Publications

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

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