A major focus of our lab is engineering innovation for analysis of complex biological systems — as is required to address questions important to both fundamental biological systems and applied clinical research. We employ a combination of approaches drawn from bioengineering, chemical engineering, mechanical engineering, and electrical engineering with strong foundations in biology, materials science, and analytical chemistry. In essence, we strive to advance the “mathematization” of biology & medicine.
We are part of the UC Berkeley Department of Bioengineering and the UC Berkeley/UCSF Graduate Group in Bioengineering. A primary focus of our research is in tools to push the frontier of single-cell biology. To accomplish this, we design and create instrumentation that exploits scale-dependent physics and chemistry. Our work accelerates development of bioanalytical methods, streamlines sample preparation strategies, improves biomarker validation studies, and advances clinical diagnostics.
Affiliations: QB3: The California Institute of Quantitative Biosciences, The Chan Zuckerberg Biohub, The Berkeley Stem Cell Center, Jacobs Institute of Design Innovation, and The Lawrence Berkeley National Laboratory.
Graduate student researchers join us from UC Berkeley & UCSF Graduate Programs: Bioengineering, Chemical Biology, and Applied Science & Technology, and various engineering & chemistry programs.
News
- A warm welcome to postdoctoral scholars Kin Gomez, Ph.D. and Harrison Khoo, Ph.D. both starting at the Herr Lab in July 2026. Looking forward to breakthroughs in collaboration with two rising stars in bioengineering.
- Congratulations (again) to Maya & co-authors at Biohub for being recognized with a Best Poster Award at the Single-Cell Proteomics SCP Conference 2026.
- Congratulations to Maya & co-authors at Biohub on our work “Single-Cell Mass Spectrometry Proteomics Paired with Imaging-Based Morphology” selected for a poster at MicroTAS 2026.
- New publication accepted at Analyst: “Bead-free deterministic DNA barcoding using vacuum-driven loading of aqueous oligonucleotides to microwell arrays” on a novel microwell barcoding technique.
- New preprint available on our research with the Rosenbluth Lab at UCSF: “AutoBlot: deterministic single-cell western blotting reveals proteomic diversity in rare cell populations“, with peer review underway.
- Congratulations on graduation from the UC Berkeley MEng program to Samantha, Bhavya, and Maylee. Big thanks PhD candidate Maya for exceptional mentorship during that MEng year.
- Preprint on our work “Bead-free deterministic DNA barcoding using vacuum-driven loading of aqueous oligonucleotides to microwell arrays” is available and under peer review.
- Collaboration with Rosenbluth Lab at UCSF has a preprint available “EpiBlot: A Data-Informed Chromatin Accessibility and Proteoform-Resolved Profiling Workflow” and under peer review.
- Amy is named a Weill Neurohub Investigator.
- Congratulations to Nazibul for receiving a Berkeley Stem Cell Center Postdoc Fellowship (CIRM) through 2027!
- Congrats to Xin on being selected to present a talk at qBio in Feb 2026. Amy will also deliver a talk.
- Amy appointed to the DARPA Biological Sciences & Technology working group.
- Pacifichem arrives just once every 5 years, and Amy will present a handful of invited talks on our lab’s research in Dec 2025.
- Iyla and Maya each deliver podium presentations at the American Chemical Society – Western Regional Meeting in San Jose, CA. Congratulations Iyla & team, and Maya & team.
- Our paper “Single-cell nucleus extraction with cellular indexing” is accepted at Advanced Science. Congratulations to Trinh, Ana, Alison, Anna, Xin, Nazibul, Paul.
- Our paper “Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms” is accepted at Analyst.