Chris Sander
A5008166270- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Renal cell carcinoma treatment
- RNA modifications and cancer
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Sarcoma Diagnosis and Treatment
- Cancer Treatment and Pharmacology
- Advanced Breast Cancer Therapies
- Colorectal Cancer Treatments and Studies
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Renal and related cancers
- Prostate Cancer Treatment and Research
- Advanced Proteomics Techniques and Applications
- Cancer, Hypoxia, and Metabolism
Deutsche Morbus Crohn/Colitis ulcerosa Vereinigung
2025
Harvard University
2015-2024
Dana-Farber Cancer Institute
2007-2024
Center for Systems Biology
2005-2024
Dana-Farber/Harvard Cancer Center
2023-2024
Broad Institute
2007-2024
Athinoula A. Martinos Center for Biomedical Imaging
2024
Massachusetts General Hospital
2024
Memorial Sloan Kettering Cancer Center
2013-2023
Boston University
2017-2022
Abstract The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to from more than 5,000 tumor samples 20 studies. significantly lowers the barriers between complex genomic and researchers who want rapid, intuitive, high-quality molecular profiles clinical attributes large-scale projects empowers translate these rich sets into biologic insights applications....
The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource exploring, visualizing, and analyzing multidimensional cancer genomics data. portal reduces molecular profiling data from tissues cell lines into readily understandable genetic, epigenetic, gene expression, proteomic events. query interface combined with customized storage enables researchers to interactively explore genetic alterations across samples, genes, pathways and, when available in the underlying...
Current clinical practice is organized according to tissue or organ of origin tumors. Now, The Cancer Genome Atlas (TCGA) Research Network has started identify genomic and other molecular commonalities among a dozen different types cancer. Emerging similarities contrasts will form the basis for targeted therapies future repurposing existing by rather than histological diseases. profiled analyzed large numbers human tumors discover aberrations at DNA, RNA, protein epigenetic levels. resulting...
Immune checkpoint inhibitors, which unleash a patient’s own T cells to kill tumors, are revolutionizing cancer treatment. To unravel the genomic determinants of response this therapy, we used whole-exome sequencing non–small cell lung cancers treated with pembrolizumab, an antibody targeting programmed death-1 (PD-1). In two independent cohorts, higher nonsynonymous mutation burden in tumors was associated improved objective response, durable clinical benefit, and progression-free survival....
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The function most mammalian miRNAs is unknown. We have predicted on 3' untranslated regions human gene transcripts for all currently known 218 facilitate focused experiments. report about 2,000 genes miRNA conserved in mammals and 250 as targets between fish. prediction algorithm optimizes sequence complementarity using position-specific rules relies strict requirements...
The recent discoveries of microRNA (miRNA) genes and characterization the first few target regulated by miRNAs in Caenorhabditis elegans Drosophila melanogaster have set stage for elucidation a novel network regulatory control. We present computational method whole-genome prediction miRNA genes. is validated using known examples. For each miRNA, are selected on basis three properties: sequence complementarity position-weighted local alignment algorithm, free energies RNA-RNA duplexes,...
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical contain key features representing the democratized nature collection process. To ensure proper use this large dataset associated genomic features, we developed standardized named Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major outcome endpoints. In...
Highlights•Alteration map of 10 signaling pathways across 9,125 samples from 33 cancer types•Reusable, curated pathway templates that include a catalogue driver genes•57% tumors have at least one potentially actionable alteration in these pathways•Co-occurrence alterations suggests combination therapy opportunitiesSummaryGenetic control cell-cycle progression, apoptosis, and cell growth are common hallmarks cancer, but the extent, mechanisms, co-occurrence differ between individual tumor...
MicroRNA.org ( http://www.microrna.org ) is a comprehensive resource of microRNA target predictions and expression profiles. Target are based on development the miRanda algorithm which incorporates current biological knowledge rules use an up-to-date compendium mammalian microRNAs. MicroRNA profiles derived from sequencing project large set tissues cell lines normal disease origin. Using improved graphical interface, user can explore (i) genes that potentially regulated by particular...
A genetic interaction network containing approximately 1000 genes and 4000 interactions was mapped by crossing mutations in 132 different query into a set of 4700 viable gene yeast deletion mutants scoring the double mutant progeny for fitness defects. Network connectivity predictive function because often occurred among functionally related genes, similar patterns tended to identify components same pathway. The exhibited dense local neighborhoods; therefore, position on partially is other...
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary acquired disease processes. are annotated as ordered network transformations single consistent data model. thus functions digital archive human tool for discovering functional relationships such gene expression profiles or somatic mutation catalogs from tumor...
As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction their likely functional impact becomes important practical goal. Here, we introduce a new score (FIS) for amino acid residue changes using evolutionary conservation patterns. The information these patterns is derived from aligned families and sub-families sequence homologs within between species combinatorial entropy formalism. performs well on large set mutations separating...
RNA silencing processes are guided by small RNAs that derived from double-stranded RNA. To probe for function of during infection human cells a DNA virus, we recorded the profile infected Epstein-Barr virus (EBV). We show EBV expresses several microRNA (miRNA) genes. Given miRNAs in pathways either targeting messenger degradation or repressing translation, identified viral regulators host and/or gene expression.
Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three-level system of networks by using additional derived from alignments. a position-specific conservation weight part the increases performance. number insertions and deletions reduces tendency for overprediction overall Addition global amino acid content yields further improvement,...