idekeradmin – IDEKER LAB

PubMed

An open invitation to the Understudied Proteins Initiative 2022-05-09
No abstract
Georg Kustatscher
Understudied proteins: opportunities and challenges for functional proteomics 2022-05-09
No abstract
Georg Kustatscher
Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance 2022-02-12
In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in Saccharomyces cerevisiae. Sequence analysis identified many genes contributing to the resistance phenotype as well as numerous amino acids in potential targets that may play a role in compound binding. Our work shows that compound-target pairs can […]
Sabine Ottilie
Prospecting whole cancer genomes 2022-02-05
No abstract
Jason F Kreisberg
Deep distributed computing to reconstruct extremely large lineage trees 2022-01-07
Phylogeny estimation (the reconstruction of evolutionary trees) has recently been applied to CRISPR-based cell lineage tracing, allowing the developmental history of an individual tissue or organism to be inferred from a large number of mutated sequences in somatic cells. However, current computational methods are not able to construct phylogenetic trees from extremely large numbers of […]
Naoki Konno
Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR 2021-12-16
Oncogenesis relies on the alteration of multiple driver genes, but precisely which groups of alterations lead to cancer is not well understood. To chart these combinations, Zhao and colleagues use the CRISPR-Cas9 system to knockout all pairwise combinations among 52 tumor suppressor genes, with the goal of identifying groups of alterations that collaborate to promote […]
Samson H Fong
A multi-scale map of cell structure fusing protein images and interactions 2021-11-25
The cell is a multi-scale structure with modular organization across at least four orders of magnitude¹. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately^(2,3). Here we integrate immunofluorescence images in the Human Protein Atlas⁴ with affinity […]
Yue Qin
A protein interaction landscape of breast cancer 2021-09-30
Cancers have been associated with a diverse array of genomic alterations. To help mechanistically understand such alterations in breast-invasive carcinoma, we applied affinity purification–mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer (BC) proteins, with and without relevant mutations, across three human breast cell lines. These networks identify cancer-specific protein-protein […]
Minkyu Kim
Interpretation of cancer mutations using a multiscale map of protein systems 2021-09-30
A major goal of cancer research is to understand how mutations distributed across diverse genes affect common cellular systems, including multiprotein complexes and assemblies. Two challenges—how to comprehensively map such systems and how to identify which are under mutational selection—have hindered this understanding. Accordingly, we created a comprehensive map of cancer protein systems integrating both […]
Fan Zheng
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity 2021-09-30
We outline a framework for elucidating tumor genetic complexity through multidimensional protein-protein interaction maps and apply it to enhancing our understanding of head and neck squamous cell carcinoma. This network uncovers 771 interactions from cancer and noncancerous cell states, including WT and mutant protein isoforms. Prioritization of cancer-enriched interactions reveals a previously unidentified association of […]
Danielle L Swaney