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
Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics Nature Reviews Molecular Cell Biology
Gulati GS
D'Silva JP
Liu Y
Wang L
Newman AM
Mapping single-cell developmental potential in health and disease with interpretable deep learning bioRxiv
Kang M
Armenteros JJA
Gulati GS
Gleyzer R
Avagyan S
Brown EL
Zhang W
Usmani A
Earland N
Wu Z
Zou J
Fields RC
Chen DY
Chaudhuri AA
Newman AM
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE Nature Biotechnology
Vahid MR
Brown EL
Steen CB
Zhang W
Jeon HS
Kang M
Gentles AJ
Newman AM
Researchers invent a tool to create high-resolution maps of gene activity, opening a path to improved diagnostics and therapies Stanford press release
Stanford's CytoSPACE Looks to Improve Single-Cell Transcriptomics Alignment GenomeWeb
New computational method to identify location of cell types in a sample Phys.org
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
Institute data scientists identify who may be at risk from revolutionary cancer treatments: Stanford press release
Spotlight: Bello, E., Dougan, M. Elevated circulating memory T cells precede immunotherapy toxicities in melanoma. Trends in Cancer (2022): Article
Viewpoint: Johnson, D.B., Balko, J.M. Primed for toxicity: CD4+ T cells and immune checkpoint inhibitors. Med (2022): Article
Spotlight: Goswami, S., Siddiqui, B.A., Subudhi, S., Basu, S., Yadav, S.S., Diab, A., Sharma, P. A composite T cell biomarker in pre-treatment blood samples correlates with detection of immune-related adverse events. Cancer Cell (2022): Article
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
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
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
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
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
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
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
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
Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy Nature Cancer
Subramanian A
Nemat-Gorgani N
Ellis-Caleo TJ
van IJzendoorn DGP
Sears TJ
Somani A
Luca BA
Zhou MY
Bradic M
Torres IA
Oladipo E
New C
Kenney DE
Avedian RS
Steffner RJ
Binkley MS
Mohler DG
Tap WD
D'Angelo SP
van de Rijn M
Ganjoo KN
Bui NQ
Charville GW
Newman AM
Moding EJ
CD4 T cells and toxicity from immune checkpoint blockade Immunological Reviews
Earland N
Zhang W
Usmani A
Nene A
Bacchiocchi A
Chen DY
Sznol M
Halaban R
Chaudhuri AA
Newman AM
Profiling cellular ecosystems at single-cell resolution and at scale with EcoTyper Methods in Molecular Biology
Steen CB
Luca BA
Alizadeh AA
Gentles AJ
Newman AM
p53 governs an AT1 differentiation programme in lung cancer suppression Nature
Kaiser AM
Gatto A
Hanson KJ
Zhao RL
Raj N
Ozawa MG
Seoane JA
Bieging-Rolett KT
Wang M
Li I
Trope WL
Liou DZ
Shrager JB
Plevritis SK
Newman AM
Van Rechem C
Attardi LD
Single-cell mapping identifies MSI+ cells as a common origin for diverse subtypes of pancreatic cancer Cancer Cell
Rajbhandari N
Hamilton M
Quintero CM
Ferguson LP
Fox R
Schürch CM
Wang J
Nakamura M
Lytle NK
McDermott M
Diaz E
Pettit H
Kritzik M
Han H
Cridebring D
Wen KW
Tsai S
Goggins MG
Lowy AM
Wechsler-Reya RJ
Von Hoff DD
Newman AM
Reya T
Diversity of intratumoral regulatory T cells in B-cell non-Hodgkin lymphoma Blood Advances
Spasevska I
Sharma A
Steen CB
Josefsson SE
Blaker YN
Kolstad A
Rustad EH
Meyer S
Isaksen K
Chellappa S
Kushekhar K
Beiske K
Førsund MS
Spetalen S
Holte H
Østenstad B
Brodtkorb M
Kimby E
Olweus J
Taskén K
Newman AM
Lorenz S
Smeland EB
Alizadeh AA
Huse K
Myklebust JH
Identification of a minority population of LMO2+ breast cancer cells that integrate into the vasculature and initiate metastasis Science Advances
Sikandar S
Gulati GS
Antony J
Fetter I
Kuo AH
Dang Ho WH
Haro-Acosta V
Das S
Steen CB
Pereira TA
Qian D
Beachy PA
Dirbas F
Red-Horse K
Rabbitts TH
Thiery JP
Newman AM
Clarke MF
Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer Theranostics
Wang J
Fite BZ
Kare AJ
Wu B
Raie M
Tumbale SK
Zhang N
Davis RR
Tepper CG
Aviran S
Newman AM
King DA
Ferrara KW
Inferring gene expression from cell-free DNA fragmentation profiles Nature Biotechnology
Esfahani MS
Hamilton EG
Mehrmohamadi M
Nabet BY
Alig SK
King DA
Steen CB
Macaulay CW
Schultz A
Nesselbush MC
Soo J
Schroers-Martin JG
Chen B
Binkley MS
Stehr H
Chabon JJ
Sworder BJ
Hui AB
Frank MJ
Moding EJ
Liu CL
Newman AM
Isbell JM
Rudin CM
Li BT
Kurtz DM
Diehn M
Alizadeh AA
Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis Nature Communications
Farshidfar F
Rhrissorrakrai K
Levovitz C
Peng C
Knight J
Bacchiocchi A
Su J
Yin M
Sznol M
Ariyan S
Clune J
Olino K
Parida L
Nikolaus J
Zhang M
Zhao S
Wang Y
Huang G
Wan M
Li X
Cao J
Yan Q
Chen X
Newman AM
Halaban R
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
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
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
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
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
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
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
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
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).
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
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
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences BMC Bioinformatics
Newman AM
Cooper JB