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!