New article in Journal of Autoimmunity

New article in Journal of Autoimmunity

February 1, 2024

A new publication from Trevor Chan, Prof. Ilias Tagokopoulos, and collaborators about IL-23 induces CLEC5A+ IL-17A+ neutrophils and elicit skin inflammation associated with psoriatic arthritis. Abstract: IL-23-activation of IL-17 producing T cells is involved in many rheumatic diseases. Herein, we investigate the role of IL-23 in the activation of myeloid cell subsets that contribute to skin inflammation in mice and […]

New article in Biomedicines

August 13, 2023

A new publication from Fangzhou Li, Dr. Ilias Tagkopoulos, and collaborators about Profile Characterization of Biogenic Amines in Glioblastoma Patients Undergoing Standard-of-Care Treatment. Introduction: Biogenic amines play important roles throughout cellular metabolism. This study explores a role of biogenic amines in glioblastoma pathogenesis. Here, we characterize the plasma levels of biogenic amines in glioblastoma patients undergoing […]

New article in Current Research in Food Science

April 19, 2023

A new publication from Tarini Naravane and Dr. Ilias Tagkopoulos about Machine learning models to predict micronutrient profile in food after processing. Abstract: The information on nutritional profile of cooked foods is important to both food manufacturers and consumers, and a major challenge to obtaining precise information is the inherent variation in the composition of the raw […]

New article in AAAI-23 AIAFS

February 4, 2023

A new publication from Jason Youn, Fangzhou Li, and Dr. Ilias Tagkopoulos about Semi-automated construction of food composition knowledge base is accepted as a lightning talk in the 37th AAAI Conference on Artificial Intelligence, AI for Agriculture and Food Systems Workshop (AAAI-23 AIAFS). Abstract: A food composition knowledge base, which stores the essential phyto-, micro-, and […]

New article in PLOS One

December 5, 2022

A new publication from Trevor Chan, Cheng-En Tan, and Dr. Ilias Tagkopoulos about Audit lead selection and yield prediction from historical tax data using artificial neural networks. Abstract: Tax audits are a crucial process adopted in all tax departments to ensure tax compliance and fairness. Traditionally, tax audit leads have been selected based on empirical […]

New article in the Journal of Agricultural and Food Chemistry

November 25, 2022

A new publication from Dr. Ilias Tagkopoulos and collaborators about Chardonnay Marc as a New Model for Upcycled Co-products in the Food Industry: Concentration of Diverse Natural Products Chemistry for Consumer Health and Sensory Benefits. Abstract: Research continues to provide compelling insights into potential health benefits associated with diets rich in plant-based natural products (PBNPs). […]

New article in Journal of the American Medical Informatics Association

October 31, 2022

A new publication from Dr. Ameen Eetemadi and Dr. Ilias Tagkopoulos, about Algorithmic Lifestyle Optimization. Abstract: A hallmark of personalized medicine and nutrition is to identify effective treatment plans at the individual level. Lifestyle interventions (LIs), from diet to exercise, can have a significant effect over time, especially in the case of food intolerances and […]

New article in Scientific Reports

August 25, 2022

A new publication from collaborators and Dr. Ilias Tagkopoulos, about An Early Prediction Model for Canine Chronic Kidney Disease Based on Routine Clinical Laboratory Tests. Abstract: The aim of this study was to derive a model to predict the risk of dogs developing chronic kidney disease (CKD) using data from electronic health records (EHR) collected […]

New article in Computational and Structural Biotechnology Journal

July 20, 2022

A new publication from collaborators and Dr. Ilias Tagkopoulos, about A Computational Algorithm to Assess the Physiochemical Determinants of T Cell Receptor Dissociation Kinetics. Abstract: The rational design of T Cell Receptors (TCRs) for immunotherapy has stagnated due to a limited understanding of the dynamic physiochemical features of the TCR that elicit an immunogenic response. […]

New article in International Journal of Molecular Sciences

June 3, 2022

A new publication from Dr. Navneet Rai, Dr. Minseung Kim, and Dr. Ilias Tagkopoulos, about Understanding the Formation and Mechanism of Anticipatory Responses in Escherichia coli. Abstract: Microorganisms often live in complex habitats, where changes in the environment are predictable, providing an opportunity for microorganisms to learn, anticipate the upcoming environmental changes and prepare in […]

New article in Nature Communications

April 29, 2022

A new publication from Jason Youn, Dr. Navneet Rai, and Dr. Ilias Tagkopoulos, about Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Abstract: We present a machine learning framework to automate knowledge discovery through knowledge graph construction, inconsistency resolution, and iterative link prediction. By incorporating knowledge from 10 publicly available sources, […]

New article in Applied Sciences

December 4, 2021

A new publication from Dr. Bo Mi Lee, Dr. Ameen Eetemadi, and Dr. Ilias Tagkopoulos, about Reduced graphene oxide-metalloporphyrin sensors for human breath screening. Abstract: The objective of this study is to validate reduced graphene oxide (RGO)-based volatile organic compounds (VOC) sensors, assembled by simple and low-cost manufacturing, for the detection of disease-related VOCs in […]

New article in Metabolic Engineering

November 24, 2021

A new publication from collaborators and our lab members, Dr. Erol S. Kavvas, Dr. Xiaokang Wang, and Dr. Ilias Tagkopoulos, about Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli. Abstract: Previously, Escherichia coli was engineered to produce isobutyl acetate (IBA). Titers greater than the toxicity threshold (3 g/L) were achieved by using layer-assisted production. […]

New article in Journal of Dairy Science

September 20, 2021

A new publication from collaborators and our lab members, Jaesung Youn and Dr. Tagkopoulos, about Integration of statistical inferences and machine learning algorithms for prediction of metritis cure in dairy cows. Abstract: The study’s objectives were to identify cow-level and environmental factors associated with metritis cure to predict metritis cure using traditional statistics and machine […]

Ameen Eetemadi

Ameen Eetemadi graduates!

July 26, 2021

Ameen graduates with a Ph.D. in Computer Science with a designated emphasis in biotechnology, specializing areas of machine learning, bioinformatics, and computational biology on Jul 26th, 2021! Congratulations to Dr. Eetemadi! Wish you a new journey filled with success!

New article in Frontiers in Microbiology

June 23, 2021

A new publication from Dr. Beatriz Merchel Piovesan Pereira, Muhammad Adil Salim, Dr. Navneet Rai, and Dr. Ilias Tagkopoulos about Tolerance to glutaraldehyde in Escherichia coli mediated by overexpression of the aldehyde reductase YqhD by YqhC. Abstract: Glutaraldehyde is a widely used biocide on the market for about 50 years. Despite its broad application, several reports on the emergence of bacterial […]

New article in Scientific Reports

April 9, 2021

A new publication from Dr. Ki-Jo Kim, Dr. Su-Jin Moon, Dr. Kyung-Su Park, and Dr. Ilias Tagkopoulos about drug effects modeling on disease module in systemic sclerosis. Abstract: The network-based proximity between drug targets and disease genes can provide novel insights regarding the repercussions, interplay, and repositioning of drugs in the context of disease. Current […]

New article in Frontiers in Microbiology

February 26, 2021

A new publication from Dr. Beatriz Pereira, Dr. Xiaokang Wang, and Dr. Ilias Tagkopoulos about the response of Escherichia coli to biocides (antiseptics and disinfectants) after adaptive laboratory evolution. The work explores the differences between biocides when selecting for mutations in the E. coli genome, their effect on biofilm formation, biocide, and antibiotic susceptibility. Reference: Pereira, Beatriz Merchel Piovesan, […]

New article in Clinical Nutrition

January 11, 2021

A new Clinical Nutrition article by Ameen Eetemadi and Professor Ilias Tagkopoulos investigating the role of the gut microbiome in dietary treatments for irritable bowel syndrome (IBS). We integrated and analyzed raw microbiome data from multiple IBS studies and showed for the first time that methane and fatty acid metabolism pathways are predictive of Low-FODMAP […]

Beatriz Pereira graduates!

December 31, 2020

Beatriz graduates with a Ph.D. in Microbiology with a designated emphasis in biotechnology on Dec 31st, 2020! Congratulations to Dr. Pereira! Wish you a new journey filled with success! Also see this Beatriz’s fantastic blog about her Ph.D. journey!

New article in Foods

December 10, 2020

A new publication from Derrick Risner, Fangzhou Li, Dr. Jason S. Fell, Dr. Sara A. Pace, Dr. Justin B. Siegel, Dr. Ilias Tagopolous, and Dr. Edward S. Spang, providing a model for assessing the projected cost of animal cell-based meat. A sensitivity analysis of the model identified the nine most influential cost factors for ACBM […]

New article in Frontiers in Artificial Intelligence

December 8, 2020

A new Front. Artif. Intell. article by Jason, Tarani, and Prof. Tagkopoulos! In this work, we applied the learning ontologies via embeddings (LOVE) framework, which takes advantage of the semantic similarity of the word embeddings to the field of food ontologies. The automated method we proposed here is a solution to the manual burden of […]

New article in Nature Communication

October 6, 2020

A new publication from Xiaokang Wang, Navneet Rai, Beatriz Merchel Piovesan Pereira, Ameen Eetemadi, and Ilias Tagkopoulos. How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. In this paper we designed an optimal experimental design (coined OPEX) framework to guide omics experimentation by selecting the most informative experiments to […]

Gabriel Simmons joins the lab!

September 28, 2020

Gabe joins the lab as a CS PhD student in 2020! Gabe received his B.S. in mechanical engineering at UC Davis, and before joining the lab, he was working as a data scientist at Process Integration and Predictive Analytics, LLC. Learn more from Gabe’s CV!

Christian Millsop joins the lab!

September 28, 2020

Christian joins the lab as a CS PhD student in 2020! Christian acquired his B.S. in biochemical engineering at UC Davis, and the Master of Information and Data Science degree at UC Berkeley. Before joining the lab, Christian was also working as a data engineer at Genentech. Learn more from Christian’s CV!

New article in Biochemistry

September 16, 2020

A new publication from Dr. Wai Shun Mak, Dr. Xiaokang Wang, Rigoberto Arenas, Youtian Cui, Dr. Steve J Bertolani, Wen Qiao Deng, Dr. Ilias Tagkopoulos, Dr. David K Wilson, Dr. Justin B Siegel, combining structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs). They discovered latent ADO-like […]

Erol Kavvas joins the lab!

September 11, 2020

Erol joins the lab as a postdoctoral associate in 2020! Erol received his Ph.D. degree at University of California, San Diego in 2020, and he specializes in bioengineering with the emphasis on machine learning. Learn more from Erol’s CV.

NSF grant awarded $20M for AIFS, AI Institute for Next Generation Food Systems

August 29, 2020

The U.S. National Science Foundation (NSF) and the U.S. Department of Agriculture’s National Institute of Food and Agriculture (USDA) awarded $100M and $40M respectively, $140M in total, to seven newly established artificial intelligence institutes. UC Davis AI Institute for Next Generation Food Systems led by Prof. Ilias Tagkopoulos was selected as one of the seven […]

New article in Clinical and Experimental Rheumatology

July 25, 2020

A new publication from Dr. Young Bin Joo, Dr. In-Woon Baek, Dr. Kyung-Su Park, Dr. Ilias Tagkopoulos, and Dr. Ki-Jo Kim, investigating whether unbiased clustering analysis of phenotypic data can lead to coherent subgroups of axSpA patients with a distinct risk of radiographic progression. They found out that phenotype mapping results in a clinically relevant […]

Xiaokang Wang graduates!

May 22, 2020

Xiaokang graduates as a Ph.D.! Xiaokang received the offer of a quantitative analyst position from Point72 Asset Management. Congratulations to you, and wish you a good fortune and every success!

New article in Applied and Environmental Microbiology

May 4, 2020

A new publication from Beatriz Pereira, Xiaokang Wang, and Dr. Ilias Tagkopoulos on E. coli’s stress response to everyday use biocides. The work highlights the differences between short- and long-term exposure to biocides in the bacterial transcriptome. Novel correlations between zinc-homeostasis genes and tolerance to biocides were explored, and targets for future investigation of resistance […]

New article in Frontiers in Microbiology

April 3, 2020

A new publication from our lab with Ameen, Navneet, Beatriz, Minseung and Prof. Tagkopoulos reviewing the computational methods across diet, microbiome, and health including an overview of the current knowledge about diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning methods, recommendation system approaches, the intellectual property landscape and new scenarios to be unlocked in […]

Muhammad Adil Salim joins the lab!

April 1, 2020

Adil joins the lab as a Ph.D. student in Microbiology! Adil received his B.S. (Hons) and M.Phil. degrees at University of Peshawar, respectively in 2013 and 2016. Adil focuses on the area in microbiology with a designated emphasis in biotechnology. Learn more from Adil’s resume!

Fangzhou Li joins the lab!

November 5, 2019

Fang joins the lab as a junior specialist in November, 2019! Fang will start his Ph.D. from Fall 2020!

New article in Applied and Environmental Microbiology

April 29, 2019

A new publication from Beatriz Pereira and Dr. Ilias Tagkopoulos reviewing benzalkonium chlorides (BACs). The review overviewed the current market and regulations of BACs as well as available safety data and the correlation between BACs and increasing of microbial tolerance to chemicals. The work suggested a role of BACs in generating selective environments that favor […]

New article in Clinical Immunology

March 25, 2019

A new publication from our lab with Ki-Jo, Minseung, Iannis and Prof. Tagkopoulos on curating a Rheumatoid arthritis (RA) synovial genome-scale transcriptomic profiles which cover an intersection of 11769 genes from 11 datasets. Three clusters with different pathway signatures are observed and the prediction model using gene expression level as input for drug effectiveness are […]

New article in Biotechnology and Bioengineering

February 2, 2019

A new publication from our lab with Navneet, Linh, Minseung and Prof. Tagkopoulos on observing a reproducible phenomenon of abrupt population decrease followed by a rapid increase during long‐term chemostat cultivations in specific E.coli strains. Genetic basis of this phenomenon is identified by genome and transcription profiling. Rai, Navneet, et al. “Population collapse and adaptive rescue […]

New article in The Korean Journal of Internal Medicine

February 2, 2019

A new publication from our lab with Ki-Jo and Prof. Tagkopoulos on reviewing different machine approaches for clinical data analysis in rheumatic diseases research. Kim, Ki-Jo, and Ilias Tagkopoulos. “Application of machine learning in rheumatic disease research.” The Korean journal of internal medicine(2018). doi:10.3904/kjim.2018.349 (link)  

New article in Biotechnology and Bioengineering

December 17, 2018

A new publication from our lab with Navneet, Linh, Minseung and Prof. Tagkopoulos on a new reproducible phenomenon on chemostat cultivation, where the population collapses around 100h and it recovers through adaptive mutations in key membrane and tRNA genes. Rai, Navneet, et al. “Population collapse and adaptive rescue during long‐term chemostat fermentation.” Biotechnology and bioengineering 116.3 (2019): […]

New article in Bioinformatics

December 17, 2018

A new publication from our lab with Ameen and Prof. Tagkopoulos on novel neural network structure (Genetic Neural Network, GNN) which achieve 40% more accurate than other conventional architectures (MLP, RNN, BiRNN) on average for gene expression level predictions. Eetemadi, Ameen, and Ilias Tagkopoulos. “Genetic Neural Networks: an artificial neural network architecture for capturing gene […]