Helix Projects





Machine learning approaches for characterizing and classifying local environments in proteins.

People: Russ Altman (PI), Inbal Halperin, Jessica Ebert, Shirley Wu, Dariya Glazer, Megan So, Joseph Chan, Samanth Chui, Randy Radmer

This work is supported by NIH R01 LM05652.

PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. PharmGKB's mission is to catalyze pharmacogenomics research.


This work is supported by NIH/NIGMS U01 GM061374.

RNA Dynamics & Folding

Methods for combining experiments and theory to model RNA structure and folding.

People: Russ Altman (PI), Alain Laederach, Magda Jonikas, Randy Radmer, Chris Bruns, and the Herschlag Lab collaborators

This work is supported by NIH P01 GM66275.

Linking Collagen Genotypes to Molecular Phenotypes

Use of genomic technologies to survey the variation in key collagen genes throughout the human population, link the discovered polymorphisms to their structural effects and develop an understanding of the mechanism of collagenous disorders including Osteogenesis Imperfecta.

People: Helix Group: Teri Klein (PI), Dale Bodian, James Gallerani, Kasey Miller, Randy Radmer; Stanford/Pande Group: Vijay Pande, Sanghyun Park; UCSF: Pui-Yan Kwok, Tingfung Chan; U. Washington: Peter Byers

This work is supported by NIH/NIAMS R01 AR051582.

Physics-based simulation of the motion and dynamics of biological structures.


This work is supported by the NIH Roadmap for Medical Research Grant U54 GM072970.

Myosin Force Chain Using Bioinformatics

Using comparative analysis to identify conserved structural features in molecular motors.

People: Russ Altman (PI), Jung-Chi Liao, Susan Tang, Jeanette Schmidt

Liver drug-related phenotyping project

Using bioinformatics databases to find organ-specific cell markers.

People: Russ Altman (PI), Bernie Daigle, Caroline Thorn, Shirley Wu


Malaria Bioinformatics

Ontologies to support the representation, distribution, and use of scientific data related to the parasite Plasmodium falciparum.

Defining Average Core Structures

Methods for probabilistic representation of structural variability and structural similarity.

RiboWeb: Biological collaboration on the Web

An ontology and knowledge base of ribosomal biochemical structural data.

Probabilistic Methods for Structure Computation and Display

Computing 3D molecular structures with sparse and noisy information.

The Structure of 30S rRNA in procaryotes

Low resolution models built from the RiboWEB knowledgebase

Heterogenous Database Integration Miscellaneous Small Projects

Methods for integrating databases using a common schema mapping technique.

Policy issues related to pharmacogenomics

Assessment of the identifiability of genomic DNA based on SNP frequencies.
Link to Stanford