CIRI is a risk model from the Alizadeh Lab and the Diehn Lab developed by Kurtz, Esfahani, Scherer, et al. for integrating diverse prognostic markers in cancer to produce a unified prediction of risk. CIRI incorporates serial information obtained throughout a patient’s course to provide a personalized estimate of risk over time.
PhasED-Seq (Phased variant Enrichment and Detection Sequencing) is a method from the Alizadeh Lab and the Diehn Lab for sensitive detection of circulating tumor DNA with detection limits in the parts-per-million range.
CIBERSORTx is an analytical tool from the Alizadeh Lab and Newman Lab to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.
MARIA is a machine learning tool from the Alizadeh Lab and the Altman Lab developed by Chen et al. to predict likelihood of HLA-II peptide ligand presentation given cell HLA alleles, peptide sequences, and source genes of the peptides.
Lung-CLiP is a novel approach from the Alizadeh Lab and the Diehn Lab developed by Chabon, Hamilton, Kurtz, Shahrokh, et al. for noninvasive early NSCLC detection that integrates improved sequencing library preparation and machine learning to predict the presence of tumor-derived cfDNA in a blood sample.
DIREct: this is the supplemental web site from the Alizadeh Lab and the Diehn Lab for the submitted manuscript by Nabet, Esfahani, et al.
PRECOG is a system from the Alizadeh Lab and the Gentles Lab for querying associations between genomic profiles and cancer outcomes. It enables researchers to query whether, for example, high expression of a gene is prognostic for shorter or longer patient survival.
CIBERSORT is an analytical tool from the Alizadeh Lab developed by Newman et al. to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.
iDES is a general framework from the Alizadeh Lab and the Diehn Lab for error suppression in high throughput sequencing data. A key advance within iDES is the use of computational “background polishing” to model and eliminate stereotypical sequencing artifacts. Background polishing can deliver performance gains that match, and often surpass, molecular barcoding alone. Applied together, the two techniques can improve analytical sensitivity by ~15-fold.
FACTERA is a tool from the Alizadeh Lab and the Diehn Lab for practical and robust de novo enumeration of genomic fusions and breakpoints from paired-end targeted (or genome-wide) sequencing data. FACTERA has minimal external dependencies, works directly on a preexisting BAM alignment file, and produces easily interpretable output.
Two Gene Score (TGS) calculator to determine prognosis in Diffuse Large B-cell Lymphoma (DLBCL) using the Two Gene Score (TGS) and the International Prognostic Index (IPI). Measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with DLBCL. This simple test can be used to select patients of different risk groups for clinical trials.
HEEBO/MEEBO legacy website. In collaboration with researchers at Stanford, UCSF, Stowers-Institute, Rockefeller, and Basel University, we designed and built an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and the human counterpart, HEEBOChip.
SOURCE (legacy website) is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports. It was moved to Princeton University, and the supporting database was last updated on June 10, 2015.
LLMPP legacy website - this is a web supplement for the Lymphoma/Leukemia Molecular Profiling Project originally published by Alizadeh A. et al. in 2000. It is a landmark paper and has received over 10,000 citations (as of 2020).
COSTIMULATION legacy website - this is a web supplement for the paper, Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T-Cell Activation (2002) PNAS 99(18): 11796-11801.
HOST-RESPONSE legacy website - this is a web supplement for the paper, Boldrick et al. (2002) PNAS Vol. 99: 972-977.