Members of the Saier Lab

Dr. Milton Saier

Head of laboratory

Dr.  Saier established the main research lines of the lab and coordinates/guides all lab members and projects. His expertise in a wide range of biological fields allowed the creation/maintenance/curation of  the Transporter Classification Database (TCDB) and the publication of more than 600 peer-reviewed papers.

Dr. Zhongge Zhang

Scientist/Molecular Biology

Dr. Zhang joined the Saier Lab in 2001. He has vast experience on multiple areas such environment-induced mutations in bacteria, transcriptional/metabolic regulation, protein/protein interactome and bacterial growth laws. As a supervisor, he guides students, visiting scholars and oversees all research activities in the wet lab.

Dr. Arturo Medrano-Soto

Scientist/Bioinformatics

Dr. Medrano-Soto joined the lab in 2015. He has substantial experience in multiple fields including Comparative Genomics, Functional Genomics, Molecular Evolution and Bioinformatics.  He mentors students and visiting scholars, supervises the lab’s bioinformatics projects, develops new software tools, and keeps the dry lab operational.

Grad students

Jonathan Onstead

Jonathan joined the wet lab in March, 2022. His major was in Cell and Molecular Biology.  For his Master’s degree Jonathan is working on a wet lab approach to investigate the effect of IS26 on bacterial antibiotic resistance.

Jack Ord

Jack joined the dry lab in December, 2022 and his major was in Molecular Cell Biology.  For his Master’s project, Jack is looking at how insertion elements in transferase genes result in lipopolysaccharide modifications on the surface of E. coli and cause increased resistance to strong antibiotics.

Sofia Smith

Sofia joined our wet lab in January, 2023, as an undergrad and her major was Molecular and Cell Biology. For her master’s project, she is examining a bacterial survival mechanism by investigating IS1 activity in Eschrichia coli. Specifically, looking at transposable element activity and regulation when in starvation or toxic environments.

Undergrad students

Hunter Cheng

Hunter joined the lab in April, 2021, and his major is Biology and Bioinformatics. Hunter applies his programming skills to improve established bioinformatics tools, and he will participate in projects including superfamily characterization/expansion and comparative genomics.

Juan Velo

Juan joined the wet lab in October, 2021, as an undergrad majoring in Biochemistry. In his project, Juan is attempting to determine the effects of orientation and distances of IS elements upon bglGFB operon activation.

Hanzhong (Clark) Yang

Clark joined the dry lab in January, 2022, and his major is in Bioinformatics. Clark will apply his software development skills to several bioinformatics projects in the dry lab, including superfamily characterization/expansion and comparative genomics.

Andre Chu

Andre joined the dry lab in September, 2022. His major is in Bioinformatics.  In his project, Andre is  using a computational approach to predict of molecular function of hypothetical transporters within the MFS supperfamily.

Ritviksiddha Penchala

Ritvik joined the dry lab in September, 2022. His major is in Bioinformatics.  In his project, RItvik collaborates with 3 other students to apply a comparative genomics approach to study the human microbiome and its role in the response to COVID-19 infections.

Gautham Prabhakar

Gautham joined the wet lab in September, 2022 as an undergrad majoring in Bioinformatics.  In his project, Gautham collaborates with three other students to apply a comparative genomics approach to study the human microbiome and its role in the response to COVID-19 infections.

Allyson Ho

Allyson joined the lab in November, 2022, as an undergrad. Her major is General Biology. She is our web lab technician and makes sure that the equipment and supplies are in good condition and stocked. She contributes to the experimental needs of the research projects in the lab.

Coby Lin

Coby joined the dry lab in December, 2022 as an undergrad. His major is in Bioinformatics.  In his project, Coby is working on developing a fast method to identify transportomes for high-throughput processing of genomes.

Jialu (Steve) Huo

Steve joined the wet lab in January, 2023 as an undergrad.  In his project, Steve is  studying insertion sequence IS1 in E. coli to determine which of the six IS1 copies in the genome shows the most significant activity.

Wenhua Tang

Wenhua joined our bioinformatics lab in October, 2023, as an undergrad majoring in Data Science.  In his project, Wenhua will apply data mining and machine learning techniques to generate tools that will improve the quality of annotations  and the structure of knowledge representation in TCDB.

Volunteers

MSc. Sophia Beliaev

Sophia joined our lab in January, 2022. Her major was in Molecular and Cell Biology. For her Master’s project she used bioinformatic methods to expand the MFS superfamily with the Sar TMS10 Membrane Protein (S10MP) Family. She successfully defended her thesis on March, 2024. She is currently working on the manuscript to publish her results.

Collaborators

Dr. Gabriel Moreno-Hagelsieb

Professor/WLU Canada

Dr. Moreno-Hagelsieb took a sabbatical leave in our lab in 2015 as a bioinformatics specialist. Since then, he continues to collaborate with us in multiple projects involving Comparative Genomcis, Superfamily characterization/expansion, and the creation of novel annotation/curation pipelines for TCDB.

Dr. Vamsee Reddy

MD/St. Clare’s Denville Hospital

Dr. Reddy is our current database developer for TCDB. Over the years, he has contributed to multiple projects in the dry lab, including the adaptation of the ChEBI ontology to transported substrates in TCDB, characterization and expansion of superfamilies, characterization of transportormes, and comparative genomics.

Dr. Hassan Zafar

Professor/UO Pakistan

Dr. Zafar first joined our lab as a visiting scholar in 2016. Since then, he has worked on various projects involving comparative genomics of gut microbes, such as Salmonella, E. coli, Lactobacillus, Bacteroides, and Bifidobacterium. He continues to actively collaborate with us.

MSc. Kevin J. Hendargo

Kevin obtained his master’s degree in our lab on April 2023. Thanks to his expertise in Bioinformatics and Structural Biology, Kevin has contributed to multiple published articles. He continues to collaborate with us on multiple projects.

MSc. Nicholas Wong

Alumnus/SBP

Nicholas obtained his Master’s degree on November 2021 in our lab, when he defended his thesis “Stages of Early Replication and Membrane Rearrangement in Coronaviruses: The Replication Organelle”.  He’s contributed to several projects.

Dr. Bhaskara L. Reddy

Professor/LACCD

Dr. Reddy has collaborated with the lab multiple times over the years in projects ranging from famiiy/superfamily characterization and evolution, psychobiotics and their impact in mental health, the relationship between autism and the microbiome, the realtioship between eating meat and epidemics, and more.

Dr. Diego Romero-Pérez

Professor/UABC

Dr. Romero-Pérez collaborates with our lab by mining the literature to identify relevant transport-related papers to keep TCDB up to date.

Dr. Mohammad Aboulwafa

Professor/ASU Egypt

Dr. Aboulwafa has visited us several times and has collaborated with our wet lab  on a variety of topics, including  transport of sugars and vitamins, regulation of crp gene expression,  protein-protein interactions, and  more.

Previous lab members

MSc. Madison Baxter

Madison joined the lab in August, 2020, as an undergrad and her major was Human Biology.  She obtained her Master’s degree in June 2023 and it has already been published.

MSc. Aditi Dubey

Aditi obtained her master’s degree in our lab on March 2023. She contributed to several  published bioinformatics projects including her Master’s thesis.

Visvesh Jegadheesh

Visvesh joined the wet lab in September, 2022 as an undergrad majoring in Bioinformatics.  In his project, Visvesh collaborated with three other students to apply a comparative genomics approach to study the human microbiome and its role in the response to COVID-19 infections.

Yiran Xu

Yiran joined the lab in April, 2023 as a volunteer international exchange undergrad student from the Chinese University of Hong Kong. His major is Bioinformatics. Yiran worked on upgrading in-house bioinformatics tools that benefited several projects in the lab.

MSc. Chang (Owen) Zhang

Owen joined the lab in February, 2023. He studied Cognitive Science and majored in Machine Learning and Neural Computation. He then completed a master’s degree in Computer Science. As a volunteer in the lab, he worked on developing algorithms to classify proteins in their families based on the organization of their domain content.

MSc. Harry Zhou

Harry joined the lab in March, 2018, as an undergrad majoring in Human Biology. He completed his Master’s degree on April 20, 2023, where he elucidated the molecular mechanism behind IS5-driven activation of the fucOA operon in Escherichia coli.

MSc. Jianing Wang

Jianing received his master’s degree in our lab in March 2023. In addition to his project, he contributed to several published bioinformatics projects. Currently he is working on the preparation of the manuscript to publish his Master’s thesis project.

BSc. Charlene Ramtin

Charlene joined the lab in April, 2021 as an undergrad and she majored in Global Health. During here time in the lab, Charlene worked on a comparative genomics study involving endosymbionts of amoebas and clams.

BSc. Bowen Li

Bowen joined the lab in February, 2021, as an undergrad. His major is Pharmaceutical Chemistry. After his graduation in 2022, he volunteers in the lab to complete his project  where he studies the relationship between ABC uptake systems and ABC2 export systems,  which requires both sequence- and structure-based approaches.

BSc. Vince Ly

Vince joined the lab in April, 2021 as an undergrad. His major is Molecular and Cell Biology. After his graduation in 2022, he volunteers in the lab to complete his project where we studies the relationship between ABC uptake systems and ABC2 export systems. This includes the characterization and relationships between the different components of ECF uptake systems.

Toheeb Balogun

PhD Student

Toheeb is a PhD student in the School of Biological Sciences that rotated in our lab in the fall quarter 2022. Toheeb worked on the bioinformatic identification and characterization of novel superfamilies of spanin proteins.

MSc. Peter Kopkowski

Peter obtained his Master’s degree in October 2022, by defending the thesis: The Effects of DNA-Binding Proteins on IS Element Insertion Upstream of the bgl Operon in Escherichia coli. He has contributed to other project in the lab and his thesis is being prepared for publication.

MSc. Katie Jing Kay Lam

Alumna

Katie obtained her Master’s degree on April 2022, by defending the thesis: Histone-like Nucleoid Structuring (H-NS) Protein Silences the Beta-Glucoside (bgl) Utilization Operon by Formation of a DNA Loop in Escherichia coli. She also contributed to several published projects from the lab involving bioinformatics and wet lab work.

BSc. Xiaojuan (Farah) Chen

Alumna

Farah joined the lab in October, 2020 as an undergrad. She double majored in pharmacological chemistry and chemical engineering. She was our wet lab assistant for one year.

BSc. Hin (Edward) So

Alumnus

Edward worked in the lab until November 2022 as a lab technician. He majored in Molecular en Cell biology.  During his time in the lab Edward was responsible for keeping the wet lab equipment in good shape and helped with the experimental needs of several projects.

BSc. Nicole Hatakeyama

Alumna

Nicole joined the lab in March, 2021.  She completed her BSc in General Biology. Nicole contributed to two comparative genomics projects involving 1)  four Metagenome Assembled Genomes from  the bacterial Candidate Phyla Radiation group; and 2) six sulfate-reducing bacteria.

BSc. Yichi Zhang

Alumnus/Boston University

Yichi joined the lab in 2017 as an undergrad majoring in Bioinformatics and Environmental Chemistry. He developed several programs to help our research efforts in the dry lab. As a student, he contributed to several bioinformatics projects.

MD. Jingxia Meng

WUSTL

Dr. Meng joined the lab in October, 2020.  She worked with two other undergrad students on collecting evidence to determine whether the LIC family, which includes GABA receptors, is a distant member of the VIC superfamily.

BSc. Blaine Safir

Alumnus

Blaine joined the lab in the 2020 fall quarter as an undergrad majoring in Molecular & Cellular Biology. He participated in a Comparative Genomics project and studied the mechanism of IS5 insertion into the glpFK operon in Escherichia coli.

BSc. Ahmed Mabrouk

Alumnus

Ahmed joined the lab from October 2020 to  August 2021. He majored is General Biology and Global Health. In his wet lab project, Ahmed designed experiments to investigate the role of c-di-GMP in the regulation of the FlhDB operon of Escherichia coli during stationary phase.

MSc. Dennis Tran

Alumnus

On June 2021, Dennis obtained his Master’s degree by defending the thesis: The effects of global and specific DNA-binding proteins on transcriptional regulation of the bgl operon. Some of his results have been published.

BSc. Mai Kishinevsky

Alumna

Mai joined the lab in September, 2020, as an undergrad. During 10 months, 1) she curated ABC  systems in TCDB; 2) she studied the relationship of the ABC LptBFG family to ABC type 2 systems; and 3) in collaboration with other students, she studied the relationship between the S and T subunits within ECF systems.

MSc. Daniel Tyler

Alumnus

On January 28, 2021, Daniel obtained his Master’s degree  by defending the thesis: Discovery and characterization of the Phospholemman/SIMP/Viroporin (PSV) superfamily (published results).

MSc. Nuo Tian

Alumna/UCSF

On January 12, 2021, Nuo obtained her Master’s degree by defending the thesis: Structural and evolutionary relationships within the ATP-binding cassette (ABC) superfamily. Her experience allowed her to contribute to the curation of information in TCDB.

BSc. Vasu Pranav Sai Iddamsetty

Alumnus/Illumina

Pranav joined the lab in 2016 as an undergrad majoring in Bioinformatics. He developed and improved web applications and  stand-alone programs to help our research efforts in the dry lab. As a student, he contributed to several projects in the Saier lab.

MSc. Steven Russum

Alumnus

On March 19, 2020, Steven obtained his Master’s degree by defending the thesis: Comparative Metagenomic Analyses of Transporters Within the Archaeal Superphylum, Asgard.  (Published results). In addition, his experience allowed him to contribute to the curation of information in TCDB.

Andrew Bodnar

Andrew joined the lab in July, 2017, as an undergrad with major in Molecular Biology. He studied how the expression of a metal ion efflux gene cluster in the bacterium Cupriavidus metallidurans can be influenced by insertion elements and the role of  the three-dimensional structure of the DNA in this process.

BSc. Cassidy Lee

Alumna

Cassidy joined the lab in July 2019 as a  volunteer undergrad. She used bioinformatic techniques to characterize the transportome of the sulfate-reducing bacterium Desulfobacterium autotrophicum HRM2.

 

Dr. Sehrish Khan

Scientist/Pakistan

Dr Khan joined our lab in 2018 as a visiting scholar. As part of her PhD, she worked for a year on the use of the CRISPR/Cas9 system for the generation of disease-resistant plants. She developed most of the protocols of the CRISPR/Cas9 system in our lab.

MSc. Pauldeen Davejan

Alumnus

On July 26, 2018, Pauldeen obtained his Master’s degree by defending the thesis: Expansion of the Major Facilitator Superfamiy (MFS) to include novel transporters and the potential relationship between MFS and the LysE Superfamily (Published results).

Dr. Fereshteh Heidari

Scientist/Iran

Dr. Heidari joined the lab in 2017 and spent over a year doing research as part of her PhD. She worked on two projects: the characterization and comparative genomics of transportomes within the genus Bdellovibrio, as well as an experimental study of a riboflavin transporter in Bdellovibrio exovorous JSS.