The Team

Ashley’s career has focused on the study of host-microbe interactions mediated by microbial factors, specifically within inflammatory bowel disease (IBD). Her interest in studying biological components through analytical methods began during her undergraduate career at Florida State University where she received a B.S. in Biochemistry and developed a competitive immunoassay for the detection of islet amylin polypeptide by capillary electrophoresis under the mentorship of Dr. Michael G. Roper. This experience inspired her to pursue a PhD in Chemistry within the laboratory of Dr. Erin E. Carlson at Indiana University-Bloomington (IU). During her PhD at IU, she developed untargeted mass spectrometry methods for the discovery of metabolites from microbial communities. It was during her PhD that she became extremely interested in the effect of microbial-derived components on human health and sought to apply her chemistry and analytical backgrounds to the study of microbial metabolites in host-microbe disease mechanisms which led her to the University of Chicago.

While at the University of Chicago as a postdoctoral fellow, scholar and Staff Scientist, she was mentored by Dr. Dionysios A. Antonopoulos and Dr. Eugene B. Chang. Her training included several collaborative projects within the UChicago, MBL and ANL communities to quantitatively and qualitatively explore peptides and metabolites from continuous microbial culture, IBD patients and murine model systems. She has studied the impact of secreted metabolites on intestinal barrier function from a defined microbial community, analyzed metabolite profiles from IBD patients to explore their anxiety/depression comorbidities through targeted and untargeted methods, and established an in vivo murine model to study the impact of bile acids on microbe engraftment. She received several grants to support this work through The Microbiome Center, the Digestive Disease Research Core Center (DDRCC), and the Gastro-intestinal Research Foundation Associate’s Board (GIRF AB). She has also served as a Scientific Advisor on the GIRF AB since 2020.

Ashley is dedicated to providing targeted and untargeted metabolomics platforms to the host-microbe community to elucidate and define disease state-specific metabolite profiles for the discovery of early detection and prevention strategies as well as the discovery of novel treatments.

• Email: asidebottom@bsd.uchicago.edu

Metabolomics Team

Amber Rose attended the University of Texas in Austin, TX, where she received a BSA degree in Chemistry. During her undergraduate career, Amber became interested in research and joined an inorganic chemistry research lab. She worked with her graduate student mentor to utilize alkali metal counter-ions to produce stable, highly reducing FeS clusters, allowing for characterization of previously unstable products. After graduation, Amber was hired as a R&D lab technician at Albemarle Corporation in Pasadena, TX. She performed various inorganic synthesis procedures and material preparation using lab and pilot plant equipment, which resulted in the improvement and development of FCC catalyst materials. After two years of work, Amber decided to further her education in a field of study she had always found fascinating—forensic science. She joined an accredited graduate program at Cedar Crest College in Allentown, PA, where she obtained a MS degree in Forensic Science. While at Cedar Crest, Amber completed a thesis research project, which involved gathering and analyzing GC-MS data for a lesser-known class of novel psychoactive substances known as aminoindanes. She and her research advisor have recently submitted a manuscript for publication to the Rapid Communications in Mass Spectrometry Journal. Amber remains passionate about research and is excited to grow as a professional scientist while learning more about the human microbiome and various techniques used to analyze metabolites of interest.

 

Antonio grew up in the northwest suburbs of Chicago and has always had an interest in science. He earned his BS in Biological Sciences at the University of Illinois at Chicago (UIC) and went on to earn his Ph.D. at UIC in Dr. Brian T. Murphy’s lab. During his time in the Murphy lab, his research focus was twofold: i) isolation, purification, and structure elucidation of antibacterial and antimalarial compounds sourced from bacteria and ii) rapid identification of unknown environmental bacteria using mass spectrometry. In his free time Antonio likes to go bouldering, running, and taking his cat on walks. 

 

David was born in Nebraska and grew up in Northwest Missouri.  He attended the University of Nebraska Lincoln (UNL) for his undergrad and majored in Biological Sciences.  He then attended the University of Nebraska Medical Center (UNMC) in Omaha and obtained a BS in Medical Technology, now known as Medical Laboratory Science.  Since then, he’s worked predominantly in the hospital laboratory setting.  In 2009, he took a position at UNMC under the CDC’s Laboratory Response Network for Chemical Threats program (LRN-C).  There he began his work in the mass spectrometry field, with biannual trips to either the CDC in Atlanta or other state labs for training and updates from the network.  His mass spectrometry work has been in clinical applications, performing quantitative analyses on small molecules utilizing GC-, LC-, and ICP-MS.  In 2016, he started work on bringing up a new lab for identification and quantitation of seized narcotics using FTIR and mass spectrometry.  His lab went live in October of 2017 and began serving the Omaha Police Department.  He finished his Master of Public Health degree in December of 2020, with a focus in environmental and occupational health.  His capstone project involved measuring blood mercury and cadmium levels in children living near a coal-fired power plant in Omaha.  He relocated to Chicago in December of 2020 and began work at the University of Chicago in January of 2021.

 

Jessica did her undergraduate work in Biology at Taylor University in Upland, Indiana. After discovering her love for science, she opted to continue her education by getting her PhD  in Pharmacognosy (Natural Products) at the University of Illinois in Chicago. She spent much of her time there studying the way bacteria interacts in cheese, and, suprisingly, she still loves to eat cheese!  In her spare time she likes to play soccer and ultimate frisbee.

 

Mary received her BS in Forensic Science from Loyola University of Chicago. Since then, she has worked as a forensic toxicologist with the Cook County Medical examiner performing routine drug and alcohol tests on biological specimens utilizing GC-MS, LC-MS, HS-MS, and Elisa techniques to assist the Medical Examiner in determining the cause of death during autopsies. Mary then shifted gears to work in a clinical setting in the Mass Spectrometry Lab at Lurie Children’s hospital here in Chicago. It was there where she performed therapeutic drug monitoring via different Mass Spec techniques and trained in the Biochemical Genetics Lab which analyzed amino and organic acid levels for the diagnosis of and monitoring of patients with inborn errors of intermediary metabolism. During the beginning stages of the Covid pandemic, Mary was asked to help the Lurie Children’s Special Infectious Diseases lab in performing PCR Covid testing for Lurie patients, staff, and members of the community. In her spare time, Mary worked in Loyola’s Forensic Science Mass Spectrometry lab doing research and method development for the biomarker Phoshatidyl Ethanol (PEth) trying to create a GC-MS method for analysis of PEth from a dried blood spot card to which the method is currently in the process of becoming patented. For a short period of time, Mary worked in Indiana performing routine drug analysis via LC/MS for Pain Management Clinics in addition to PCR testing on Covid samples, but is happy to be back in Chicago doing research via Mass Spectrometry.

 

After earning his BFA in ‘Intermedia’ (with a focus on illustration, video, and animation) from Arizona State University in 2002, Michael attended DePaul University from 2009–2012 for post-bacc studies in the sciences. While there, he conducted research with Prof. Justin Maresh, synthesizing halogenated plant biosynthesis precursors and maintaining plant cell cultures for the biotransformation of the precursors into “non-natural” natural products.

Michael then earned his PhD in Pharmacognosy in 2016 as an AFPE and NIH NCCIH T32 predoctoral fellow in the lab of Prof. Brian T. Murphy at the University of Illinois at Chicago, where he discovered and led preclinical studies on novel tuberculosis antibiotic leads from freshwater- and marine-derived actinomycete bacteria.

As an NIH NCI NRSA Postdoctoral Fellow working under the co-mentorship of Prof. Neil L. Kelleher and Prof. Regan J. Thomson, Michael advanced the “metabologenomics,” platform of correlating microbial genomics and mass-spectrometry–based metabolomics to drive the discovery of novel specialized metabolites. Specifically, he collaborated with leading natural products bioinformatics groups to aid in the development and provide proof-of-concept for the discovery platform known as BiGSCAPE-CORASON.

As Senior Scientist in the Duchossois Family Institute (DFI) Host-Microbe Metabolomics Facility at the University of Chicago, Michael’s interests involve the discovery of new small molecules and functions in the human microbiome related to health and disease.

 

Bioinformatics

Ramanujam Ramaswamy (Ram) is from India. He graduated with a bachelor’s degree in Mechanical Engineering following which, he worked for Toyota manufacturing for four years. He came to the US in 2019 to pursue a Master’s in Industrial Engineering and while exploring different areas, found his curiosity and calling pointed towards bioinformatics. He joined the Duchossois Family Institute at the University of Chicago in 2022. Ram loves swimming, ice skating (not a big fan of cold though…), talking about philosophy,  and trying out new things.

Administration

Shannon graduated from Indiana University in 2022 with a BFA in photography and a BA in Art History. She joined the DFI in September, 2023 and helps support the members of the core facilities. She is passionate about the intersection of STEM and the arts.

• Office Phone: 773.834.3080
• Email: shannon.hocker@bsd.uchicago.edu