Members of the Saier Lab

Dr. Milton Saier

Professor/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 about 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

Kevin J. Hendargo

Kevin joined the lab in spring, 2016, as an undergrad majoring in Biochemistry and Cell Biology. Thanks to his expertise in Bioinformatics and Structural Biology, Kevin has contributed to multiple projects. His Master’s thesis is about the refinement of bioinformatic techniques to better classify families/superfamilies and improve structure/function predictions.

Andrew Bodnar

Andrew joined the lab in July, 2017, as an undergrad with major in Molecular Biology. For his Master’s project, Andrew is investigating how the expression of a metal ion efflux gene cluster in the bacterium Cupriavidus metallidurans can be influenced by insertion elements and the three-dimensional structure of the DNA.

Harry Zhou

Harry joined the lab in March, 2018, as an undergrad majoring in Human Biology. He is expanding his original project for his Master’s degree, which seeks to elucidate the molecular mechanism following IS5-insertion into the fuc regulon in Escherichia coli.

Katie Jing Kay Lam

Katie joined the lab in October, 2018, as an undergrad with major in Human Biology. She has contributed to several projects involving Comparative Genomics and Superfamily expansion. Currently, she is working on her Master’s project, where she studies non-insertional mutations in the bgl operon in Escherichia coli.

Peter Kopkowski

Peter joined the lab in July, 2019, as an undergrad majoring in General Biology. His Master’s project is to determine the effect DNA binding proteins have on transposition frequency into the bgl operon in Escherichia coli.

Jianing Wang

Jianing joined the lab in October, 2019, as an undergrad majoring in Bioinformatics. He has participated in two bioinformatics projects. Currently, he is working on his Master’s project about the comparative genomics of viral genomes from the order Nidovirales with emphasis in family and functional associations.

Aditi Dubey

Aditi joined the lab in April, 2020 as a Microbiology major undergrad. She has contributed to two comparative genomics projects. In her Master’s project, she collaborates with another student to study the relationship between the LIC family and the VIC superfamily using sequence-based and 3D structural-based approaches.

Blaine Safir

Blaine joined the lab in the 2020 fall quarter as an undergrad majoring in Molecular & Cellular Biology. He has contributed to one Comparative Genomics project in the dry lab. His Master’s project is to elucidate the mechanism of IS5 insertion into the glpFK operon in Escherichia coli.

Undergrad students

Madison Baxter

Madison joined the lab in August, 2020, and her major is Human Biology. She has contributed to two bioinformatics projects. In her currently project, she collaborates with another student to study the relationship between the LIC family and the VIC superfamily using a 3D structure-based approach.

Xiaojuan (Farah) Chen

Farah joined the lab in October, 2020. She is double majoring in pharmacological chemistry and chemical engineering. As our wet lab assistant, her efforts contribute to multiple experimental projects in the lab.

Ahmed Mabrouk

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

Bowen Li

Bowen joined the lab in February, 2021. His major is Pharmaceutical Chemistry. Bowen’s project applies bioinformatic methods to study the relationship between ABC uptake systems and ABC2 export systems,  which requires both sequence- and structure-based approaches.

Charlene Ramtin

Charlene joined the lab in April, 2021, and an undergrad and her major is Global Health. She is working on a comparative genomics study involving endosymbionts of amoebas and clams.

Hunter Cheng

Hunter joined the lab in April, 2021, and his major is Biology and Bioinformatics. Hunter will apply his software development skills to several bioinformatics projects in the dry lab, including superfamily characterization/expansion and comparative genomics.

Vince Ly

Vince joined the lab in April, 2021. His major is Molecular and Cell Biology. Vince is contributing to the project where we study the relationship between ABC uptake systems and ABC2 export systems. This includes the characterization and relationships between the different components of ECF uptake systems.

Solomon Kim

Solomon joined the lab in October, 2021, as lab assistant. His major is Biochemistry and he is interested in our bioinformatics team where he will contribute to several of our projects.

Volunteers

MD. Jingxia Meng

Dr. Meng joined the lab in October, 2020.  She is working 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. Nicole Hatakeyama

Nicole joined the lab in March, 2021.  She completed her BSc in General Biology. Nicole is contributing to three comparative genomics projects involving 1)  four Metagenome Assembled Genomes from  the bacterial Candidate Phyla Radiation group; 2) six sulfate-reducing bacteria; and 3) eight endosymbionts of amoebas and clams.

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. 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. 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.

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.

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 and continues to collaborate with the Saier lab.

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 projects and continues to collaborate with the Saier lab.

MSc. Nicholas Wong

Alumnus/SBP

Nicholas joined the lab in 2017 as an undergrad student. He obtained his Master’s degree on November 5. 2021, when he defended his thesis “Stages of Early Replication and Membrane Rearrangement in Coronaviruses: The Replication Organelle”.  He’s contributed to several projects.

Previous lab members

MSc. Dennis Tran

Alumnus

On June 23, 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.

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.

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.

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.

BSc. Cassidy Lee

Volunteer

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.