Publications and Research

Our group combines computational and experimental techniques to study the cellular organization of complex tissues, with a focus on determining the phenotypic diversity and clinical significance of tumor cell subsets.

denotes a member of the Newman Lab
co-first author
corresponding author
co-senior author

Major

T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma
Nature Medicine
Lozano AX Chaudhuri AA Nene A Bacchiocchi A Earland N Vesely MD Usmani A Turner BE Steen CB Luca BA Badri T Gulati GS Vahid MR Kahemeneh F Harris PK Chen DY Dhodapkar K Sznol M Halaban R Newman AM
2022. In Press.
Atlas of clinically distinct cell states and ecosystems across human solid tumors
Cell
Luca BA Steen CB Matusiak M Azizi A Varma S Zhu C Przybyl J Espín-Pérez A Diehn M Alizadeh AA van de Rijn M Gentles AJ Newman AM
2021. DOI:10.1016/j.cell.2021.09.014.
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  • Tool can reveal cancer subtypes by cell communities they’re found in: Stanford press release
  • Preview: Rolong, A., Chen, B., Lau, K.S. Deciphering the cancer microenvironment from bulk data with EcoTyper. Cell (2021): Article
  • Cell Papers on Tumor Cell States, Rift Valley Fever Virus Host Factors, Recombinant SARS-CoV-2: GenomeWeb
Single-cell transcriptional diversity is a hallmark of developmental potential
Science
Gulati GS Sikandar SS Wesche DJ Manjunath A Bharadwaj A Berger MJ Ilagan F Kuo AH Hsieh RW Cai S Zabala M Scheeren FA Lobo NA Qian D Yu FB Dirbas FM Clarke MF Newman AM
2020. 367:405-411.
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  • A single number helps Stanford data scientists find most dangerous cancer cells: Stanford press release
  • Bagby G: F1000Prime Recommendation: F1000Prime
  • Tiwari V and Lavin D: F1000Prime Recommendation: F1000Prime
  • Research Highlight: Burgess, D.J. Transcriptomics of developmental fate. Nat Rev Genet (2020): Article
  • Science Studies Use Single-Cell RNA Sequencing to Study Cell States, Apply Deep Phenotyping to Pregnancy: GenomeWeb
  • A single number to mark the deadliest cancer cells: Ludwig Cancer Research press release
Determining cell type abundance and expression from bulk tissues with digital cytometry
Nature Biotechnology
Newman AM Steen CB Liu CL Gentles AJ Chaudhuri AA Scherer F Khoudadoust MS Esfahani MS Luca BA Steiner D Diehn M Alizadeh AA
2019. doi:10.1038/s41587-019-0114-2.
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Integrated digital error suppression for improved detection of circulating tumor DNA
Nature Biotechnology
Newman AM Lovejoy AF Klass DM Kurtz DM Chabon JJ Scherer F Stehr H Liu C Bratman SV Say C Zhou L Carter JN West RB Sledge Jr GW Shrager JB Loo Jr BW Neal JW Wakelee HA Diehn M Alizadeh AA
2016. 34:547-555.
The prognostic landscape of genes and infiltrating immune cells across human cancers
Nature Medicine
Gentles AJ Newman AM Liu CL Bratman SV Feng W Kim D Nair VS Xu Y Khuong A Hoang CD Diehn M West RB Plevritis SK Alizadeh AA
2015. 21:938-945.
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  • F1000 Recommendation: Tolar J & H Fey (2016) doi: 10.3410/f.725660593.793520921
  • News in Brief: Gene expression database may lead to more-accurate prognoses (2015)
  • Cancer Discov, doi: 10.1158/2159-8290.CD- NB2015-117.
  • Research highlight (2015) Nat Biotechnol, 33:932, doi: 10.1038/nbt.3337
Robust enumeration of cell subsets from tissue expression profiles
Nature Methods
Newman AM Liu C Green MR Gentles AJ Feng W Xu Y Hoang CD Diehn M Alizadeh AA
2015. 12:453-457.
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
Nature Medicine
Newman AM Bratman SV To J Wynne JF Eclov NCW Modlin LA Liu CL Neal JW Wakelee HA Merritt RE Shrager JB Loo Jr BW Alizadeh AA Diehn M
2014. 20:548-554.
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  • News and Views: Spellman PT and JW Gray, Detecting cancer by monitoring circulating tumor DNA (2014) Nat Med, 20:474-475.
Identification of a colonial chordate histocompatibility gene
Science
Voskoboynik A Newman AM Corey DM Sahoo D Pushkarev D Neff NF Passarelli B Koh W Ishizuka KJ Palmeri KJ Dimov I Keasar C Fan CH Mantalas G Sinha R Penland L Quake SR Weissman IL
2013. 341:384-387.
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  • Editors’ choice: KL Mueller, A gene for early acceptance (2013) Sci Signal, 6:ec179
Lab-specific gene expression signatures in pluripotent stem cells
Cell Stem Cell
Newman AM Cooper JB
2010. 7:258.

2021

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma
Cancer Cell
Steen C Luca BA Esfahani MS Azizi A Sworder BJ Nabet BY Kurtz DM Liu CL Khameneh F Advani RH Natkunam Y Myklebust JH Diehn M Gentles AJ Newman AM Alizadeh AA
2021. DOI 10.1016/j.ccell.2021.08.011.
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  • Preview: McNally, D.R., Elemento, O., Melnick, A. Dissecting bulk transcriptomes of diffuse large B cell lymphoma. Cancer Cell (2021): Article
Integrated spatial multiomics reveals fibroblast fate during tissue repair
Proceedings of the National Academy of Sciences of the United States of America
Foster DS Januszyk M Yost KE Chinta MS Gulati GS Nguyen AT Burcham AR Salhotra A Chase Ransom R Henn D Chen K Mascharak S Tolentino K Titan AL Jones RE da Silva O Tripp Leavitt W Marshall CD des Jardins-Park HE Hu MS Wan DC Wernig G Wagh D Coller J Norton JA Gurtner GC Newman AM Chang HY Longaker MT
2021. DOI 10.1073/pnas.2110025118.
Landscape of innate lymphoid cells in human head and neck cancer reveals divergent NK cell states in the tumor microenvironment
Proceedings of the National Academy of Sciences of the United States of America
Moreno-Nieves UY Tay JK Saumyaa S Horowitz NB Shin JH Mohammad IA Luca BA Mundy DC Gulati GS Bedi N Chang S Chen C Kaplan MJ Rosenthal EL Holsinger FC Divi V Baik FM Sirjani DB Gentles AJ Newman AM Freud AG Sunwoo JB
2021. 118:e2101169118.

2020

LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis
Cell Stem Cell
Zabala M Lobo NA Antony J Heitink LS Gulati GS Lam J Parashurama N Sanchez K Adorno M Sikandar SS Kuo AH Qian D Kalisky T Sim S Li L Dirbas FM Somlo G Newman AM Quake SR Clarke MF
2020. 27:284-299.e8.
Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition
Cell
Nabet BY Esfahani MS Moding EJ Hamilton EG Chabon JJ Rizvi H Steen CB Chaudhuri AA Liu CL Hui AB Almanza D Stehr H Gojenola L Bonilla RF Jin MC Jeon YJ Tseng D Liu C Merghoub T Neal JW Wakelee HA Padda SK Ramchandran KJ Das M Plodkowski AJ Yoo C Chen EL Ko RB Newman AM Hellmann MD Alizadeh AA Diehn M
2020. 183:363-376.
Profiling cell type abundance and expression in bulk tissues with CIBERSORTx
Methods in Molecular Biology
Steen CB Liu CL Alizadeh AA Newman AM
2020. 2117:135-157.

2019

Computational approaches for characterizing the tumor immune microenvironment
Immunology
Liu CC Steen CB Newman AM
2019. doi:10.1111/imm.13101.
A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
Nature Communications
Myers LM Tal MC Torrez Dulgeroff LB Carmody AB Messer RJ Gulati GS Yiu YY Staron MM Angel CL Sinha R Markovic M Pham EA Fram B Ahmed A Newman AM Glenn JS Davis MM Kaech SM Weissman IL Hasenkrug KJ
2019. 10:794.
Functional significance of U2AF1 S34F mutations in lung adenocarcinomas
Nature Communications
Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N Kildebeck E Newman AM Bratman SV Porteus MH Chang HY Alizadeh AA Diehn M
2019. 10:5712.
Circulating Tumor DNA Analysis for Detection of Minimal Residual Disease After Chemoradiotherapy for Localized Esophageal Cancer
Gastroenterology
Azad TD Chaudhuri AA Fang P Qiao Y Esfahani MS Chabon JJ Hamilton EG Yang YD Lovejoy A Newman AM Kurtz DM Jin M Schroers-Martin J Stehr H Liu CL Hui AB Patel V Maru D Lin SH Alizadeh AA Diehn M
2019. 10.1053/j.gastro.2019.10.039.
Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction
Cell
Kurtz DM Esfahani MS Scherer F Soo J Jin MC Liu CL Newman AM Dührsen U Hüttmann A Casasnovas O Westin JR Ritgen M Böttcher S Langerak AW Roschewski M Wilson WH Gaidano G Rossi D Bahlo J Hallek M Tibshirani R Diehn M Alizadeh AA
2019. 178:699-713.

2018

Profiling tumor infiltrating immune cells with CIBERSORT
Methods in Molecular Biology
Chen B Khodadoust MS Liu CL Newman AM Alizadeh AA
2018. Cancer Systems Biology, Vol 1711, von Stechow, L., ed. (Springer).
Urochordata: Botryllus – Natural Chimerism and Tolerance Induction in a Colonial Chordate
Advances in Comparative Immunology
Voskoboynik A Newman AM Kowarsky M Weissman IL
2018. Cooper EL, ed. (Springer), pp. 503-519.
Complex mammalian-like haematopoietic system found in a colonial chordate
Nature
Rosental B Kowarsky M Seita J Corey DM Ishizuka KJ Palmeri KJ Chen SY Sinha R Okamoto J Mantalas G Manni L Raveh T Clarke DN Tsai JM Newman AM Neff NF Nolan GP Quake SR Weissman IL Voskoboynik A
2018. 564:425-429.
Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma
Journal of Clinical Oncology
Kurtz DM Scherer F Jin MC Soo J Craig AFM Esfahani MS Chabon JJ Stehr H Liu CL Tibshirani R Maeda LS Gupta NK Khodadoust MS Advani RH Levy R Newman AM Dührsen U Hüttmann A Meignan M Casasnovas RO Westin JR Roschewski M Wilson WH Gaidano G Rossi D Diehn M Alizadeh AA
2018. 36:2845-2853.
Combination approach for detecting different types of alterations in circulating tumor DNA in leiomyosarcoma
Clinical Cancer Research
Przybyl J Chabon JJ Spans L Ganjoo K Vennam S Newman AM Forgó E Varma S Zhu S Debiec-Rychter M Alizadeh AA Diehn M van de Rijn M
2018. doi 10.1158/1078-0432.CCR-17-3704.
Feature selection by coverage design optimization
Journal of Applied Statistics
Reid S Newman AM Diehn M Alizadeh AA Tibshirani R
2018. org/10.1080/02664763.2018.1432577.
Early B cell changes predict autoimmunity following combination immune checkpoint blockade
Journal of Clinical Investigation
Das R Bar N Ferreira M Newman AM Zhang L Bailur JK Bacchiocchi A Kluger H Wei W Halaban R Sznol M Dhodapkar MV Dhodapkar MM
2018. 10.1172/JCI96798.

2017

Data normalization considerations for digital tumor dissection
Genome Biology
Newman AM Gentles AJ Liu CL Diehn M Alizadeh AA
2017. 18:128.
Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling
Cancer Discovery
Chaudhuri AA Chabon JJ Lovejoy AF Newman AM Stehr H Azad TD Khodadoust MS Esfahani MS Liu CL Zhou L Scherer F Kurtz DM Say C Carter JN Merriott DJ Dudley JC Binkley MS Modlin L Padda SK Gensheimer MF West RB Shrager JB Neal JW Wakelee HA Loo BW Alizadeh AA Diehn M
2017. 10.1158/2159-8290.CD-17-0716.
Targeted chromatic ligation, a robust epigenetic profiling technique for small cell numbers
Nucleic Acids Research
Zarnegar M Reinitz F Newman AM Clarke M
2017. 10.1093/nar/gkx648.
Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas
JCI Insight
Przybyl J Kowalewska M Quattrone A Dewaele B Vanspauwen V Varma S Vennam S Newman AM Swierniak M Bakula-Zalewska E Siedlecki JA Bidzinski M Cools J van de Rijn M Debiec-Rychter M
2017. 2:94033.
Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens
Nature
Khodadoust M Olsson N Wagar L Haabeth OAW Chen B Swaminathan K Rawson K Liu CL Steiner D Lund P Rao S Zhang L Marceau C Stehr H Newman AM Czerwinski D Carlton V Moorhead M Faham M Kohrt H Carette J Green MR Davis M Levy R Elias J Alizadeh AA
2017. 10.1038/nature21433.

2016

Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA
Science Translational Medicine
Scherer F Kurtz DM Newman AM Stehr S Craig AFM Esfahani MS Lovejoy AF Chabon JJ Klass DM Liu CL Zhou L Glover C Visser BC Poultsides GA Advani RH Maeda LS Gupta NK Levy R Ohgami RS Kunder CA Diehn M Alizadeh AA
2016. 8:364ra155.
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  • Research highlight (2016) Nat Rev Cancer, doi: 10.1038/nrc.2016.146
High-throughput genomic profiling of tumor-infiltrating leukocytes
Current Opinion in Immunology
Newman AM Alizadeh AA
2016. 41:77-84.
Circulating tumor DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients
Nature Communications
Chabon JJ Simmons AD Lovejoy AF Esfahani MS Newman AM Haringsma HJ Kurtz DM Stehr H Florian Scherer Karlovich CA Harding TC Goldman JW Sequist LV Piotrowska Z Wakelee HA Neal JW Alizadeh AA Diehn M
2016. 7:11815.
Role of KEAP1/NRF2 and TP53 mutations in lung squamous cell carcinoma development and radiation resistance
Cancer Discovery
Jeong Y Hoang N Lovejoy A Stehr H Newman AM Gentles A Kong W Truong D Martin S Chaudhuri A Heiser D Zhou L Say C Carter JN Hiniker SM Loo Jr. B West RB Beachy PA Alizadeh AA Diehn M
2016. doi: 10.1158/2159-8290.CD-16-0127.
Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors
PNAS
Krampitz GW George BM Willingham SB Volkmer JP Weiskopf K Jahchan N Newman AM Sahoo D Zemek AJ Yanovsky RL Nguyen JK Schnorr PJ Mazur PK Sage J Longacre TA Vissera BC Poultsides GA Nortona JA Weissman IL
2016. doi: 10.1073/pnas.1600007113.

2015

Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq
Expert Review of Molecular Diagnostics
Bratman SV Newman AM Alizadeh AA Diehn M
2015. 15:715-719.
Identification and isolation of a dermal lineage with intrinsic fibrogenic potential
Science
Rinkevich Y Walmsley GG Hu MS Maan ZN Newman AM Drukker M Januszyk M Gurtner GC Lorenz HP Weissman IL Longaker MT
2015. 348, doi:10.1126/science.aaa2151.
Large-scale and comprehensive immune profiling and functional analysis of normal human aging
PLOS ONE
Whiting C Siebert J Newman AM Du H Alizadeh AA Goronzy J Weyand C Krishnan E Fathman CG Maecker HT
2015. 10:e0133627.

2014

FACTERA: A practical method for the discovery of genomic rearrangements at breakpoint resolution
Bioinformatics
Newman AM Bratman SV Stehr H Lee LJ Liu CL Diehn M Alizadeh AA
2014. In Press.
In vivo clonal analysis reveals lineage-restricted progenitor characteristics in mammalian kidney development, maintenance, and regeneration
Cell Reports
Rinkevich Y Montoro DT Contreras-Trujillo H Harari-Steinberg O Newman AM Tsai JM Lim X Van-Amerongen R Bowman A Januszyk M Pleniceanu O Nusse R Longaker MT Weissman IL Dekel B
2014. 7:1270-1283.
Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering
ACS Nano
Bawazer LA Newman AM Gu Q Ibish A Arcila M Cooper JB Meldrum FC Morse DE
2014. 8:387-395.

2013

The genome sequence of the colonial chordate, Botryllus schlosseri
eLife
Voskoboynik A Neff NF Sahoo D Newman AM Pushkarev D Koh W Passarelli B Fan CH Mantalas G Palmeri KJ Ishizuka KJ Gissi C Griggio F Ben-Shlomo R Corey DM Penland L White III RA Weissman IL Quake SR
2013. 2:e00569.

2012 and older

Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks
Genome Medicine
Newman AM Gallo NB Hancox L Miller N Radeke CM Maloney MA Cooper JB Anderson DH Hageman GS Johnson LV Radeke MJ
2012. 4:16 (BioMed Central press release; highly accessed).
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  • Commentary: Whitmore SS and RF Mullins, Transcriptome changes in age-related macular degeneration (2012) BMC Med, 10:21.
clusterMaker: A multi-algorithm clustering plugin for Cytoscape
BMC Bioinformatics
Morris JH Apelstin A Newman AM Baumbauch J Wittkop T Su G Bader GD Ferrin TE
2011. 12:436 (highly accessed).
A proteomic approach for the identification of novel lysine methyltransferase substrates
Epigenetics and Chromatin
Levy D Liu CL Yang Z Newman AM Alizadeh AA Utz PJ Gozani O
2011. 259.0.
Global analysis of proline-rich tandem repeat proteins reveals broad phylogenetic diversity in plant secretomes
PLOS ONE
Newman AM Cooper JB
2011. 6:e23167.
AutoSOME: A clustering method for identifying gene expression modules without prior knowledge of cluster number
BMC Bioinformatics
Newman AM Cooper JB
2010. 11:117 (highly accessed).
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
BMC Bioinformatics
Newman AM Cooper JB
2007. 8:382.