Publications

* = Equal contribution. ^ = Correspondence. Lab members are underlined. For an updated publication please see Google Scholar.

2021

[35] Promises and challenges of adoptive T-cell therapies for solid tumours

M Morotti, A Albukhari, A Alsaadi, M Artibani, JD Brenton, SM Curbishley, T Dong, ML Dustin, Z Hu, N McGranahan, ML Miller, L SantanaGonzalez, LW Seymour, T Shi, P VanLoo, C Yau, H White, N Wietek, DN Church, DC Wedge, AA Ahmed

British journal of cancer (February), 1--18 (2021) | doi | pubmed

2020

[34] Integrated Multi-Tumor Radio-Genomic Marker of Outcomes in Patients with High Serous Ovarian Carcinoma

H Veeraraghavan, HA Vargas, A Sanchez, M Micco, E Mema, Y Lakhman, M CrispinOrtuzar, EP Huang, DA Levine, RN Grisham, N AbuRustum, JO Deasy, A Snyder, ML Miller, JD Brenton, E Sala

Cancers 12(11), 1--27 (2020) | doi | pubmed

[33] Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases

R Rabbie, N AnsariPour, O Cast, D Lau, F Scott, SJ Welsh, C Parkinson, L Khoja, L Moore, M Tullett, K Wong, I Ferreira, JMM Gomez, M Levesque, FA Gallagher, A JimenezSanchez, L Riva, ML Miller, K Allinson, PJ Campbell, P Corrie, DC Wedge, DJ Adams

Nature Communications 11(1), 4306 (2020) | doi | pubmed

[32] Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

A JimenezSanchez, P Cybulska, KL Mager, S Koplev, O Cast, D Couturier, D Memon, P Selenica, I Nikolovski, Y Mazaheri, Y Bykov, FC Geyer, G Macintyre, LM Gavarro, RM Drews, MB Gill, AD Papanastasiou, RE Sosa, RA Soslow, T Walther, R Shen, DS Chi, KJ Park, T Hollmann, JS ReisFilho, F Markowetz, P Beltrao, HA Vargas, D Zamarin, JD Brenton, A Snyder, B Weigelt, E Sala, ML Miller

Nature Genetics (), (2020) | doi | pubmed

2019

[31] Comprehensive Benchmarking and Integration of Tumour Microenvironment Cell Estimation Methods

A JimenezSanchez, O Cast, ML Miller

Cancer Research (), 1--42 (2019) | doi | pubmed

[30] Lack of detectable neoantigen depletion signals in the untreated cancer genome

J VandenEynden, A JimenezSanchez, ML Miller, E Larsson

Nature Genetics 51(12), 1741--1748 (2019) | doi | pubmed

[29] UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma

Y Wolf, O Bartok, S Patkar, GB Eli, S Cohen, K Litchfield, R Levy, A JimenezSanchez, S Trabish, JS Lee, H Karathia, E Barnea, C Day, E Cinnamon, I Stein, A Solomon, L Bitton, E PerezGuijarro, T Dubovik, SS ShenOrr, ML Miller, G Merlino, Y Levin, E Pikarsky, L Eisenbach, A Admon, C Swanton, E Ruppin, Y Samuels

Cell 179(1), 219--235.e21 (2019) | doi | pubmed

[28] Centriolar satellites are acentriolar assemblies of centrosomal proteins

V Quarantotti, J Chen, J Tischer, C GonzalezTejedo, EK Papachristou, CS DSantos, JV Kilmartin, ML Miller, F Gergely

The EMBO Journal 38(14), e101082 (2019) | doi | pubmed

2018

[27] Mutational Analysis Identifies Therapeutic Biomarkers in Inflammatory Bowel Disease-Associated Colorectal Cancers

S Din, K Wong, MF Mueller, A Oniscu, J Hewinson, CJ Black, ML Miller, A JimenezSanchez, R Rabbie, M Rashid, J Satsangi, DJ Adams, MJ Arends

Clinical Cancer Research 24(20), 5133--5142 (2018) | doi | pubmed

[26] The protein kinase SIK downregulates the polarity protein Par3

M Vanlandewijck, MS Dadras, M Lomnytska, T Mahzabin, ML Miller, C Busch, S Brunak, C Heldin, A Moustakas

Oncotarget 9(5), 5716--5735 (2018) | doi | pubmed

2017

[25] Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient

A JimenezSanchez, D Memon, S Pourpe, H Veeraraghavan, Y Li, HA Vargas, MB Gill, KJ Park, O Zivanovic, J Konner, J Ricca, D Zamarin, T Walther, C Aghajanian, JD Wolchok, E Sala, T Merghoub, A Snyder, ML Miller

Cell 170(5), 927--938.e20 (2017) | doi | pubmed | pdf

2016

[24] Integrin-Alpha10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma

T Okada, AY Lee, L Qin, N Agaram, T Mimae, Y Shen, R OConnor, MA LopezLago, A Craig, ML Miller, P Agius, E Molinelli, ND Socci, AM Crago, F Shima, C Sander, S Singer

Cancer Discovery 6(10), 1148--1165 (2016) | doi | pubmed

[23] Mitochondrial DNA copy number variation across human cancers

E Reznik, ML Miller, Y Senbabaoglu, N Riaz, J Sarungbam, SK Tickoo, HA AlAhmadie, W Lee, VE Seshan, AA Hakimi, C Sander

eLife 5(), 1--20 (2016) | doi | pubmed | pdf

[22] MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

NP Gauthier, E Reznik, J Gao, SO Sumer, N Schultz, C Sander, ML Miller

Nucleic Acids Research 44(D1), D986--91 (2016) | doi | pubmed | pdf

2015

[21] Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

ML Miller, E Reznik, NP Gauthier, BA Aksoy, A Korkut, J Gao, G Ciriello, N Schultz, C Sander

Cell Systems 1(3), 197--209 (2015) | doi | pubmed

[20] Genomic Classification of Cutaneous Melanoma

The Cancer Genome Atlas Consortium

Cell 161(7), 1681--1696 (2015) | doi | pubmed | pdf

[19] Mutational landscape determines sensitivity to PD-1 blockage in non-small cell lung cancer

NA Rizvi, MD Hellmann, A Snyder, P Kvistborg, V Makarov, JJ Havel, W Lee, J Yuan, P Wong, TS Ho, ML Miller, N Rekhtman, AL Moreira, F Ibrahim, C Bruggeman, B Gasmi, R Zappasodi, Y Maeda, C Sander, EB Garon, T Merghoub, J Wolchok, T Schumacher, TA Chan

Science 348(6230), 124--129 (2015) | doi | pubmed

[18] Friends not foes: CTLA-4 blockade and mTOR inhibition cooperate during CD8+ T cell priming to promote memory formation and metabolic readiness

VA Pedicord, JR Cross, W MontalvoOrtiz, ML Miller, JP Allison

Journal of Immunology 194(5), 2089--98 (2015) | doi | pubmed

2014

[17] KinomeXplorer: an integrated platform for kinome biology studies

H Horn, EM Schoof, J Kim, X Robin, ML Miller, F Diella, A Palma, G Cesareni, LJ Jensen, R Linding

Nature Methods 11(6), 603--4 (2014) | doi | pubmed

[16] Spatial Normalization of Reverse Phase Protein Array Data

P Kaushik, EJ Molinelli, ML Miller, W Wang, A Korkut, W Liu, Z Ju, Y Lu, G Mills, C Sander

PLoS ONE 9(12), e97213 (2014) | doi | pubmed | pdf

2013

[15] Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments

NP Gauthier, B Soufi, WE Walkowicz, VA Pedicord, KJ Mavrakis, B Macek, DY Gin, C Sander, ML Miller

Nature Methods 10(8), 768--73 (2013) | doi | pubmed | pdf

[14] Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets

ML Miller, EJ Molinelli, JS Nair, T Sheikh, R Samy, X Jing, Q He, A Korkut, AM Crago, S Singer, GK Schwartz, C Sander

Science Signaling 6(294), ra85 (2013) | doi | pubmed | pdf

[13] Perturbation biology: inferring signaling networks in cellular systems

EJ Molinelli, A Korkut, W Wang, ML Miller, NP Gauthier, X Jing, P Kaushik, Q He, G Mills, DB Solit, CA Pratilas, M Weigt, A Braunstein, A Pagnani, R Zecchina, C Sander

PLoS Computational Biology 9(12), e1003290 (2013) | doi | pubmed | pdf

[12] Emerging landscape of oncogenic signatures across human cancers

G Ciriello, ML Miller, BA Aksoy, Y Senbabaoglu, N Schultz, C Sander

Nature Genetics 45(10), 1127--1133 (2013) | doi | pubmed | pdf

[11] The Cancer Genome Atlas Pan-Cancer analysis project

The Cancer Genome Atlas Consortium

Nature Genetics 45(10), 1113--20 (2013) | doi | pubmed | pdf

[10] The SH2 domain interaction landscape

M Tinti, L Kiemer, S Costa, ML Miller, F Sacco, JV Olsen, M Carducci, S Paoluzi, F Langone, CT Workman, N Blom, K Machida, CM Thompson, M Schutkowski, S Brunak, M Mann, BJ Mayer, L Castagnoli, G Cesareni

Cell Reports 3(4), 1293--305 (2013) | doi | pubmed | pdf

2011

[9] Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes

TH Pers, NT Hansen, K Lage, P Koefoed, P Dworzynski, ML Miller, TJ Flint, E Mellerup, H Dam, Oa Andreassen, S Djurovic, I Melle, AD Borglum, T Werge, S Purcell, Ma Ferreira, I Kouskoumvekaki, CT Workman, T Hansen, O Mors, S Brunak

Genetic Epidemiology 35(5), 318--32 (2011) | doi | pubmed

2010

[8] Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

JV Olsen, M Vermeulen, A Santamaria, C Kumar, ML Miller, LJ Jensen, F Gnad, J Cox, TS Jensen, EA Nigg, S Brunak, M Mann

Science Signaling 3(104), ra3 (2010) | doi | pubmed

2009

[7] Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

AA Khan, D Betel, ML Miller, C Sander, CS Leslie, DS Marks

Nature Biotechnology 27(6), 549--55 (2009) | doi | pubmed | pdf

[6] NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins

ML Miller, B Soufi, C Jers, N Blom, B Macek, I Mijakovic

Proteomics 9(1), 116--25 (2009) | doi | pubmed

[5] Kinase-specific prediction of protein phosphorylation sites

ML Miller, N Blom

Methods in Molecular Biology 527(1), 299--310 (2009) | doi | pubmed

2008

[4] Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

ML Miller, S Hanke, AM Hinsby, C Friis, S Brunak, M Mann, N Blom

Molecular and Cellular Proteomics 7(1), 181--92 (2008) | doi | pubmed | pdf

[3] Linear motif atlas for phosphorylation-dependent signaling

ML Miller, LJ Jensen, F Diella, C Jorgensen, M Tinti, L Li, M Hsiung, SA Parker, J Bordeaux, T SicheritzPonten, M Olhovsky, A Pasculescu, J Alexander, S Knapp, N Blom, P Bork, S Li, G Cesareni, T Pawson, BE Turk, MB Yaffe, S Brunak, R Linding

Science Signaling 1(35), ra2 (2008) | doi | pubmed | pdf

2007

[2] NetPhosYeast: prediction of protein phosphorylation sites in yeast

CR Ingrell, ML Miller, ON Jensen, N Blom

Bioinformatics 23(7), 895--7 (2007) | doi | pubmed | pdf

2006

[1] Characterization and location of secretory phospholipase A2 groups IIE, V, and X in the rat brain

M Kolko, NR Christoffersen, SG Barreiro, ML Miller, AJ Pizza, NG Bazan

Journal of Neuroscience Research 83(), 874--882 (2006) | doi | pubmed