Multiplexed Immunofluorescent Images. This paper presents an innovative approach to enhancing the capabilities of medical image searches, significantly benefiting the field of pathology.
June 7th 2023
Raj and Indra Nooyi have made a pilot philanthropic donation of $18k to the lab.
June 1st 2023
Congratulations to Jillur Rahman Saurav, Mohammad Sadegh Nasr, Helen H Shang, Paul Koomey, Michael Robben, Manfred Huber, Jon Weidanz, Bríd Ryan, Eytan Ruppin, Peng Jiang, and Jacob M. Luber for their co-authored paper titled A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels, published at IEEE. This innovative research presents a novel cGAN architecture guided by SSIM for clinically driven generative image synthesis of multiplexed spatial proteomics channels.
May 11th 2023
Congrats to Saurav, Md Jillur Rahman for passing his PhD diagnostic exam!
May 1st 2023
Congratulations to Saurav, for being featured on UTA news for Google Mentorship program
April 18th 2023
Congratulations to Nasr, Mohammad Sadegh, who has secured a summer internship at University of Texas MD Anderson Cancer Center, the number one cancer hospital in the world. Mohammad will be working on a feature extraction algorithm applied to pathology slides of breast cancer patients.
April 18th 2023
Congrats to Nasr, Mohammad Sadegh and Hajighasemi, Amir! For their poster on Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides Through Variational Autoencoder Based Image Compression at “2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)”
April 18th 2023
Jacob will be an invited speaker at ACM The Web Conference Health Day 2023 in Austin on May 1st, where he will present work on generative sythesis of multiplexed spatial proteomics and fast seach of histopathology slides.
April 7th 2023
Congrats to PhD student Jillur Rahman Saurav for being selected for the highly competitive 2023 Google CS Research Mentorship Program (CSRMP)! CSRMP matches students from historically marginalized groups with peers and a Google mentor to support their pursuit of computing research pathways. Saurav was selected for this based on the strength of his preprint A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels.
April 6th 2023
Congrats to PhD students Anne Alsup and Kelli Fowlds on their new preprint BetaBuddy - An end-to-end computer vision pipeline for the automated analysis of insulin secreting β-cells!
March 23rd 2023
Congrats to postdoctoral fellow Michael Robben, Ph.D., whose paper “Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial-Gene Pathway Annotation and its Effects on Reconstructed Network Topology” has been accepted at the Journal of Computational Biology. PhD candidate Mohammad Nasr and PhD student Avishek Das also made contributions to the paper.
March 6th 2023
Congrats to masters student Aarushi Jain for securing internship offers at Argonne National Laboratory, Lawrence Berkeley National Laboratory, and Los Alamos National Laboratory!
February 21st 2023
Congrats to Veerla, Jai Prakash for passing his PhD diagnostic exam!
February 15th 2023
Congrats to undergraduate Paul Koomey on being accepted to the PhD program in the School of Computer Science at Carnegie Mellon University! This is currently the number 1 ranked CS PhD program in the world.
January 19th 2023
Congrats to PhD students Mohammad Nasr and Amir Hajighasemi for having their co-first author paper Clinically Relevant Latent Space Embedding of Cancer Histopathology Slides Through Variational Autoencoder Based Image Compression accepted at the 2023 IEEE International Symposium on Biomedical Imaging (ISBI)! Visiting Assistant Professor Helen Shang, MD, MS did the clinical work for this paper and is extending it to retrospective concordance studies in the ER.
October 1st 2022
Congrats to undergraduate Paul Koomey on receving a full time job offer at Goldman Sachs! The lab is recruiting stellar UTA CS undergraduates who want to become involved in research that will jumpstart careers.
October 1st 2022
Congrats to undergraduate Paul Koomey on winning the UTA CSE undergraduate academic achievment award for having the top GPA out of 2,055 undergraduates in the department!
July 19th 2022
Congrats to postdoc Michael Robben, Ph.D. for having his paper Selection of an Ideal Machine Learning Framework for Predicting Perturbation Effects on Network Topology of Bacterial KEGG Pathways accepted at the ACM BCB CNB-MAC workshop! We are using this algorithm to perform directed evolution experiments/crispri screens to design phage that “shape” the microbiome so that it ideally synergizes with checkpoint blockade inhibitors. Michael will give a talk on this at the ACM BCB conference in Chicago next month.
April 19th 2022
Congrats to PhD Students Kelli & Anne for winning second place in the graduate research category at the annual UTA College of Engineering Innovation Day poster competition!
April 1st 2022
Welcome to our new postdoctoral fellow, Michael Robben, PhD!
March 15th 2022
Welcome Mohammad!
February 25th 2022
Congrats to lab members Kelli and Anne for being selected to give the Department of Bioengineering showcase poster at the annual UTA College of Engineering Banquet!
January 22nd 2022
Congrats to junior year undergraduate lab member and CS major Paul Koomey, who has landed a summer SWE internship at Goldman Sachs!
November 18th 2021
The Lab receives a 5 year/$2 Million dollar grant from CPRIT for developing deep learning accelerated search approaches for cancer drug discovery!
November 15th 2021
Welcome Paul!
November 10th 2021
Welcome Jai!
November 1st 2021
Welcome Avishek & Saurav!
October 15th 2021
Welcome Fiza!
September 23rd 2021
Welcome Kelli!
September 23rd 2021
Welcome Anne!
September 15th 2021
Welcome Demetra!
September 1st 2021
The lab receives a 3 year/$250,000 rising STARs grant from The University of Texas System.
September 1st 2021
The lab officially starts at The University of Texas at Arlington!