News
2023
- 9.16,2023. Congrats on Yongchao as the co-first author of a paper published at JCI Insight! A successful collaborative work with leading researchers on uterine fibroids.
- 9.13,2023. Yongchao's paper, "Iterative Geometric Depression in Early Pregnancy using EMR in a Minority Projection Method for Bias Mitigation in Predicting Population" has been selected as a rapid-fire presentation at the IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) in Pittsburgh (October 15-18) 2023. Congrats also on receiving the NSF travel award.
- 7.17.2023. Brandon's first conference paper, "An Integrative Approach to Building Regulatory Potential-Weighted Gene Regulatory Networks: A Leiomyoma Case Study," has been accepted by the 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Sept.3-6, 2023, Huston. Congrats!
- 6.30.2023. Congratulations to Kaustubh on a successful MS dissertation defense: "MOMMI-MP: A Comprehensive Database for Integrated Analysis of Metabolic and Microbiome Profiling of Mouse Pregnancy"!
2022
- 11.25.2022. Congrats to Mehrdad on receiving the IEEE BIBM 2022 Student Travel Award for oral presentation on the paper: "Information retrieval in single cell chromatin analysis using TF-IDF transformation methods"!
- 8.29.2022. Congratulations to Shang on a successful Ph.D. dissertation defense: "Development of Machine Learning Approaches for the Integration and Analysis of Multi-omics Data"!
- 7.13.2022. Shang's paper: "Assessing comparative importance of DNA sequence and epigenetic modifications on gene expression using a deep convolutional neural network," is published in Comput Struct Biotechnol Journal. Congrats!
2021
- 12.13.2021. The team of Dr. Dai and alumni (Dr. Peter Larsen and Dr. Derek Reiman) is the second winner of the GSK Bio-Manufacturing Omics Data Challenges.
- 9.15.2021. Derek started a faculty position at the Toyota Technological Institute at Chicago (TTIC). Congrats!
- 9.1.2021. Congratulations to Derek on the successful PhD dissertation defense: "Deep Learning Frameworks for Multi-omics Analyses of the Microbiome in Disease Studies."
- 6.2021. Congrats to Daiqing on a new position as a research technician at the Section of Cardiology, University of Chicago.
- 6.7.2021. Tina's paper: "Integrating microbiome and metabolome data for host disease prediction via deep learning neural networks," has been accepted for oral presentation at IEEE Biomedical and Health Informatics (BHI 2021), July 27-30, 2021. Congratulations!
- 5.26.2021. Shang's BITFAM paper: "A Bayesian Inference Transcription Factor Activity Model for the Analysis of Single Cell Transcriptomes," has been accepted by Genome Research. Congrats!
- 5.12.2021. Congrats to Tina on giving an oral presentation: "Is Gut Metabolome More Informative than Microbiome in Predicting Host Phenotype?" at GLBIO 2021!
- 4.29.2021. Derek's paper "MiMeNet: Exploring the Microbiome-Metabolome Relationships using Neural Networks" has been accepted by PLoS Computational Biology. Congrats!
2020
- 7.15.2020. Derek gives a short talk at ISMB 2020 on his paper, "MiMeNet: Exploring the Microbiome-Metabolome Relationships using Neural Networks." Congrats!
- 7.8.2020. Derek gives a talk at DelTA 2020 on his paper, "Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets." Congrats!
- 5.9.2020. Derek's paper, "PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype from Metagenomic Data," has been accepted by IEEE JBHI. Congrats!
2019
- 11.2019. Congrats to Jingting on the job position as a Clinical Data Scientist at Gilead Sciences, CA.
- 11.03.2019. Derek received a Student Travel Award to the IEEE BIBM conference at San Diego. Congrats!
- 10.22.2019. Congrats to Jingting for a successful PhD dissertation defense! Title: "Computational Analysis of DNA Methylation and Gene Expression".
- 10.20.2019. Shang presented a poster presentation at Cell Symposia of Transcriptional Regulation in Evolution, Development, and Disease. Title: "A Bayesian Inference Transcription Factor Activity Model for the Analysis of Single Cell Transcriptomes".
- 10.20.2019. Jingting, Derek and Shang's paper, "Using Convolutional Neural Network to Study the Regulatory Relationship Between DNA Methylation and Gene Expression," was accepted by the IEEE BIBM19 Workshop for oral presentation. Congrats!
- 10.1.2019. Derek's paper, "Using Autoencoders for Predicting Latent Microbiome Community Shifts Responding to Dietary Changes," was accepted by the IEEE BIBM19 Workshop for oral presentation. Congrats!
2018
- 11.12.2018. Jingting passed the Ph.D. Preliminary Exam. Title: Computational Analysis of DNA Methylation and Gene Regulation. Congrats!
- 05.16.2018. The R package "MetaLonDA" enjoyed more than 2100 downloads since its release in January 2018. Well done, Ahmed!
- 05.16.2018. Congrats to Ahmed on a successful Ph.D. thesis defense (Title: Computational Methods for Longitudinal Microbiome Analysis: Identification, Modeling, and Classification)!
- 02.13.2018. Ahmed released MetaLonDA R package and the paper "MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies" in Microbiome. Congrats!
2017
- 08.30.2017. Congrats to Peter Larsen on a successful Ph.D. thesis defense (Title: Modeling Host-Microbiome Interactions)!
- 06.07.2017. Ahmed's paper "Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA" was accepted as a regular paper for oral presentation at the ACM-BCB held at Boston. Congrats!
- 06.01.2017. Derek's paper "Using Convolutional Neural Networks to Explore the Microbiome" was accepted for oral presentation at EMBC2017 held in Korea
- 05.25.2017. Ahmed passed the Ph.D. Preliminary Exam with the proposed thesis project "Computational Methods For Longitudinal Microbiome Analysis: Identification, Modeling, and Classification". Congrats!
- 05.18.2017. Ahmed won the 2nd place for poster "Microbiome Dynamics as Predictors of Lung Transplant Rejection" at Great Lakes Bioinformatics Conference (GLBIO'17) at Chicago. Congrats!
- 5.17.2017. Dr. Dai organized a special session "Host-Microbiome Integrations: data analysis, modeling and applications at GLBIO 2017 (Chicago)
- 05.15.2017. Dr. Dai received a GPU grant from NVIDIA based on Derek's project "Convolutional Neural Networks (CNNs) for microbiome data analysis".
- 05.15.2017. Ahmed received a CCTS Pre-doctoral Education for Clinical and Translational Scientists (PECTS) Fellowship. Congrats!
- 03.22.2017. Ahmed won the Scientific Excellence Award for 1st place poster at UIC Department of Medicine Scholarly Activities Day. Congrats!
2016
- 11.1.2016. Ahmed was elected as Student Representative of IEEE EMBS (Terms Ends 2018). Congrats!
- 04.22.2016. Ahmed won 1st place in 2016 UIC Student Research Forum. Congrats!