Aaron M. Newman

发表

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

Aaron M. Newman, James B. Cooper, A. Newman, 2010, BMC Bioinformatics.

XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences

Aaron M. Newman, James B. Cooper, A. Newman, 2007, BMC Bioinformatics.

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

Ash A. Alizadeh, Chih Long Liu, Maximilian Diehn, 2014, Bioinform..

Noninvasive Cancer Classification Using Diverse Genomic Features in Circulating Tumor DNA

Robert Tibshirani, Ash A. Alizadeh, Mohammad Shahrokh Esfahani, 2016, BCB.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

Gary D. Bader, Gang Su, Gary D Bader, 2011, BMC Bioinformatics.

Abstract 1690: A tumor deconvolution DREAM Challenge: Inferring immune infiltration from bulk gene expression data

Thomas Yu, Justin Guinney, Aaron M. Newman, 2019 .

EcoTyper: a machine learning framework for large-scale identification of cell type-specific transcriptional states and cellular ecosystems

Ash A. Alizadeh, Aaron M. Newman, Andrew J. Gentles, 2021 .

Corrigendum: Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients

Ash A. Alizadeh, Maximilian Diehn, Aaron M. Newman, 2016, Nature Communications.

Identification of a Colonial Chordate Histocompatibility Gene

Debashis Sahoo, Irving L. Weissman, Ivan K. Dimov, 2013, Science.

Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging

Ash A. Alizadeh, Aaron M. Newman, C. Garrison Fathman, 2015, PloS one.

Data normalization considerations for digital tumor dissection

Ash A. Alizadeh, Maximilian Diehn, Aaron M. Newman, 2017, Genome Biology.

Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2018, Clinical Cancer Research.

CDK19 is a Regulator of Triple-Negative Breast Cancer Growth

Aaron M. Newman, A. Newman, Robert W. Hsieh, 2018, bioRxiv.

Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors

Aaron M. Newman, D. Sahoo, A. Newman, 2016, Proceedings of the National Academy of Sciences.

Abstract PR09: The prognostic landscape of genes and infiltrating immune cells across human cancers

Ash A. Alizadeh, Aaron M. Newman, Chuong D. Hoang, 2015 .

Robust enumeration of cell subsets from tissue expression profiles

Ash A. Alizadeh, Aaron M. Newman, Michael R. Green, 2015, Nature Methods.

Determining cell-type abundance and expression from bulk tissues with digital cytometry

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2019, Nature Biotechnology.

Single Cell Spatial Biology for Precision Cancer Medicine.

Laura M. Heiser, Aaron M. Newman, A. Newman, 2022, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Lab-specific gene expression signatures in pluripotent stem cells.

Aaron M. Newman, Aaron M Newman, A. Newman, 2010, Cell stem cell.

Identifying stem cell gene expression patterns and phenotypic networks with AutoSOME.

Aaron M. Newman, A. Newman, J. Cooper, 2014, Methods in molecular biology.

Stem Cell Gene Expression Analysis using AutoSOME Computational Biology of Embryonic Stem Cells

Aaron M. Newman, A. Newman, J. Cooper, 2010 .

Profiling Tumor Infiltrating Immune Cells with CIBERSORT.

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2018, Methods in molecular biology.

Atlas of clinically distinct cell states and ecosystems across human solid tumors

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2021, Cell.

Antigen Presentation Profiling Reveals Recognition of Lymphoma Immunoglobulin Neoantigens

Ash A. Alizadeh, Aaron M. Newman, Lisa E. Wagar, 2017, Nature.

Urochordata: Botryllus – Natural Chimerism and Tolerance Induction in a Colonial Chordate

Aaron M. Newman, A. Voskoboynik, A. Newman, 2018 .

The genome sequence of the colonial chordate, Botryllus schlosseri

Aaron M. Newman, Dmitry Pushkarev, A. Voskoboynik, 2013, eLife.

T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma

Milad R. Vahid, Aaron M. Newman, Alexander X. Lozano, 2022, Nature Medicine.

Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma.

Ash A. Alizadeh, Aaron M. Newman, R. Tibshirani, 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling.

Ash A. Alizadeh, Aaron M. Newman, R. West, 2017, Cancer Discovery.

Integrated digital error suppression for improved detection of circulating tumor DNA

Ash A. Alizadeh, Aaron M. Newman, Justin N. Carter, 2016, Nature Biotechnology.

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2013, Nature Medicine.

The Immune Landscape of Cancer.

James A. Eddy, David L. Gibbs, Evan O. Paull, 2019, Immunity.

High-throughput genomic profiling of tumor-infiltrating leukocytes.

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2016, Current opinion in immunology.

Single-cell transcriptional diversity is a hallmark of developmental potential

Aaron M. Newman, Mark J. Berger, A. Newman, 2019, Science.

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

Milad R. Vahid, Aaron M. Newman, A. Newman, 2023, Nature Biotechnology.

Robust alignment of single-cell and spatial transcriptomes with CytoSPACE

Milad R. Vahid, Aaron M. Newman, Chloé B. Steen, 2022, bioRxiv.

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma.

Aaron M. Newman, A. Newman, A. Alizadeh, 2021, Cancer cell.

Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx.

Ash A. Alizadeh, Aaron M. Newman, Chloé B. Steen, 2020, Methods in molecular biology.

Inferring gene expression from cell-free DNA fragmentation profiles

Aaron M. Newman, A. Newman, A. Alizadeh, 2022, Nature Biotechnology.

Inferring gene expression from cell-free DNA fragmentation profiles

Aaron M. Newman, A. Newman, A. Alizadeh, 2022, Nature Biotechnology.

Determining cell-type abundance and expression from bulk tissues with digital cytometry

Ash A. Alizadeh, Aaron M. Newman, Chloé B. Steen, 2019, Nature Biotechnology.

Landscape of innate lymphoid cells in human head and neck cancer reveals divergent NK cell states in the tumor microenvironment

Aaron M. Newman, A. Newman, A. Gentles, 2021, Proceedings of the National Academy of Sciences.

SUPPLEMENTARY NOTE

Ash A. Alizadeh, Aaron M. Newman, Michael R. Green, 1879, Botanical Gazette.

Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2016, Science Translational Medicine.

Circulating tumor DNA analysis for detection of minimal residual disease after chemoradiotherapy for localized esophageal cancer.

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2019, Gastroenterology.

Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2020, Cell.

Complex Mammalian-like Hematopoietic System Found in a Colonial Chordate

Aaron M. Newman, G. Nolan, A. Voskoboynik, 2018, Nature.

Evolutionary Origin of the Mammalian Hematopoietic System Found in a Colonial Chordate

Aaron M. Newman, G. Nolan, A. Voskoboynik, 2017, bioRxiv.

Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

Aaron M. Newman, Don H. Anderson, A. Newman, 2012, Genome Medicine.

Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients

Ash A. Alizadeh, Aaron M. Newman, Kathleen A. Durkin, 2016, Nature Communications.

Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis

Aaron M. Newman, James E. Clune, S. Ariyan, 2022, Nature Communications.

Integrative molecular and clinical profiling of acral melanoma identifies LZTR1 as a key tumor promoter and therapeutic target

Aaron M. Newman, James E. Clune, S. Ariyan, 2021, bioRxiv.

Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance.

Ash A. Alizadeh, Aaron M. Newman, Justin N. Carter, 2017, Cancer discovery.

Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq

Ash A. Alizadeh, Maximilian Diehn, Aaron M. Newman, 2015, Expert review of molecular diagnostics.

Integrated spatial multiomics reveals fibroblast fate during tissue repair

Howard Y. Chang, Aaron M. Newman, Deshka S. Foster, 2021, Proceedings of the National Academy of Sciences.

Computational approaches for characterizing the tumor immune microenvironment

Aaron M. Newman, Aaron M Newman, Candace C Liu, 2019, Immunology.

Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

Ash A. Alizadeh, Howard Y. Chang, Aaron M. Newman, 2019, Nature Communications.

The Response of Vascular Dermal Enodethial Cells to House Dust Mite Extracts

Aaron M. Newman, A. Newman, A. Newman, 2008 .

Molecular and Immunologic Signatures are Related to Clinical Benefit from Treatment with Vocimagene Amiretrorepvec (Toca 511) and 5-Fluorocytosine (Toca FC) in Patients with Glioma

Ash A. Alizadeh, Aliz R. Rao, Aaron M. Newman, 2020, Clinical Cancer Research.

A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer

Aaron M. Newman, Sky W. Brubaker, Garry P. Nolan, 2023, Research square.

A spatial map of human macrophage niches links tissue location with function

Aaron M. Newman, Sky W. Brubaker, Garry P. Nolan, 2022, bioRxiv.

Identification and isolation of a dermal lineage with intrinsic fibrogenic potential

Aaron M. Newman, A. Newman, I. Weissman, 2015, Science.

In vivo clonal analysis reveals lineage-restricted progenitor characteristics in mammalian kidney development, maintenance, and regeneration.

Aaron M. Newman, Daniel T. Montoro, A. Newman, 2014, Cell reports.

Method of Isolating and Transplanting the Hematopoietic Stem Cell with Its Microenvironment Which Improves Functional Hematopoietic Engraftment

Aaron M. Newman, A. Newman, I. Weissman, 2018, Journal of the American College of Surgeons.

LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis.

Aaron M. Newman, A. Newman, S. Quake, 2020, Cell stem cell.

Analytical validation of digital cytometry (iSort) for leukocyte enumeration using stored blood.

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2020 .

A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression

Aaron M. Newman, Mark M. Davis, A. Newman, 2019, Nature Communications.

Early B cell changes predict autoimmunity following combination immune checkpoint blockade

Aaron M. Newman, A. Newman, M. Dhodapkar, 2018, The Journal of clinical investigation.

Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers

Aaron M. Newman, A. Newman, M. Clarke, 2017, Nucleic acids research.

Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas.

Aaron M. Newman, A. Newman, M. van de Rijn, 2017, JCI insight.

Global Analysis of Proline-Rich Tandem Repeat Proteins Reveals Broad Phylogenetic Diversity in Plant Secretomes

Aaron M. Newman, A. Newman, J. Cooper, 2011, PloS one.

Reply to J. Wang et al.

Ash A. Alizadeh, Aaron M. Newman, R. Tibshirani, 2019, Journal of Clinical Oncology.

p53 governs an AT1 differentiation programme in lung cancer suppression

Aaron M. Newman, A. Newman, S. Plevritis, 2023, Nature.

Analysis of circulating tumor DNA in localized lung cancer for detection of molecular residual disease and personalization of adjuvant strategies.

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2017 .

Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer

Aaron M. Newman, A. Newman, S. Aviran, 2022, Theranostics.

CD4 T cells and toxicity from immune checkpoint blockade

Aaron M. Newman, A. Newman, A. Chaudhuri, 2023, Immunological reviews.

LMO2 is critical for early metastatic events in breast cancer

Aaron M. Newman, A. Newman, J. Thiery, 2021, bioRxiv.

Abstract 5666: A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer

Ash A. Alizadeh, Aaron M. Newman, K. Ramchandran, 2020, Tumor Biology.

Pooled mutation analysis for the NP28673 and NP28761 studies of alectinib in ALK+ non-small-cell lung cancer (NSCLC).

Aaron M. Newman, A. Shaw, S. Ou, 2016 .

A proteomic approach for the identification of novel lysine methyltransferase substrates.

Ash A. Alizadeh, Aaron M. Newman, C. Liu, 2011, Epigenetics & Chromatin.

A proteomic approach for the identification of novel lysine methyltransferase substrates

Ash A. Alizadeh, Aaron M. Newman, C. Liu, 2011 .

Data normalization considerations for digital tumor dissection

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2017, Genome Biology.

Methodology Open Access

Ash A. Alizadeh, Aaron M. Newman, C. Liu, 2022 .

Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum

Xavier Franceries, Thomas Filleron, Pierre Celsis, 2012, Malaria Journal.

Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling.

Ash A. Alizadeh, Aaron M. Newman, Justin N. Carter, 2017, Cancer discovery.

Diversity of intratumoral regulatory T cells in B-cell non-Hodgkin lymphoma

Ash A. Alizadeh, Aaron M. Newman, J. Myklebust, 2023, Blood advances.

Genomic feature selection by coverage design optimization

Robert Tibshirani, Ash A. Alizadeh, Maximilian Diehn, 2018, Journal of applied statistics.

Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer

Aaron M. Newman, S. Aviran, C. Tepper, 2022, Theranostics.

Abstract PR09: The prognostic landscape of genes and infiltrating immune cells across human cancers

Ash A. Alizadeh, Aaron M. Newman, Chuong D. Hoang, 2015 .

Early prediction of clinical outcomes in resected stage II and III colorectal cancer (CRC) through deep sequencing of circulating tumor DNA (ctDNA).

Ash A. Alizadeh, Aaron M. Newman, A. Newman, 2017 .

Quantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis

Aaron M. Newman, Justin N. Carter, A. Alizadeh, 2024, medRxiv.

Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum

Aaron M. Newman, C. Liu, Daniel Levy, 2012, Malaria Journal.

The Diffuse Large B-Cell Lymphoma Infiltrating Macrophage Transcriptome Signature Is Enriched for Both M1 and M2 Genes and Provides an Excellent Platform for Functional Validation of Macrophage Biology in DLBCL

Ash A. Alizadeh, Aaron M. Newman, J. Gribben, 2012 .

Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering.

Aaron M. Newman, D. Morse, F. Meldrum, 2014, ACS nano.

A proteomic approach for the identification of novel lysine methyltransferase substrates

Ash A. Alizadeh, Or Gozani, Aaron M. Newman, 2011, Epigenetics & Chromatin.