We have developed several, groundbreaking technologies that contribute to advancing:
-
our understanding of transcription factor (TF) function & gene regulation, including an automated yeast one-hybrid platform that enables large-scale protein-DNA interaction mapping (Hens et al., Nat. Methods, 2011; Gubelmann et al., Mol. Syst. Biol., 2013), a multiplexed, targeted proteomics pipeline to count TFs or other lowly abundant proteins during cellular differentiation (Simicevic et al., Nat. Methods, 2013; a Nature Biotech Highlight), a microfluidic approach (SMiLE-seq; patented), enabling de novo, quantitative TF-DNA binding analyses across a wide range of TF monomers and dimers (Isakova et al., Nature Methods, 2017; a Nature Genetics Reviews Highlight), and scTF-seq to study the role of TF dose in gene regulation (Liu et al., BioRxiv, 2024).
- our ability to profile or analyze single cells, including novel approaches to perform single cell transcriptomics on low-input cell samples or rare cells (Bues et al., 2022; patented) or to derive the transcriptome of a cell without killing it, Live-seq, enabling downstream molecular or functional profiling of that same cell (Chen et al., Nature, 2022; Highlighted by Nature Biotechnology, Nature Methods, Cell Reports Methods & PreLights). In addition, we developed the web portal ‘ASAP’ to enable standardized, straight-forward analysis of single cell omic datasets (Gardeux et al., Bioinformatics, 2017)
We also developed an ultra-affordable, highly multiplexed transcriptomics assay, BRB-seq (Alpern et al., Genome Biology, 2019), which led to a new start-up: Alithea Genomics.
My lab’s overall contribution to Life Sciences Tech development was recognized by Nature Methods.