Publications
2023
May 29
Human microglia show unique transcriptional changes in Alzheimer’s diseaseMay 29
Machine learning in rare diseaseMay 17
Open drug discovery in Alzheimer’s diseaseMay 8
STOP-AD portal: Selecting the optimal pharmaceutical for preclinical drug testing in Alzheimer’s diseaseApril 21
Genetic Subdivisions of Follicular Lymphoma Defined by Distinct Coding and non-coding Mutation PatternsApril 19
Young people’s data governance preferences for their mental health data: MindKind Study findings from India, South Africa, and the United KingdomMarch 28
Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challengeMarch 9
PREPRINT: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth ResearchFebruary 16
Leveraging IP for AI governance
2022
December 21
Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER ProgramsDecember 9
A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation ModelsDecember 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 CancerNovember 21
External Model for Automated Mammography Interpretation by Artificial IntelligenceOctober 20
The Post-Roe Political Landscape Demands a Morality of Caution for Women’s HealthOctober 19
COVID-19 in people with neurofibromatosis 1, neurofibromatosis 2, or schwannomatosisOctober 7
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responsesOctober 6
GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMAAugust 4
Disentangling personalized treatment effects from “time-of-the-day” confounding in mobile health studiesAugust 1
A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid ArthritisJuly 12
Preprint: AACR Project GENIE: 100,000 cases and beyondJuly 1
The Mobile Toolbox for monitoring cognitive functionJuly 1
Big Health Data Research and Group Harm: The Scope of IRB ReviewJune 28
Preprint: The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP modelsJune 23
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools DatabaseMay 12
Preprint: MindKind: A mixed-methods protocol for the feasibility of global digital mental health studies in young peopleApril 21
Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorderApril 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 brainsMarch 19
MITI minimum information guidelines for highly multiplexed tissue imagesMarch 14
Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort CollaborativeMarch 3
U.S. Adult Perspectives on Facial Images, DNA, and Other BiometricsMarch 1
From paper to screen: regulatory and operational considerations for modernizing the informed consent processFebruary 22
A Scalable Quality Assurance Process for Curating Oncology Electronic Health Records: The Project GENIE Biopharma Collaborative ApproachFebruary 1
Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic StudiesJanuary 18
A community challenge for a pancancer drug mechanism of action inference from perturbational profile dataJanuary 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 samplesDecember 1
Characterizing Long COVID: Deep Phenotype of a Complex ConditionNovember 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 implementationNovember 11
Ten simple rules on writing clean and reliable open-source scientific softwareNovember 10
GA4GH: International policies and standards for data sharing across genomic research and healthcareNovember 5
Pursuing Better Biomarkers for Immunotherapy Response in Cancer Through a Crowdsourced Data ChallengeOctober 17
Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowdOctober 1
A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and HospitalizationSeptember 14
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM ChallengeAugust 9
Remote smartphone monitoring of Parkinson’s disease and individual response to therapyJuly 29
Machine Learning in Rare DiseaseJuly 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 pandemicJuly 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 leukemiaJuly 15
Brigatinib causes tumor shrinkage in both NF2-deficient meningioma and schwannoma through inhibition of multiple tyrosine kinases but not ALKJuly 1
Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort CollaborativeJuly 1
Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non-Small Cell Lung or Colorectal CancerJune 28
Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myelomaJune 16
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discoveryJune 15
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birthJune 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 StudyJune 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 CancerApril 12
Brain proteome-wide association study implicates novel proteins in depression pathogenesisMarch 29
Comprehensive identification of somatic nucleotide variants in human brain tissue.March 25
Sex differences in the human brain transcriptome of cases with schizophreniaMarch 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 ChallengeFebruary 5
Limb and trunk accelerometer data collected with wearable sensors from subjects with Parkinson’s diseaseFebruary 5
Accelerometer data collected with a minimum set of wearable sensors from subjects with Parkinson’s diseaseFebruary 1
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesisFebruary 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 medicineJanuary 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 AgingDecember 23
Preprint: A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile DataDecember 15
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II—practical challengesDecember 4
Assessment of the All of Us research program’s informed consent processDecember 3
Molecular estimation of neurodegeneration pseudotime in older brainsDecember 1
COVID-19 in Patients With Inflammatory Arthritis: A Prospective Study on the Effects of Comorbidities and Disease-Modifying Antirheumatic Drugs on Clinical OutcomesNovember 27
Real-world longitudinal data collected from the SleepHealth mobile app studyNovember 23
Model organism development and evaluation for late‐onset Alzheimer’s disease: MODEL‐ADNovember 10
A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s diseaseNovember 9
Stable predictions for health related anticausal prediction tasks affected by selection biases: the need to deconfound the test set featuresOctober 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 PredictionAugust 14
Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and eliminationAugust 1
Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling.July 28
Bringing Code to Data: Do Not Forget GovernanceJuly 14
Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse ModelsJuly 8
Developing pathways for community-led research with big data: a content analysis of stakeholder interviewsJuly 1
Effects of mood and aging on keystroke dynamics metadata and their diurnal patterns in a large open-science sample: A BiAffect iOS studyJune 19
A Clinically and Genomically Annotated Nerve Sheath Tumor Biospecimen RepositoryMay 18
Research Ethics in a Pandemic: considerations for the use of research infrastructure and resources for public health activitiesApril 28
Who Are the People in Your Neighborhood? Personas Populating Unregulated mHealth ResearchApril 28
Unregulated Health Research Using Mobile Devices: Ethical Considerations and Policy RecommendationsMarch 30
Connected Medical Technology and Cybersecurity Informed Consent: A New ParadigmMarch 30
mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor DataMarch 16
Informed Consent in Two Alzheimer’s Disease Research Centers: Insights From Research CoordinatorsMarch 13
Modernizing and designing evaluation frameworks for connected sensor technologies in medicineMarch 2
Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening MammogramsFebruary 21
Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1February 20
Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM ChallengeFebruary 17
Indicators of retention in remote digital health studies: a cross-study evaluation of 100,000 participantsFebruary 9
Data Science Approaches for Effective Use of Mobile Device–Based Collection of Real‐World DataFebruary 3
Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive diseaseFebruary 2
Bringing Code to Data: Don’t Forget GovernanceFebruary 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 ReleaseJanuary 8
Crowdsourced mapping of unexplored target space of kinase inhibitorsJanuary 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 applicationsDecember 13
Engaging a community to enable disease-centric data sharing with the NF Data PortalDecember 4
An open toolkit for tracking open science partnership implementation and impactNovember 21
Welcome to the TidyverseNovember 20
Contemporary Views of Research Participant Willingness to Participate and Share Digital Data in Biomedical ResearchNovember 19
Causality-based tests to detect the influence of confounders on mobile health diagnostic applications: a comparison with restricted permutationsOctober 19
Assessing Tele-Health Outcomes in Multiyear Extensions of Parkinson’s Disease Trials (AT-HOME PD): An Update on Recruitment: 1067October 2
Indicators of retention in remote digital health studies: A cross-study evaluation of 100,000 participantsSeptember 20
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challengesSeptember 6
CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.August 15
The “All of Us” Research ProgramAugust 6
The Rise of Citizen Science in Health and Biomedical ResearchJuly 19
Mobiletoolbox for mobile monitoring of cognitive changeJuly 17
Community-powered, radically open technologies to acceslerate Alzheimer’s Disease therapeutic discoveryJuly 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 platformJuly 1
Developing an electronic consent for ADRCJuly 1
Agora: A platform for the democratization of Alzheimer’s Disease target evidenceJune 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 skinMay 2
Supporting Coping with Parkinson’s Disease Through Self TrackingApril 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 StudyMarch 1
Importance of Participant-Centricity and Trust for a Sustainable Medical Information CommonsJanuary 29
Identifying and ranking potential driver genes of Alzheimer’s Disease using multi-view evidence aggregationJanuary 21
Implementing a universal informed consent process for the All of Us Research ProgramJanuary 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 aggregationJanuary 19
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regionsJanuary 10
Open science precision medicine in Canada: Points to considerJanuary 6
Ethical Issues in Consumer Informatics and Online ContentJanuary 3
Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approachJanuary 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 infectionDecember 7
The Role of Government in Precision Medicine, Precision Public Health and the Intersection With Healthy LivingOctober 22
Spatiotemporal loss of NF1 in Schwann cell lineage leads to different types of cutaneous neurofibroma susceptible to modification by the Hippo pathwayOctober 8
Remote Assessment, in Real-World Setting, of Tremor Severity in Parkinson’s Disease Patients Using Smartphone Inertial SensorsSeptember 11
The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s diseaseSeptember 5
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit appAugust 21
The accuracy of passive phone sensors in predicting daily moodAugust 20
Probing the chemical–biological relationship space with the Drug Target ExplorerAugust 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 researchAugust 1
The Emerging Imperative for a Consensus Approach Toward the Rating and Clinical Recommendation of Mental Health AppsJuly 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 2June 12
Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cellsJune 8
Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust ClustersJune 7
Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWASMay 22
The asthma mobile health study, smartphone data collected using ResearchKitApril 26
Cutaneous neurofibromas in the genomics era: current understanding and open questionsApril 18
Smartphone-Based Passive Assessment of Mobility in Depression: Challenges and OpportunitiesApril 5
Machine Learning Identifies Stemness Features Associated with Oncogenic DedifferentiationApril 5
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome AnalyticsApril 1
Introduction to the “Technology in Practice” Special Issue.April 1
Review and Comparison of Electronic Patient-Facing Family Health History ToolsMarch 27
Design Issues in E-ConsentMarch 7
Engaging populations underrepresented in research through novel approaches to consentFebruary 1
A community approach to mortality prediction in sepsis via gene expression analysisJanuary 1
Democratizing Health Data for Translational Research
2017
December 21
The inconvenience of data of convenience: computational research beyond post-mortem analysesOctober 23
KRAS Mutation and Consensus Molecular Subtypes 2 and 3 Are Independently Associated with Reduced Immune Infiltration and Reactivity in Colorectal CancerOctober 17
Targeted metabolomics and medication classification data from participants in the ADNI1 cohortOctober 16
The efficacy of smartphone-based mental health interventions for depressive symptoms: a meta-analysis of randomized controlled trialsOctober 10
An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenomeSeptember 28
Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiologyAugust 30
Consent Processes for Mobile App Mediated Research: Systematic ReviewAugust 30
Consent Processes for Mobile App Mediated Research: Systematic ReviewAugust 29
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer CellsAugust 3
Cancer: A precision approach to tumour treatmentJune 1
Large-Scale Identification of Common Trait and Disease Variants Affecting Gene ExpressionJune 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 studyApril 11
A high-throughput molecular data resource for Cutaneous NeurofibromasMarch 28
Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivativesFebruary 16
Formative Evaluation of Participant Experience With Mobile eConsent in the App-Mediated Parkinson mPower Study: A Mixed Methods StudyFebruary 16
Formative Evaluation of Participant Experience With Mobile eConsent in the App-Mediated Parkinson mPower Study: A Mixed Methods StudyFebruary 14
The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKitFebruary 14
The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKitJanuary 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 genesDecember 1
Systems Approaches to Cancer BiologyNovember 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 dataOctober 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 schizophreniaAugust 23
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritisJuly 15
Crowdsourcing biomedical research: leveraging communities as innovation enginesJuly 11
Spatiotemporal reconstruction of the human blastocyst by single-cell gene expression analysis informs induction of naive pluripotencyJuly 6
Mobile health: the power of wearables, sensors, and apps to transform clinical trialsJune 10
Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s diseaseJune 9
Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cell from the Progenitor Cell Biology ConsortiumJune 3
Understanding the contribution of family history to colorectal cancer risk and its clinical implications: A state-of-the-science reviewMay 5
Developing a Transparent, Participant-Navigated Electronic Informed Consent for Mobile-Mediated ResearchApril 11
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseasesApril 8
DREAMTools: a Python package for scoring collaborative challengesMarch 15
A large dataset of protein dynamics in the mammalian heart proteomeMarch 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 TissueFebruary 22
Empirical assessment of causal network inference through a community-based effort.
2015
November 25
The PsychENCODE projectOctober 12
The consensus molecular subtypes of colorectal cancer.September 7
rCGH : a comprehensive array-based genomic profile platform for precision medicineAugust 26
TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stabilityJuly 13
The NIH BD2K center for big data in translational genomicsJuly 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 metricJanuary 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 sensitivityJanuary 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 CarcinomaDecember 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 adenocarcinomaDecember 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 principleNovember 15
MyoD is a tumor suppressor gene in medulloblastomaNovember 13
Tumor Growth Rate is an early indicator of anti-tumor drug activity in phase I trialsSeptember 26
The Cancer Genome Atlas Pan-Cancer analysis projectSeptember 26
Enabling Transparent and Collaborative Computational Analysis of 12 tumor types within The Cancer Genome AtlasSeptember 2
HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolismAugust 28
A statin-dependent QTL for GATM expression is associated with statin-induced myopathyAugust 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 DatabaseAugust 15
Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in clinical oncologyAugust 10
Parallel globally optimal structure learning of Bayesian networksAugust 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 eQTLsJuly 18
A phase II flexible screening design allowing for interim analysis and comparison with historical controlJune 25
hARACNe: improving the accuracy of regulatory model reverse engineering via higher order data processing inequality testsMay 9
Genome-wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella VaccinationMay 9
Improving Breast Cancer Survival Analysis Through Competition-Based Multidimensional ModelingMay 2
IGF-1R targeting increases the antitumor effects of DNA damaging agents in SCLC model: an opportunity to increase the efficacy of standard therapyMay 1
Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast CancerApril 26
Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder ChallengeApril 25
Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s DiseaseApril 15
A network-heuristic approach to improve the impact of genomic data on drug discoveryApril 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 commonsMarch 28
A Fool’s ErrandMarch 28
A system biology framework identifies molecular underpinings of coronary heart diseaseMarch 18
Modeling causality for pairs of phenotypes in systems geneticsMarch 18
clearScience: Infrastructure for communicating Data-intensive scienceMarch 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 pseudoprogressionJanuary 16
GSVA: Gene Set Variation Analysis