People
Senior Investigators
Mark Akeson, Professor of Biomolecular Engineering, and member UC Santa Cruz Genomics Institute. Beginning in 1996, our group has been developing nanopore devices for analysis of individual biological polymers. Our main contributions in this field have been coupling enzyme motors to biological pores to regulate polymer displacement past integral sensors within the pores. More recent experiments have focused on epigenetic modifications of DNA (principally 5-ˇmethylcytosine and 5-ˇhydroxymethylcytosine), and on single protein characterization. Over the last nine years we have worked with Oxford Nanopore Technology (ONT) in their efforts to develop a commercial nanopore DNA sequencer. This includes experiments where we evaluated their MinION sequencer (Jain, M., et al., “Improved data analysis for the MinION nanopore sequencer”. Nat Methods, 2015. 12(4): p. 351-356. We have also developed approaches for improving accuracy, and adapting the MinION to simultaneously read canonical and methylated cytosine bases (see Jain, M.O.,Hugh E.; and Akeson, M.. Methods For Determining Base Locations in a Polynucleotide, USPO, Editor. April 2015, Univ of California: USA. Over the coming years we will also focus on using nanopore sequencing devices like the MinION to elucidate relevant unresolved biological questions in cellular differentiation, neurological disorders, and cancer.
David Deamer, Research Professor of Biomolecular Engineering at the University of California (Santa Cruz) is Director of a newly established Astrobiology Center, a collaboration of NASA Ames and University of California researchers. He has recently published two new books. First Life: Discovering the Connections between Stars, Cells, and How Life Began (University of California Press, 2011). Deamer also co-edited Origins of Life with Jack Szostak, published by Cold Spring Harbor Press in 2010. Deamer's research focuses on how linear macromolecules traverse nanoscopic channels. Single-stranded nucleic acid molecules can be driven electrophoretically through a nanoscopic channel embedded in a lipid-bilayer membrane. The presence of the polynucleotide in the channel affects the ionic conductance in a manner related to chain length, concentration and base sequence. This observation has considerable potential for characterizing DNA and RNA in microscopic volumes of nucleic acid solutions. Recent reviews by Deamer (2011) and Branton, Deamer et al.(2008) describe the promise and challenges of nanopore sequencing.
Hugh Olsen. My research interests have historically focused on gene expression at the RNA and protein level with genes involved in cancer, in cellular homeostasis , and with the general gene class of G-protein coupled receptors. Currently, my interests have shifted to more practical applications of gene expression and protein engineering. These include engineering of mesophilic proteins to extreme conditions, as well as, discovery and expression of genes from extremophiles. These studies are aimed to provide new enzymes/proteins for research and industry.
Miten Jain, Assistant Research Scientist. My research interests include: 1) developing tools for analyzing genomics data; 2) developing wet-lab methods for long read sequencing of DNA and RNA; 3) developing wet-lab methods and software for resolving homopolymers and base modifications; 4) developing the nanopore MinION and PromethION sequencing platforms; 5) developing methods for sequencing and analysis of different classes of RNA (mRNA, rRNA, tRNA, non-coding RNA); 6) interfacing with a host of collaborations within UCSC and outside, including international consortiums and NASA, on nanopore sequencing applications. Learn more about Dr. Jain here.
Research Staff
Graduate Students
Niki Thomas
Lab Alumni
Andrew Smith
Doug Marks
Jacob Schreiber
Jeff Nivala
Kate Lieberman
Wenonah Vercoutere