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List of works by Chris Sander

(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway

scholarly article

18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers

scientific article

3D RNA and Functional Interactions from Evolutionary Couplings

scientific article

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets

scientific article published on 23 January 2017

A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data

scientific article published on 01 January 2018

A Landscape of Metabolic Variation across Tumor Types

scientific article published on 26 January 2018

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers

scientific article

A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity ⬇️

scientific article published on April 27, 2012

A flexible search system for high-accuracy identification of biological entities and molecules

scientific article published on 12 November 2021

A mammalian microRNA expression atlas based on small RNA library sequencing

scientific article

A novel class of small RNAs bind to MILI protein in mouse testes

scientific journal article

A series of PDB related databases for everyday needs

scientific article

A specificity map for the PDZ domain family

scientific article

Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma

scientific article published on 01 April 2019

Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network

scientific article

AlignmentViewer: Sequence Analysis of Large Protein Families

scientific article published on 27 March 2020

AlignmentViewer: Sequence Analysis of Large Protein Families

scientific article published on 15 October 2020

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

scientific article (publication date: 28 April 2015)

Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity.

scientific article

An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma

scientific article published on January 2016

An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of microRNA-target interactions across diverse cancer types

scientific article

Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection.

scientific article

Analyzing causal relationships in proteomic profiles using CausalPath

scientific article published on 24 November 2021

Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development

scientific article

Applications of targeted proteomics in systems biology and translational medicine

scientific article

Author-sourced capture of pathway knowledge in computable form using Biofactoid

scientific article published on 03 December 2021

Automated network analysis identifies core pathways in glioblastoma

scientific article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network

scientific article published in January 2017

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

scientific article (publication date: 3 April 2015)

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

scientific article published on 15 August 2019

CancerGenes: a gene selection resource for cancer genome projects

scientific article published on 6 November 2006

Capturing scientific knowledge in computable form

scientific article published on 11 March 2021

Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments

scientific article published on 30 June 2013

CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy

scientific article published on 21 December 2020

CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics

scientific article published on 16 November 2020

CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines

Cellular cofactors affecting hepatitis C virus infection and replication

scientific article

Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB.

scientific article

Characterizing gene sets with FuncAssociate

scientific article published on December 2003

ChiBE: interactive visualization and manipulation of BioPAX pathway models

scientific article

Collection, integration and analysis of cancer genomic profiles: from data to insight

scientific article

Combining Evolutionary Covariance and NMR Data for Protein Structure Determination

scientific article published on 23 December 2018

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

scientific article

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification

scientific article

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites ⬇️

scientific article published on August 27, 2010

Computational analysis of mouse piRNA sequence and biogenesis ⬇️

scientific article (publication date: November 2007)

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Computer-guided design of optimal microbial consortia for immune system modulation

scientific article published on 17 April 2018

Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis

scientific article published on 26 April 2009

Copy number alteration burden predicts prostate cancer relapse

scientific article published on 14 July 2014

Correction: Human MicroRNA Targets

scientific article

Correlated mutations and residue contacts in proteins

scientific article

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

DGCR8-dependent microRNA biogenesis is essential for skin development

scholarly article

Detection of activity centers in cellular pathways using transcript profiling

scientific article published in August 2004

Determinants of protein function revealed by combinatorial entropy optimization

scientific article (publication date: 2007)

Diabetes, Weight Change, and Pancreatic Cancer Risk

scientific article published on 13 August 2020

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

scientific article

Discovering modulators of gene expression

scientific article

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors

scientific article published on 12 September 2012

Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets.

scientific article published on 24 September 2013

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota

scientific article

Emerging landscape of oncogenic signatures across human cancers

scientific article

Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

scientific article published on March 2017

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Evaluating cell lines as tumour models by comparison of genomic profiles

scientific article published on January 2013

Evaluation of annotation strategies using an entire genome sequence

scientific article

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

scientific article

Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App

scientific article published in 2022

Extensive decoupling of metabolic genes in cancer

scientific article published on 11 May 2015

Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas

scientific article published on December 2011

Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy

scientific article

From bytes to bedside: data integration and computational biology for translational cancer research

scientific article

From genome sequences to protein function

Functional copy-number alterations in cancer

scientific article

GENO-15IDENTIFICATION AND GENOMIC ANALYSIS OF HYPER-MUTATED AND ULTRA-MUTATED GBMS.

scientific article

Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma.

scientific article

Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas

scientific article

Genetic variation in DNA repair pathways and risk of non-Hodgkin's lymphoma

scientific article

Genome Sequencing Identifies a Basis for Everolimus Sensitivity ⬇️

scientific article published on August 23, 2012

Genome-wide analysis of noncoding regulatory mutations in cancer

scientific article published on 28 September 2014

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response

scientific article

Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers.

scientific article published on 15 February 2016

Genomic complexity and AKT dependence in serous ovarian cancer

scientific article published on January 2012

Global mapping of the yeast genetic interaction network

scientific article

Human MicroRNA targets

scientific article

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

scientific article

Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression

scientific article

Identification of microRNAs of the herpesvirus family

scientific article (publication date: April 2005)

Identification of virus-encoded microRNAs

scientific article

Identifying actionable targets through integrative analyses of GEM model and human prostate cancer genomic profiling

scientific article

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

scientific article (publication date: July 2015)

Inferring protein 3D structure from deep mutation scans

scientific article published on 17 June 2019

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma

scientific article (publication date: 2012)

Integrating biological pathways and genomic profiles with ChiBE 2.

scientific article

Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

scientific article

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

article

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

scientific article

Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDB

Integrative genomic profiling of human prostate cancer

scientific article (publication date: 13 July 2010)

Integrative subtype discovery in glioblastoma using iCluster

scientific article

Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma.

scientific article published on 30 August 2016

International network of cancer genome projects

scientific article

Introducing meta-services for biomedical information extraction

scientific article published on September 2008

LLGL2 rescues nutrient stress by promoting leucine uptake in ER+ breast cancer

scientific article published on 17 April 2019

MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes

scientific article published on January 2013

MYC Cooperates with AKT in Prostate Tumorigenesis and Alters Sensitivity to mTOR Inhibitors ⬇️

scientific article published on March 4, 2011

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

scientific article published in April 2018

MatchMiner: An open source computational platform for real-time matching of cancer patients to precision medicine clinical trials using genomic and clinical criteria

Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma

scientific article published on 8 March 2007

MicroRNA profiling of the murine hematopoietic system

scientific article

MicroRNA targets in Drosophila

scientific article

Mitochondrial DNA copy number variation across human cancers

scientific article published on 22 February 2016

Mitochondrial respiratory gene expression is suppressed in many cancers

scientific article published on 18 January 2017

Models from experiments: combinatorial drug perturbations of cancer cells

scientific article published on 02 September 2008

Molecular response to PARP1 inhibition in ovarian cancer cells as determined by mass spectrometry based proteomics

scientific article published on 22 October 2021

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma

scientific article published on 2 March 2016

Mutation effects predicted from sequence co-variation

scientific article published on 16 January 2017

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

scientific article

Mutual exclusivity analysis identifies oncogenic network modules

scientific article published on 9 September 2011

NetPath: a public resource of curated signal transduction pathways

scientific article

Network modeling of the transcriptional effects of copy number aberrations in glioblastoma ⬇️

scientific article published on April 2011

Objectively judging the quality of a protein structure from a Ramachandran plot ⬇️

scientific article published on August 1, 1997

Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2

scientific article (publication date: 14 March 2011)

Oncogenic Signaling Pathways in The Cancer Genome Atlas

scientific article published in April 2018

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

scientific article published on 23 September 2015

Pathguide: a pathway resource list

scientific article

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

scientific article published on 01 January 2020

Pathway Commons, a web resource for biological pathway data

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Pathway information for systems biology

scientific article

Pattern discovery and cancer gene identification in integrated cancer genomic data

scientific article

Pattern search in BioPAX models

scientific article

PaxtoolsR: pathway analysis in R using Pathway Commons

scientific article published on 18 December 2015

PconsFold: improved contact predictions improve protein models

scientific article (publication date: September 2014)

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

scientific article published on 15 July 2020

Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells

scientific article

Perturbation biology: inferring signaling networks in cellular systems

scientific article (publication date: 2013)

PiHelper: an open source framework for drug-target and antibody-target data ⬇️

scientific article published on June 12, 2013

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.

scientific article

PredictProtein--an open resource for online prediction of protein structural and functional features

scientific article

Predicting cancer involvement of genes from heterogeneous data

scientific article

Predicting the functional impact of protein mutations: application to cancer genomics ⬇️

scientific article published on July 3, 2011

Prediction of human microRNA targets

scientific article published on January 2006

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

scientific article

Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer

scientific article published on 29 July 2013

Principle of system balance for drug interactions

scientific article published on 01 April 2010

Protein 3D structure computed from evolutionary sequence variation

scientific article published in 2011

Protein Structure from Experimental Evolution

scientific article published on 11 December 2019

Protein structure determination by combining sparse NMR data with evolutionary couplings

scientific article (publication date: August 2015)

Protein structure prediction assisted with sparse NMR data in CASP13

scientific article published on 01 December 2019

Protein structure prediction from sequence variation ⬇️

scientific article (publication date: November 2012)

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

scientific article published on 31 October 2019

RNA targets of wild-type and mutant FET family proteins

scientific article published on 13 November 2011

Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells

SARS-CoV-2 infects blood monocytes to activate NLRP3 and AIM2 inflammasomes, pyroptosis and cytokine release

SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer

scientific article published on December 2013

Sequence co-evolution gives 3D contacts and structures of protein complexes

scientific article published on 25 September 2014

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

scientific article published on 16 April 2018

Signal processing in the TGF-beta superfamily ligand-receptor network

scientific article

Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma

scientific article

Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis

scientific article

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies

scientific article published on 29 November 2009

Spatial normalization of reverse phase protein array data

scientific article

Structured States of Disordered Proteins from Genomic Sequences

scientific article published on September 2016

Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy

scientific article

Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines

scientific article

Systematic Assessment of Tumor Purity and Its Clinical Implications

scientific article published on 04 September 2020

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

scientific article

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer.

scientific article

TCEB1-mutated renal cell carcinoma: a distinct genomic and morphological subtype

scientific article published on 13 February 2015

Target mRNA abundance dilutes microRNA and siRNA activity

scientific article (publication date: 20 April 2010)

The BioPAX Validator

scientific article

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Cancer Genome Atlas Pan-Cancer analysis project

scientific article

The EVcouplings Python framework for coevolutionary sequence analysis

scientific article published on 01 May 2019

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

The Somatic Genomic Landscape of Glioblastoma

article

The amino-acid mutational spectrum of human genetic disease

scientific article

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data

scientific article

The developmental miRNA profiles of zebrafish as determined by small RNA cloning

scientific article

The microRNA.org resource: targets and expression

scientific article

The molecular diversity of Luminal A breast tumors

scientific article published on 06 October 2013

The mutational landscape of adenoid cystic carcinoma

scientific article published on 19 May 2013

The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma

scientific article

The reactome pathway knowledgebase 2022

scientific article published on 14 October 2021

The somatic genomic landscape of glioblastoma

scientific article

The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers

scientific journal article

Three-dimensional structures of membrane proteins from genomic sequencing

scientific article

Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles

scientific article

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

scientific article (publication date: June 2009)

Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy

scientific article

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

scientific article

Using MEMo to discover mutual exclusivity modules in cancer

scientific article published on March 2013

Using biological pathway data with paxtools

scientific article

What's in a genome?

scientific article published in Nature

ZIC1 overexpression is oncogenic in liposarcoma

scientific article published on 16 August 2010

cPath: open source software for collecting, storing, and querying biological pathways

scientific article published on 13 November 2006

mRNA turnover rate limits siRNA and microRNA efficacy

scientific article (publication date: 16 November 2010)

mRNA turnover rate limits siRNA and microRNA efficacy

scientific article (publication date: 21 December 2010)

miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1.

scientific article

miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis

scientific article

netboxr: Automated discovery of biological process modules by network analysis in R

scientific article published on 02 November 2020

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R

scientific article published on 03 December 2015

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