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Publications

Publications

2023

  • March 28

    Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge
  • February 16

    Leveraging IP for AI governance

2022

  • December 21

    Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs
  • December 20

    Preprint: Young people’s data governance preferences for their mental health data: MindKind Study findings from India, South Africa, and the United Kingdom
  • December 9

    A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models
  • December 8

    Rituximab is associated with worse COVID-19 outcomes in patients with rheumatoid arthritis: A retrospective, nationally sampled cohort study from the U.S. National COVID Cohort Collaborative (N3C)
  • December 8

    A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer
  • November 21

    External Model for Automated Mammography Interpretation by Artificial Intelligence
  • October 20

    The Post-Roe Political Landscape Demands a Morality of Caution for Women’s Health
  • October 19

    COVID-19 in people with neurofibromatosis 1, neurofibromatosis 2, or schwannomatosis
  • October 7

    A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
  • October 6

    GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA
  • August 4

    Disentangling personalized treatment effects from “time-of-the-day” confounding in mobile health studies
  • August 1

    A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis
  • July 12

    Preprint: AACR Project GENIE: 100,000 cases and beyond
  • July 1

    The Mobile Toolbox for monitoring cognitive function
  • July 1

    Big Health Data Research and Group Harm: The Scope of IRB Review
  • June 28

    Preprint: The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models
  • June 23

    Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database
  • May 12

    Preprint: MindKind: A mixed-methods protocol for the feasibility of global digital mental health studies in young people
  • April 21

    Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder
  • April 12

    Manifestations of genetic risk for Alzheimer’s Disease in the blood: a cross-sectional multi-omic analysis in healthy adults aged 18-90+
  • March 24

    Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains
  • March 19

    MITI minimum information guidelines for highly multiplexed tissue images
  • March 14

    Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort Collaborative
  • March 3

    U.S. Adult Perspectives on Facial Images, DNA, and Other Biometrics
  • March 1

    From paper to screen: regulatory and operational considerations for modernizing the informed consent process
  • February 22

    A Scalable Quality Assurance Process for Curating Oncology Electronic Health Records: The Project GENIE Biopharma Collaborative Approach
  • February 1

    Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies
  • January 18

    A community challenge for a pancancer drug mechanism of action inference from perturbational profile data
  • January 10

    A Smartphone Application as an Exploratory Endpoint in a Phase 3 Parkinson’s Disease Clinical Trial: A Pilot Study

2021

  • December 31

    Microglia subtype transcriptomes differ between Alzheimer Disease and control human postmortem brain samples
  • December 1

    Characterizing Long COVID: Deep Phenotype of a Complex Condition
  • November 15

    Engaged genomic science produces better and fairer outcomes: an engagement framework for engaging and involving participants, patients and publics in genomics research and healthcare implementation
  • November 11

    Ten simple rules on writing clean and reliable open-source scientific software
  • November 10

    GA4GH: International policies and standards for data sharing across genomic research and healthcare
  • November 5

    Pursuing Better Biomarkers for Immunotherapy Response in Cancer Through a Crowdsourced Data Challenge
  • October 17

    Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd
  • October 1

    A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization
  • September 14

    Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge
  • August 9

    Remote smartphone monitoring of Parkinson’s disease and individual response to therapy
  • July 29

    Machine Learning in Rare Disease
  • July 26

    Results of the Genetic Counselor SARS-CoV-2 Impact Survey from the National Society of Genetic Counselors: Progress and penalty during the COVID-19 pandemic
  • July 23

    Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study.
  • July 23

    Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
  • July 15

    Brigatinib causes tumor shrinkage in both NF2-deficient meningioma and schwannoma through inhibition of multiple tyrosine kinases but not ALK
  • July 1

    Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative
  • July 1

    Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non-Small Cell Lung or Colorectal Cancer
  • June 28

    Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma
  • June 16

    A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
  • June 15

    Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth
  • June 4

    Outcomes of COVID-19 in Patients With Cancer: Report From the National COVID Cohort Collaborative (N3C).
  • June 4

    Smartphone-Based VO2max Measurement With Heart Snapshot in Clinical and Real-world Settings With a Diverse Population: Validation Study
  • June 3

    Crowdsourced mapping of unexplored target space of kinase inhibitors.
  • May 4

    Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease.
  • April 22

    PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer
  • April 12

    Brain proteome-wide association study implicates novel proteins in depression pathogenesis
  • March 29

    Comprehensive identification of somatic nucleotide variants in human brain tissue.
  • March 25

    Sex differences in the human brain transcriptome of cases with schizophrenia
  • March 19

    Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge.
  • March 18

    Evaluation of artificial intelligence systems for assisting neurologists with fast and accurate annotations of scalp electroencephalography data.
  • March 1

    The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.
  • March 1

    Establishing the reliability of algorithms.
  • February 17

    Preprint: Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU-based disease: the Multi-Targeting Drug DREAM Challenge
  • February 5

    Limb and trunk accelerometer data collected with wearable sensors from subjects with Parkinson’s disease
  • February 5

    Accelerometer data collected with a minimum set of wearable sensors from subjects with Parkinson’s disease
  • February 1

    Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis
  • February 1

    Design of a virtual longitudinal observational study in Parkinson’s disease (AT-HOME PD)
  • January 20

    Preprint: Evaluation of crowdsourced mortality prediction models as a framework for assessing AI in medicine
  • January 8

    Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome

2020

  • December 27

    The AD Knowledge Portal: A Repository for Multi‐Omic Data on Alzheimer’s Disease and Aging
  • December 23

    Preprint: A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data
  • December 15

    Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II—practical challenges
  • December 4

    Assessment of the All of Us research program’s informed consent process
  • December 3

    Molecular estimation of neurodegeneration pseudotime in older brains
  • December 1

    COVID-19 in Patients With Inflammatory Arthritis: A Prospective Study on the Effects of Comorbidities and Disease-Modifying Antirheumatic Drugs on Clinical Outcomes
  • November 27

    Real-world longitudinal data collected from the SleepHealth mobile app study
  • November 23

    Model organism development and evaluation for late‐onset Alzheimer’s disease: MODEL‐AD
  • November 10

    A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease
  • November 9

    Stable predictions for health related anticausal prediction tasks affected by selection biases: the need to deconfound the test set features
  • October 27

    Evaluating the Utility of Smartphone-Based Sensor Assessments in Persons With Multiple Sclerosis in the Real-World Using an App (elevateMS): Observational, Prospective Pilot Digital Health Study.
  • October 12

    Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.
  • October 9

    Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
  • August 14

    Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination
  • August 1

    Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling.
  • July 28

    Bringing Code to Data: Do Not Forget Governance
  • July 14

    Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
  • July 8

    Developing pathways for community-led research with big data: a content analysis of stakeholder interviews
  • July 1

    Effects of mood and aging on keystroke dynamics metadata and their diurnal patterns in a large open-science sample: A BiAffect iOS study
  • June 19

    A Clinically and Genomically Annotated Nerve Sheath Tumor Biospecimen Repository
  • May 18

    Research Ethics in a Pandemic: considerations for the use of research infrastructure and resources for public health activities
  • April 28

    Who Are the People in Your Neighborhood? Personas Populating Unregulated mHealth Research
  • April 28

    Unregulated Health Research Using Mobile Devices: Ethical Considerations and Policy Recommendations
  • March 30

    Connected Medical Technology and Cybersecurity Informed Consent: A New Paradigm
  • March 30

    mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor Data
  • March 16

    Informed Consent in Two Alzheimer’s Disease Research Centers: Insights From Research Coordinators
  • March 13

    Modernizing and designing evaluation frameworks for connected sensor technologies in medicine
  • March 2

    Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms
  • February 21

    Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1
  • February 20

    Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge
  • February 17

    Indicators of retention in remote digital health studies: a cross-study evaluation of 100,000 participants
  • February 9

    Data Science Approaches for Effective Use of Mobile Device–Based Collection of Real‐World Data
  • February 3

    Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease
  • February 2

    Bringing Code to Data: Don’t Forget Governance
  • February 1

    IRB Management and Function, 3rd edition: mHealth, Mobile Devices, and Apps (book chapter)
  • January 17

    Open Data Sharing in the 21st Century: Sage Bionetworks’ Qualified Research Program and Its Application in mHealth Data Release
  • January 8

    Crowdsourced mapping of unexplored target space of kinase inhibitors
  • January 6

    Navigating ethical quandaries with the privacy dilemma of biomedical datasets.

2019

  • December 19

    Detecting the impact of subject characteristics on machine learning-based diagnostic applications
  • December 13

    Engaging a community to enable disease-centric data sharing with the NF Data Portal
  • December 4

    An open toolkit for tracking open science partnership implementation and impact
  • November 21

    Welcome to the Tidyverse
  • November 20

    Contemporary Views of Research Participant Willingness to Participate and Share Digital Data in Biomedical Research
  • November 19

    Causality-based tests to detect the influence of confounders on mobile health diagnostic applications: a comparison with restricted permutations
  • October 19

    Assessing Tele-Health Outcomes in Multiyear Extensions of Parkinson’s Disease Trials (AT-HOME PD): An Update on Recruitment: 1067
  • October 2

    Indicators of retention in remote digital health studies: A cross-study evaluation of 100,000 participants
  • September 20

    Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
  • September 6

    CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.
  • August 15

    The “All of Us” Research Program
  • August 6

    The Rise of Citizen Science in Health and Biomedical Research
  • July 19

    Mobiletoolbox for mobile monitoring of cognitive change
  • July 17

    Community-powered, radically open technologies to acceslerate Alzheimer’s Disease therapeutic discovery
  • July 15

    Identifying and ranking potential driver genes of Alzheimer’s disease using multiview evidence aggregation.
  • July 6

    A qualitative analysis of coordinator perceptions of the consent process: Lessons guiding the development of an electronic consent platform
  • July 1

    Developing an electronic consent for ADRC
  • July 1

    Agora: A platform for the democratization of Alzheimer’s Disease target evidence
  • June 19

    THE JOURNEY PRO STUDY: FEASIBILITY AND USER ACCEPTANCE OF A SMARTPHONE APP TO ASSESS THE BURDEN OF ANEMIA IN PATIENTS WITH MYELODYSPLASTIC SYNDROMES (MDS), β-THALASSEMIA (BT), AND MYELOFIBROSIS (MF)
  • May 20

    The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminations in the skin
  • May 2

    Supporting Coping with Parkinson’s Disease Through Self Tracking
  • April 19

    Assessing Tele-Health Outcomes in Multiyear Extensions of Parkinson’s Disease Trials (AT-HOME PD): Initiation of a Long-Term Observational Study (P2. 8-011)
  • April 11

    Physical activity, sleep and cardiovascular health data for 50,000 individuals from the MyHeart Counts Study
  • March 1

    Importance of Participant-Centricity and Trust for a Sustainable Medical Information Commons
  • January 29

    Identifying and ranking potential driver genes of Alzheimer’s Disease using multi-view evidence aggregation
  • January 21

    Implementing a universal informed consent process for the All of Us Research Program
  • January 19

    Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.
  • January 19

    Identifying and ranking potential driver genes of Alzheimer’s Disease using multi-view evidence aggregation
  • January 19

    Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
  • January 10

    Open science precision medicine in Canada: Points to consider
  • January 6

    Ethical Issues in Consumer Informatics and Online Content
  • January 3

    Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach
  • January 2

    Towards a consensus around standards for smartphone apps and digital mental health

2018

  • December 24

    A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection
  • December 7

    The Role of Government in Precision Medicine, Precision Public Health and the Intersection With Healthy Living
  • October 22

    Spatiotemporal loss of NF1 in Schwann cell lineage leads to different types of cutaneous neurofibroma susceptible to modification by the Hippo pathway
  • October 8

    Remote Assessment, in Real-World Setting, of Tremor Severity in Parkinson’s Disease Patients Using Smartphone Inertial Sensors
  • September 11

    The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease
  • September 5

    The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app
  • August 21

    The accuracy of passive phone sensors in predicting daily mood
  • August 20

    Probing the chemical–biological relationship space with the Drug Target Explorer
  • August 9

    Using Mobile Apps to Assess and Treat Depression in Hispanic and Latino Populations: Fully Remote Randomized Clinical Trial.
  • August 7

    A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
  • August 1

    The Emerging Imperative for a Consensus Approach Toward the Rating and Clinical Recommendation of Mental Health Apps
  • July 23

    Responsible sharing of biomedical data and biospecimens via the “Automatable Discovery and Access Matrix” (ADA-M)
  • June 13

    Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2
  • June 12

    Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells
  • June 8

    Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters
  • June 7

    Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS
  • May 22

    The asthma mobile health study, smartphone data collected using ResearchKit
  • April 26

    Cutaneous neurofibromas in the genomics era: current understanding and open questions
  • April 18

    Smartphone-Based Passive Assessment of Mobility in Depression: Challenges and Opportunities
  • April 5

    Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
  • April 5

    An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
  • April 1

    Introduction to the “Technology in Practice” Special Issue.
  • April 1

    Review and Comparison of Electronic Patient-Facing Family Health History Tools
  • March 27

    Design Issues in E-Consent
  • March 7

    Engaging populations underrepresented in research through novel approaches to consent
  • February 1

    A community approach to mortality prediction in sepsis via gene expression analysis
  • January 1

    Democratizing Health Data for Translational Research

2017

  • December 21

    The inconvenience of data of convenience: computational research beyond post-mortem analyses
  • October 23

    KRAS Mutation and Consensus Molecular Subtypes 2 and 3 Are Independently Associated with Reduced Immune Infiltration and Reactivity in Colorectal Cancer
  • October 17

    Targeted metabolomics and medication classification data from participants in the ADNI1 cohort
  • October 16

    The efficacy of smartphone-based mental health interventions for depressive symptoms: a meta-analysis of randomized controlled trials
  • October 10

    An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome
  • September 28

    Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology
  • August 30

    Consent Processes for Mobile App Mediated Research: Systematic Review
  • August 30

    Consent Processes for Mobile App Mediated Research: Systematic Review
  • August 29

    Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
  • August 3

    Cancer: A precision approach to tumour treatment
  • June 1

    Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression
  • June 1

    AACR Project GENIE: Powering Precision Medicine Through An International Consortium.
  • May 1

    Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study
  • April 11

    A high-throughput molecular data resource for Cutaneous Neurofibromas
  • March 28

    Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives
  • February 16

    Formative Evaluation of Participant Experience With Mobile eConsent in the App-Mediated Parkinson mPower Study: A Mixed Methods Study
  • February 16

    Formative Evaluation of Participant Experience With Mobile eConsent in the App-Mediated Parkinson mPower Study: A Mixed Methods Study
  • February 14

    The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKit
  • February 14

    The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKit
  • January 4

    Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer

2016

  • December 19

    Differential gene expression profiling of matched primary renal cell carcinoma and metastases reveals upregulation of extracellular matrix genes
  • December 1

    Systems Approaches to Cancer Biology
  • November 15

    Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
  • October 11

    Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases.
  • September 26

    Gene expression elucidates functional impact of polygenic risk for schizophrenia
  • August 23

    Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
  • July 15

    Crowdsourcing biomedical research: leveraging communities as innovation engines
  • July 11

    Spatiotemporal reconstruction of the human blastocyst by single-cell gene expression analysis informs induction of naive pluripotency
  • July 6

    Mobile health: the power of wearables, sensors, and apps to transform clinical trials
  • June 10

    Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease
  • June 9

    Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cell from the Progenitor Cell Biology Consortium
  • June 3

    Understanding the contribution of family history to colorectal cancer risk and its clinical implications: A state-of-the-science review
  • May 5

    Developing a Transparent, Participant-Navigated Electronic Informed Consent for Mobile-Mediated Research
  • April 11

    Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases
  • April 8

    DREAMTools: a Python package for scoring collaborative challenges
  • March 15

    A large dataset of protein dynamics in the mammalian heart proteome
  • March 3

    First, design for data sharing.
  • March 3

    The mPower study, Parkinson disease mobile data collected using ResearchKit.
  • March 3

    Smartphones as new tools in the management and understanding of Parkinson’s disease.
  • March 1

    Practical Guidelines for High-resolution Epigenomic Profiling of Postmortem Human Brain Tissue
  • February 22

    Empirical assessment of causal network inference through a community-based effort.

2015

  • November 25

    The PsychENCODE project
  • October 12

    The consensus molecular subtypes of colorectal cancer.
  • September 7

    rCGH : a comprehensive array-based genomic profile platform for precision medicine
  • August 26

    TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
  • July 13

    The NIH BD2K center for big data in translational genomics
  • July 12

    App-enabled trial participation: Tectonic shift or tepid rumble?
  • June 5

    Safety and Activity of the First-in-Class Sym004 Anti-EGFR Antibody Mixture in Patients with Refractory Colorectal Cancer.
  • May 18

    Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
  • May 12

    Heterogeneity of driver genes and therapeutic implications in colorectal cancer.
  • April 27

    Personalizing Colon Cancer Adjuvant Therapy: Selecting Optimal Treatments for Individual Patients.
  • March 16

    The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.
  • February 18

    Sparse expression bases in cancer reveal tumor drivers.
  • February 7

    Assessing the scale of tumor heterogeneity by complete hierarchical segmentation of MRI.
  • February 5

    Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.
  • January 28

    Bayesian Network Reconstruction using Systems Genetics Data: Comparison of MCMC Methods.
  • January 15

    Diversity matters: Historical lessons.

2014

  • December 23

    Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology.
  • December 14

    Response to “Tumor cells in search for glutamate: an alternative explanation for increased invasiveness of IDH1 mutant gliomas”.
  • November 11

    Social interactomes for enabling research communities.
  • October 28

    Patient-specific metrics of invasiveness reveal significant prognostic benefit of resection in a predictable subset of gliomas.
  • October 8

    Molecular Markers Identify Subtypes of Stage III Colon Cancer Associated with Patient Outcomes.
  • October 7

    Simulation studies as designed experiments: the comparison of penalizede regression models in the “large p, small n” setting.
  • October 1

    Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements.
  • September 10

    Game design for bioinformatics and cyberinfrastructure learning: a parallel computing case study.
  • September 10

    Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-Seq.
  • September 5

    Phase I/IIa study evaluating the safety, efficacy, pharmacokinetics, and pharmacodynamics of lucitanib in advanced solid tumors.
  • September 1

    Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning.
  • August 19

    Periostin is a novel therapeutic target that predicts and regulates glioma malignancy.
  • August 15

    Functional kinomics identifies candidate therapeutic targets in head and neck cancer.
  • August 14

    Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin.
  • July 30

    Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.
  • July 16

    Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.
  • July 15

    Optimal design of trials to demonstrate the utility of genomically-guided therapy: putting Precision Cancer Medicine to the test.
  • June 22

    Assessing the clinical utility of cancer genomic and proteomic data across tumor types.
  • June 16

    Invasion and proliferation kinetics in enhancing gliomas predict IDH1 mutation status.
  • May 30

    Clues from the resilient.
  • May 27

    Describing high-order statistical dependence using “Concurrence Topology,” with application to functional MRI brain data.
  • May 6

    Citizens as partners in the use of clinical data.
  • May 1

    TGR analysis in phase I clinical trials–letter.
  • May 1

    CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer.
  • April 4

    Standardized decision support in next generation sequencing reports of somatic cancer variants.
  • March 30

    Synapse elimination and learning rules co-regulated by MHC class I H2-Db.
  • March 27

    Global optimization of somatic variant identification in cancer genomes with a global community challenge.
  • March 1

    Coupled dimensionality reduction and classification for supervised and semi-supervised multi label learning.
  • March 1

    Synthetic lethal screens as a means to understand and treat MYC-driven cancers.
  • January 31

    ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma.
  • January 23

    Discriminating survival outcomes in patients with glioblastoma using a simulation-based, patient-specific response metric
  • January 19

    Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.
  • January 18

    The Stream Algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity
  • January 18

    Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors.
  • January 17

    Bayesian Multiview Dimensionality Reduction for Learning Predictive Subspaces.
  • January 17

    Embedding Heterogeneous Data by Preserving Multiple Kernels.
  • January 17

    The Stream Algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity.
  • January 14

    The evolution of our molecular understanding of colorectal cancer: what we are doing now, what the future holds, and how tumor profiling is just the beginning.
  • January 1

    Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.

2013

  • December 18

    Somatic Expression of ENRAGE is Associated with Obesity Status among Patients with Clear Cell Renal Cell Carcinoma
  • December 13

    Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma
  • December 12

    Modeling RAS Phenotype in Colorectal Cancer Uncovers Novel Molecular Traits of RAS Dependency and Improves Prediction of Response to Targeted Agents in Patients.
  • November 15

    Cancer, Potential of the synthetic lethality principle
  • November 15

    MyoD is a tumor suppressor gene in medulloblastoma
  • November 13

    Tumor Growth Rate is an early indicator of anti-tumor drug activity in phase I trials
  • September 26

    The Cancer Genome Atlas Pan-Cancer analysis project
  • September 26

    Enabling Transparent and Collaborative Computational Analysis of 12 tumor types within The Cancer Genome Atlas
  • September 2

    HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism
  • August 28

    A statin-dependent QTL for GATM expression is associated with statin-induced myopathy
  • August 26

    Comparison of Outcomes After Fluorouracil-Based Adjuvant Therapy for Stage II and III Colon Cancer Between 1978-1995 and 1996-2007: Findings from the ACCENT Database
  • August 15

    Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in clinical oncology
  • August 10

    Parallel globally optimal structure learning of Bayesian networks
  • August 10

    Tumor Growth Rate Provides Useful Information to Evaluate Sorafenib and Everolimus Treatment in Metastatic Renal Cell Carcinoma Patients: An Integrated Analysis of the TARGET and RECORD Phase 3 Trial Data.
  • August 9

    Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs
  • July 18

    A phase II flexible screening design allowing for interim analysis and comparison with historical control
  • June 25

    hARACNe: improving the accuracy of regulatory model reverse engineering via higher order data processing inequality tests
  • May 9

    Genome-wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination
  • May 9

    Improving Breast Cancer Survival Analysis Through Competition-Based Multidimensional Modeling
  • May 2

    IGF-1R targeting increases the antitumor effects of DNA damaging agents in SCLC model: an opportunity to increase the efficacy of standard therapy
  • May 1

    Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer
  • April 26

    Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge
  • April 25

    Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease
  • April 15

    A network-heuristic approach to improve the impact of genomic data on drug discovery
  • April 9

    Variants in triggering receptor expressed on myeloid cells 2 are associated with both behavioral variant frontotemporal lobar degeneration and Alzheimer’s disease.
  • April 5

    Metcalfe’s law and the biology information commons
  • March 28

    A Fool’s Errand
  • March 28

    A system biology framework identifies molecular underpinings of coronary heart disease
  • March 18

    Modeling causality for pairs of phenotypes in systems genetics
  • March 18

    clearScience: Infrastructure for communicating Data-intensive science
  • March 15

    US-EU Scientific Research Collaborations: Sage Bionetworks’ Experience Navigating the Complex Regulatory Landscape.
  • February 11

    Response classification based on a minimal model of glioblastoma growth is prognostic for clinical outcomes and distinguishes progression from pseudoprogression
  • January 16

    GSVA: Gene Set Variation Analysis

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