Publications

2023

Breaking the performance ceiling for neoantigen immunogenicity prediction

O’Brien H., Salm M., Morton L., Szukszto M., O’Farrell F., Boulton C., Becker P. D., Samuels Y., Swanton C., Mansour M. R., Reker Hadrup S. & Quezada S. A. (2023) Nature Cancer. 4, 12, p. 1618-1621

Neoantigens in cancer immunotherapy: quantity vs. quality

Wolf Y. & Sameuls Y. (2023) Molecular Oncology. 17, 8, p. 1457-1459

The landscape of T cell antigens for cancer immunotherapy

Peri A., Salomon N., Wolf Y., Kreiter S., Diken M. & Samuels Y. (2023) Nature Cancer. 4, 7, p. 937-954

The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC

Javitt A., Shmueli M., Kramer M., Kolodziejczyk A., Cohen I., Kamer I., Litchfield K., Bab-Dinitz E., Zadok O., Neiens V., Ulman A., Radomir L., Wolf-Levy H., Eisenberg-Lerner A., Kacen A., Alon M., Toste Rêgo A., Stacher-Priehse E., Lindner M., Koch I., Bar J., Swanton C., Samuels Y., Levin Y., da Fonseca P. C. A., Elinav E., Friedman N., Meiners S. & Merbl Y. (2023) bioArxiv.

The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC

Javitt A., Shmueli M. D., Kramer M. P., Kolodziejczyk A. A., Cohen I. J., Radomir L., Sheban D., Kamer I., Litchfield K., Bab-Dinitz E., Zadok O., Neiens V., Ulman A., Wolf-Levy H., Eisenberg-Lerner A., Kacen A., Alon M., Rêgo A. T., Stacher-Priehse E., Lindner M., Koch I., Bar J., Swanton C., Samuels Y., Levin Y., da Fonseca P. C., Elinav E., Friedman N., Meiners S. & Merbl Y. (2023) Nature Cancer. 4, 5, p. 629-647

Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes

Levy R., Alter Regev T., Paes W., Gumpert N., Cohen Shvefel S., Bartok O., Dayan-Rubinov M., Alon M., Shmueli M., Levin Y., Merbl Y., Ternette N. & Samuels Y. (2023) Molecular & Cellular Proteomics. 22, 4, 100519.

Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors

Kacen A., Javitt A., Kramer M. P., Morgenstern D., Tsaban T., Shmueli M. D., Teo G. C., Leprevost F. d. V., Barnea E., Yu F., Admon A., Eisenbach L., Samuels Y., Schueler-Furman O., Levin Y., Nesvizhskii A. & Merbl Y. (2023) Nature Biotechnology. 41, 2, p. 239-251

2022

Intratumor heterogeneity and anti-tumor immunity shape one another bidirectionally

Wolf Y. & Samuels Y. (2022) Clinical Cancer Research. 28, 14, p. 2994-3001

Mechanisms of immune activation and regulation: lessons from melanoma

Kalaora S., Nagler A., Wargo J. A. & Samuels Y. (2022) Nature reviews. Cancer. 22, 4, p. 195-207

2021

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response

Spencer C. N., McQuade J. L., Gopalakrishnan V., McCulloch J. A., Vetizou M., Cogdill A. P., Khan M. A. W., Zhang X., White M. G., Peterson C. B., Wong M. C., Morad G., Rodgers T., Badger J. H., Helmink B. A., Andrews M. C., Rodrigues R. R., Morgun A., Kim Y. S., Roszik J., Hoffman K. L., Zheng J., Zhou Y., Medik Y. B., Kahn L. M., Johnson S., Hudgens C. W., Wani K., Gaudreau P., Harris A. L., Jamal M. A., Baruch E. N., Perez-Guijarro E., Day C., Merlino G., Pazdrak B., Lochmann B. S., Szczepaniak-Sloane R. A., Arora R., Anderson J., Zobniw C. M., Posada E., Sirmans E., Simon J., Haydu L. E., Burton E. M., Wang L., Dang M., Clise-Dwyer K., Schneider S., Chapman T., Anang N. A. S., Duncan S., Toker J., Malke J. C., Glitza I. C., Amaria R. N., Tawbi H. A., Diab A., Wong M. K., Patel S. P., Woodman S. E., Davies M. A., Ross M. I., Gershenwald J. E., Lee J. E., Hwu P., Jensen V., Samuels Y., Straussman R., Ajami N. J., Nelson K. C., Nezi L., Petrosino J. F., Futreal P. A., Lazar A. J., Hu J., Jenq R. R., Tetzlaff M. T., Yan Y., Garrett W. S., Huttenhower C., Sharma P., Watowich S. S., Allison J. P., Cohen L., Trinchieri G., Daniel C. R. & Wargo J. A. (2021) Science (American Association for the Advancement of Science). 374, 6575, p. 1632-1640

Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma

Peri A., Greenstein E., Alon M., Pai J. A., Dingjan T., Reich-Zeliger S., Barnea E., Barbolin C., Levy R., Arnedo-Pac C., Kalaora S., Dassa B., Feldmesser E., Shang P., Greenberg P., Levin Y., Benedek G., Levesque M. P., Adams D. J., Lotem M., Wilmott J. S., Scolyer R. A., Jönsson G. B., Admon A., Rosenberg S. A., Cohen C. J., Niv M. Y., Lopez-Bigas N., Satpathy A. T., Friedman N. & Samuels Y. (2021) The Journal of Clinical Investigation. 131, 20, e129466.

Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics

Nagler A., Kalaora S., Barbolin C., Gangaev A., Ketelaars S. L., Alon M., Pai J., Benedek G., Yahalom-Ronen Y., Erez N., Greenberg P., Yagel G., Peri A., Levin Y., Satpathy A. T., Bar-Haim E., Paran N., Kvistborg P. & Samuels Y. (2021) Cell reports (Cambridge). 35, 13, 109305.

Melanoma models for the next generation of therapies

Patton E. E., Mueller K. L., Adams D. J., Anandasabapathy N., Aplin A. E., Bertolotto C., Bosenberg M., Ceol C. J., Chi P., Herlyn M., Holmen S. L., Karreth F. A., Kaufman C. K., Khan S., Kobold S., Leucci E., Levy C., Lombard D. B., Lund A. W., Marie K. L., Marine J. C., Marais R., McMahon M., Robles-Espinoza C. D., Ronai Z. A., Samuels Y., Soengas M. S., Villanueva J., Weeraratna A. T., White R. M., Yeh I., Zhu J., Zon L. I., Hurlbert M. S. & Merlino G. (2021) Cancer Cell. 39, 5, p. 610-631

Identification of bacteria-derived HLA-bound peptides in melanoma

Kalaora S., Nagler A., Nejman D., Alon M., Barbolin C., Barnea E., Ketelaars S. L. C., Cheng K., Vervier K., Shental N., Bussi Y., Rotkopf R., Levy R., Benedek G., Trabish S., Dadosh T., Levin-Zaidman S., Geller L. T., Wang K., Greenberg P., Yagel G., Peri A., Fuks G., Bhardwaj N., Reuben A., Hermida L., Johnson S. B., Galloway-Peña J. R., Shropshire W. C., Bernatchez C., Haymaker C., Arora R., Roitman L., Eilam R., Weinberger A., Lotan-Pompan M., Lotem M., Levin Y., Lawley T. D., Adams D. J., Levesque M. P., Besser M. J., Schachter J., Golani O., Segal E., Ruppin E., Kvistborg P., Peterson S. N., Wargo J. A., Straussman R. & Samuels Y. (2021) Nature (London). 592, 7852, p. 138-143

MEK inhibition reverses aberrant signaling in melanoma cells through reorganization of NRas and BRAF in self nano-clusters

Yakovian O., Sajman J., Arafeh R., Neve-Oz Y., Alon M., Samuels Y. & Sherman E. (2021) Cancer research (Chicago, Ill.). 81, 5, p. 1279-1292

Anti-tumour immunity induces aberrant peptide presentation in melanoma

Bartok O., Pataskar A., Nagel R., Laos M., Goldfarb E., Hayoun D., Levy R., Körner P., Kreuger I. Z. M., Champagne J., Zaal E. A., Bleijerveld O. B., Huang X., Kenski J., Wargo J., Brandis A., Levin Y., Mizrahi O., Alon M., Lebon S., Yang W., Nielsen M. M., Stern-Ginossar N., Altelaar M., Berkers C. R., Geiger T., Peeper D. S., Olweus J., Samuels Y. & Agami R. (2021) Nature (London). 590, 7845, p. 332-337

2020

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

Sadeqi Azer E., Rashidi Mehrabadi F., Malikić S., Li X. C., Bartok O., Litchfield K., Levy R., Samuels Y., Schäffer A. A., Gertz E. M., Day C. P., Pérez-Guijarro E., Marie K., Lee M. P., Merlino G., Ergun F. & Sahinalp S. C. (2020) Bioinformatics (Oxford, England). 36, suppl 1, p. i169-i176

A genome-wide CRISPR screen identifies FBXO42 involvement in resistance toward MEK inhibition in NRAS-mutant melanoma

Nagler A., Vredevoogd D. W., Alon M., Cheng P. F., Trabish S., Kalaora S., Arafeh R., Goldin V., Levesque M. P., Peeper D. S. & Samuels Y. (2020) Pigment Cell and Melanoma Research. 33, 2, p. 334-344

Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma

Kalaora S., Lee J. S., Barnea E., Levy R., Greenberg P., Alon M., Yagel G., Bar Eli G., Oren R., Peri A., Patkar S., Bitton L., Rosenberg S. A., Lotem M., Levin Y., Admon A., Ruppin E. & Samuels Y. (2020) Nature Communications. 11, 1, 896.

2019

PIK3CA in cancer: The past 30 years

Arafeh R. & Samuels Y. (2019) Seminars in Cancer Biology. 59, p. 36-49

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma

Wolf Y., Bartok O., Patkar S., Eli G. B., Cohen S., Litchfield K., Levy R., Jiménez-Sánchez A., Trabish S., Lee J. S., Karathia H., Barnea E., Day C., Cinnamon E., Stein I., Solomon A., Bitton L., Pérez-Guijarro E., Dubovik T., Shen-Orr S. S., Miller M. L., Merlino G., Levin Y., Pikarsky E., Eisenbach L., Admon A., Swanton C., Ruppin E. & Samuels Y. (2019) Cell. 179, 1, p. 219-235

Exome Sequencing of ABCB5 Identifies Recurrent Melanoma Mutations that Result in Increased Proliferative and Invasive Capacities

Sana G., Madigan J. P., Gartner J. J., Fourrez M., Lin J., Qutob N., Narayan J., Shukla S., Ambudkar S. V., Xia D., Rosenberg S. A., Gottesman M. M., Samuels Y. & Gillet J. (2019) Journal of Investigative Dermatology. 139, 9, p. 1985-1992

Cross-Talk between Receptor Tyrosine Kinases AXL and ERBB3 Regulates Invadopodia Formation in Melanoma Cells

Revach O., Sandler O., Samuels Y. & Geiger B. (2019) Cancer Research. 79, 10, p. 2634-2648

Correction: RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells (vol 8, 653, 2018)

Qutob N., Masuho I., Alon M., Emmanuel R., Cohen I., Di Pizio A., Madore J., Elkahloun A., Ziv T., Levy R., Gartner J. J., Hill V. K., Lin J. C., Hevroni Y., Greenberg P., Brodezki A., Rosenberg S. A., Kosloff M., Hayward N. K., Admon A., Niv M. Y., Scolyer R. A., Martemyanov K. A. & Samuels Y. (2019) Scientific Reports. 9, 4523.

RASA2 and NF1; two-negative regulators of Ras with complementary functions in melanoma

Arafeh R., Di Pizio A., Elkahloun A. G., Dym O., Niv M. Y. & Samuels Y. (2019) Oncogene. 38, 13, p. 2432-2434

Author Correction: Combined inhibition of MEK and nuclear ERK translocation has synergistic antitumor activity in melanoma cells (Scientific Reports, (2017), 7, 1, (16345), 10.1038/s41598-017-16558-0)

Arafeh R., Flores K., Keren-Paz A., Maik-Rachline G., Gutkind N., Rosenberg S., Seger R. & Samuels Y. (2019) Scientific Reports. 9, 1, 4672.

Correction: CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma (Oncotarget (2018) 9 (31264-31277) DOI: 10.18632/oncotarget.25805)

Alon M., Arafeh R., Lee J. S., Madan S., Kalaora S., Nagler A., Abgarian T., Greenberg P., Ruppin E. & Samuels Y. (2019) Oncotarget. 10, 13, p. 1344

Cancer exome-based identification of tumor neo-antigens using mass spectrometry

Kalaora S. & Samuels Y. (2019) Cancer Immunosurveillance : Methods and Protocols . Lopez-Soto A. & Folgueras A. R.(eds.). Vol. 1884. p. 203-214 (trueMethods in Molecular Biology).

2018

Cancer research in the era of immunogenomics

Wolf Y. & Samuels Y. (2018) ESMO Open. 3, 7, e000475.

The cancer genome

Samuels Y., Bardelli A., Wolf Y. & López-Otin C. (2018) DeVita, Hellman, and Rosenberg's Cancer: Principles & Practice of Oncology . p. 2-25

Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma

Kalaora S., Wolf Y., Feferman T., Barnea E., Greenstein E., Reshef D., Tirosh I., Reuben A., Patkar S., Levy R., Quinkhardt J., Omokoko T., Qutob N., Golani O., Zhang J., Mao X., Song X., Bernatchez C., Haymaker C., Forget M., Creasy C., Greenberg P., Carter B. W., Cooper Z. A., Rosenberg S. A., Lotem M., Sahin U., Shakhar G., Ruppin E., Wargo J. A., Friedman N., Admon A. & Samuels Y. (2018) Cancer Discovery. 8, 11, p. 1366-1375

Mutated MITF-E87R in Melanoma Enhances Tumor Progression via S100A4

Nordlinger A., Dror S., Elkahloun A., Del Rio J., Stubbs E., Golan T., Malcov H., Pricket T. D., Cronin J. C., Parikh S., Labes S., Thomas L., Yankovitz G., Tabach Y., Levy C., Samuels Y. & Khaled M. (2018) Journal of Investigative Dermatology. 138, 10, p. 2216-2223

Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures

Lee J. S., Adler L., Karathia H., Carmel N., Rabinovich S., Auslander N., Keshet R., Stettner N., Silberman A., Agemy L., Helbling D., Eilam R., Sun Q., Brandis A., Malitsky S., Itkin M., Weiss H., Pinto S., Kalaora S., Levy R., Barnea E., Admon A., Dimmock D., Stern-Ginossar N., Scherz A., Nagamani S. C. S., Unda M., Wilson D. M., Elhasid R., Carracedo A., Samuels Y., Hannenhalli S., Ruppin E. & Erez A. (2018) Cell. 174, 6, p. 1559-1570

Refinement of the endogenous epitope tagging technology allows the identification of a novel NRAS binding partner in melanoma

Alon M., Emmanuel R., Qutob N., Bakhman A., Peshti V., Brodezki A., Bassan D., Kosloff M. & Samuels Y. (2018) Pigment Cell and Melanoma Research. 31, 5, p. 641-648

Assembly and activation of the Hippo signalome by FAT1 tumor suppressor

Martin D., Degese M. S., Vitale-Cross L., Iglesias-Bartolome R., Valera J. L. C., Wang Z., Feng X., Yeerna H., Vadmal V., Moroishi T., Thorne R. F., Zaida M., Siegele B., Cheong S. C., Molinolo A. A., Samuels Y., Tamayo P., Guan K. L., Lippman S. M., Lyons J. G. & Gutkind J. S. (2018) Nature Communications. 9, 2372.

CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma

Alon M., Arafeh R., Lee J. S., Madan S., Kalaora S., Nagler A., Abgarian T., Greenberg P., Ruppin E. & Samuels Y. (2018) Oncotarget. 9, 58, p. 31264-31277

Harnessing synthetic lethality to predict the response to cancer treatment

Lee J. S., Das A., Jerby-Arnon L., Arafeh R., Auslander N., Davidson M., McGarry L., James D., Amzallag A., Park S. G., Cheng K., Robinson W., Atias D., Stossel C., Buzhor E., Stein G., Waterfall J. J., Meltzer P. S., Golan T., Hannenhalli S., Gottlieb E., Benes C. H., Samuels Y., Shanks E. & Ruppin E. (2018) Nature Communications. 9, 2546.

Erratum: Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma (Cancer Cell (2018) 33(2) (322–336.e8) (S1535610818300023) (10.1016/j.ccell.2018.01.002))

Yu Y., Schleich K., Yue B., Ji S., Lohneis P., Kemper K., Silvis M. R., Qutob N., van Rooijen E., Werner-Klein M., Li L., Dhawan D., Meierjohann S., Reimann M., Elkahloun A., Treitschke S., Dörken B., Speck C., Mallette F. A., Zon L. I., Holmen S. L., Peeper D. S., Samuels Y., Schmitt C. A. & Lee S. (2018) Cancer Cell. 33, 4, p. 785

Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma

Yu Y., Schleich K., Yue B., Ji S., Lohneis P., Kemper K., Silvis M. S., Qutob N., van Rooijen E., Werner-Klein M., Li L., Dhawan D., Meierjohann S., Reimann M., Elkahloun A., Treitschke S., Dörken B., Speck C., Mallette F. A., Zon L. I., Holmen S. L., Peeper D. S., Samuels Y., Schmitt C. A. & Lee S. (2018) Cancer Cell. 33, 2, p. 322-336.e8

RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells

Qutob N., Masuho I., Alon M., Emmanuel R., Cohen I., Di Pizio A., Madore J., Elkahloun A., Ziv T., Levy R., Gartner J. J., Hill V. K., Lin J. C., Hevroni Y., Greenberg P., Brodezki A., Rosenberg S. A., Kosloff M., Hayward N. K., Admon A., Niv M. Y., Scolyer R. A., Martemyanov K. A. & Samuels Y. (2018) Scientific Reports. 8, 653.

Analysis of enzymatic activity of matrix metalloproteinase (MMP) by collagen zymography in Melanoma

Walia V. & Samuels Y. (2018) Proteases and Cancer . Obaya A. & Cal S.(eds.). p. 97-106 (trueMethods in Molecular Biology).

2017

Combined inhibition of MEK and nuclear ERK translocation has synergistic antitumor activity in melanoma cells

Arafeh R., Flores K., Keren-Paz A., Maik-Rachline G., Gutkind N., Rosenberg S., Seger R. & Samuels Y. (2017) Scientific Reports. 7, 16345.

Genetic and Functional Analysis of GRIN2A in Tumor Samples

Prickett T. D., Gartner J. J. & Samuels Y. (2017) NMDA Receptors . p. 93-116

Synonymous Somatic Variants in Human Cancer Are Not Infamous: A Plea for Full Disclosure in Databases and Publications

Soussi T., Taschner P. E. M. & Samuels Y. (2017) Human Mutation. 38, 4, p. 339-342

2016

Vectors, compositions and methods for endogenous epitope tagging of target genes

Samuels Y. & Emmanuel R. (2016) IPC No. G01N 33/ 53 A I, Patent No. WO2016113733, 17 Nov 2015, Priority No. US201562256153P

Oncogenic PIK3CA mutations reprogram glutamine metabolism in colorectal cancer

Hao Y., Samuels Y., Li Q., Krokowski D., Guan B., Wang C., Jin Z., Dong B., Cao B., Feng X., Xiang M., Xu C., Fink S., Meropol N. J., Xu Y., Conlon R. A., Markowitz S., Kinzler K. W., Velculescu V. E., Brunengraber H., Willis J. E., LaFramboise T., Hatzoglou M., Zhang G., Vogelstein B. & Wang Z. (2016) Nature Communications. 7, 11971.

Parkin Somatic Mutations Link Melanoma and Parkinson's Disease

Levin L., Srour S., Gartner J., Kapitansky O., Qutob N., Dror S., Golan T., Dayan R., Brener R., Ziv T., Khaled M., Schueler-Furman O., Samuels Y. & Levy C. (2016) Journal of Genetics and Genomics. 43, 6, p. 369-379

Parkinson disease (PARK) genes are somatically mutated in cutaneous melanoma

Inzelberg R., Samuels Y., Azizi E., Qutob N., Inzelberg L., Domany E., Schechtman E. & Friedman E. (2016) Neurology: Genetics. 2, 3, e70.

The involvement of mutant Rac1 in the formation of invadopodia in cultured melanoma cells

Revach O. Y., Winograd-Katz S. E., Samuels Y. & Geiger B. (2016) Experimental Cell Research. 343, 1, p. 82-88

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

Kalaora S., Barnea E., Merhavi-Shoham E., Qutob N., Teer J. K., Shimony N., Schachter J., Rosenberg S. A., Besser M. J., Admon A. & Samuels Y. (2016) Oncotarget. 7, 5, p. 5110-5117

2015

Recurrent inactivating RASA2 mutations in melanoma

Arafeh R., Qutob N., Emmanuel R., Keren-Paz A., Madore J., Elkahloun A., Wilmott J. S., Gartner J. J., Di Pizio A., Winograd-Katz S., Sindiri S., Rotkopf R., Dutton-Regester K., Johansson P., Pritchard A. L., Waddell N., Hill V. K., Lin J. C., Hevroni Y., Rosenberg S. A., Khan J., Ben-Dor S., Niv M. Y., Ulitsky I., Mann G. J., Scolyer R. A., Hayward N. K. & Samuels Y. (2015) Nature Genetics. 47, 12, p. 1408-1410

The functional relevance of somatic synonymous mutations in melanoma and other cancers

Gotea V., Gartner J. J., Qutob N., Elnitski L. & Samuels Y. (2015) Pigment Cell and Melanoma Research. 28, 6, p. 673-684

Downregulation of the Ubiquitin Ligase RNF125 Underlies Resistance of Melanoma Cells to BRAF Inhibitors via JAK1 Deregulation

Kim H., Frederick D., Levesque M., Cooper Z., Feng Y., Krepler C., Brill L., Samuels Y., Hayward N., Perlina A., Piris A., Zhang T., Halaban R., Herlyn M., Brown K., Wargo J., Dummer R., Flaherty K. & Ronai Z. (2015) Cell Reports. 11, 9, p. 1458-1473

Genomic Classification of Cutaneous Melanoma

Samuels Y. (2015) Cell. 161, 7, p. 1681-1696

The cancer genome

Samuels Y., Bardelli A., Gartner J. J. & López-Otin C. (2015) Cancer: Principles & Practice of Oncology: Primer of the Molecular Biology of Cancer: Second Edition .

YAP and the drug resistance highway

Keren-Paz A., Emmanuel R. & Samuels Y. (2015) Nature Genetics. 47, 3, p. 193-194

The cancer genome

Samuels Y., Bardelli A., Gartner J. J. & López-Otin C. (2015) DeVita, Hellman, and Rosenberg's Cancer: Principles & Practice of Oncology: Tenth Edition .

2014

Mutational and functional analysis of the tumor-suppressor PTPRD in human melanoma

Walia V., Prickett T. D., Kim J. S., Gartner J. J., Lin J. C., Zhou M., Rosenberg S. A., Elble R. C., Solomon D. A., Waldman T. & Samuels Y. (2014) Human Mutation. 35, 11, p. 1301-1310

Somatic mutation of GRIN2A in malignant melanoma results in loss of tumor suppressor activity via aberrant NMDAR complex formation

Prickett T. D., Zerlanko B. J., Hill V. K., Gartner J. J., Qutob N., Jiang J., Simaan M., Wunderlich J., Gutkind J. S., Rosenberg S. A. & Samuels Y. (2014) Journal of Investigative Dermatology. 134, 9, p. 2390-2398

Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions

Lu Y. C., Yao X., Crystal J. S., Li Y. F., El-Gamil M., Gross C., Davis L., Dudley M. E., Yang J. C., Samuels Y., Rosenberg S. A. & Robbins P. F. (2014) Clinical Cancer Research. 20, 13, p. 3401-3410

Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin

Prickett T. D., Zerlanko B., Gartner J. J., Parker S. C. J., Dutton-Regester K., Lin J. C., Teer J. K., Wei X., Jiang J., Chen G., Davies M. A., Gershenwald J. E., Robinson W., Robinson S., Hayward N. K., Rosenberg S. A., Margulies E. H. & Samuels Y. (2014) Journal of Investigative Dermatology. 134, 2, p. 452-460

A highly recurrent RPS27 5'UTR mutation in melanoma

Dutton-Regester K., Gartner J. J., Emmanuel R., Qutob N., Davies M. A., Gershenwald J. E., Robinson W., Robinson S., Steven A. R., Scolyer R. A., Mann G. J., Thompson J. F., Hayward N. K. & Samuels Y. (2014) Oncotarget. 5, 10, p. 2912-2917

The head and neck cancer cell oncogenome: A platform for the development of precision molecular therapies

Martin D., Abba M., Molinolo A., Vitale-Cross L., Wang Z., Zaida M., Delic N., Samuels Y., Lyons J. & Gutkind J. (2014) Oncotarget. 5, 19, p. 8906-8923

2013

ERBB4 mutation analysis: Emerging molecular target for melanoma treatment

Lau C., Killian K. J., Samuels Y. & Rudloff U. (2013) Molecular Diagnostics For Melanoma : Methods And Protocols . Marincola F. M. & Thurin M.(eds.). p. 461-480

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

Gartner J. J., Parker S. C., Prickett T. D., Dutton-Regester K., Stitzel M. L., Lin J. C., Davis S., Simhadri V. L., Jha S., Katagiri N., Gotea V., Teer J. K., Wei X., Morken M. A., Bhanot U. K., Chen G., Elnitski L. L., Davies M. A., Gershenwald J. E., Carter H., Karchin R., Robinson W., Robinson S., Rosenberg S. A., Collins F. S., Parmigiani G., Komar A. A., Kimchi-Sarfaty C., Hayward N. K., Margulies E. H. & Samuels Y. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110, 33, p. 13481-13486

Shimmer: Detection of genetic alterations in tumors using next-generation sequence data

Hansen N. F., Gartner J. J., Mei L., Samuels Y. & Mullikin J. C. (2013) Bioinformatics. 29, 12, p. 1498-1503

Mutated PPP1R3B is recognized by T cells used to treat a melanoma patient who experienced a durable complete tumor regression

Lu Y. C., Yao X., Li Y. F., El-Gamil M., Dudley M. E., Yang J. C., Almeida J. R., Douek D. C., Samuels Y., Rosenberg S. A. & Robbins P. F. (2013) Journal of Immunology. 190, 12, p. 6034-6042

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

Robbins P. F., Lu Y., El-Gamil M., Li Y. F., Gross C., Gartner J., Lin J. C., Teer J. K., Cliften P., Tycksen E., Samuels Y. & Rosenberg S. A. (2013) Nature Medicine. 19, 6, p. 747-752

Somatic mutation of the NMDAR subunit GRIN2A in malignant melanoma results in loss of tumor suppressor activity

Prickett T., Hill V., Gartner J., Zerlanko B., Jiang J., Samaan M., Wunderlich J., Gutkind S., Rosenberg S. & Samuels Y. (2013) Cancer Research. 73, 8,

The Genetics of Melanoma: Recent Advances

Hill V. K., Gartner J. J., Samuels Y. & Goldstein A. M. (2013) Annual Review of Genomics and Human Genetics. 14, p. 257-279

2012

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

Gartner J., Davis S., Wei X., Lin J., Trivedi N., Teer J., Meltzer P., Rosenberg S. & Samuels Y. (2012) BMC Genomics. 13, 1, 505.

Molecular pathways: Dysregulated glutamatergic signaling pathways in cancer

Prickett T. & Samuels Y. (2012) Clinical Cancer Research. 18, 16, p. 4240-4246

Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes

Parker S., Gartner J., Cardenas-Navia I., Wei X., Abaan H., Ajay S., Hansen N., Song L., Bhanot U., Killian J., Gindin Y., Walker R., Meltzer P., Mullikin J., Furey T., Crawford G., Rosenberg S., Samuels Y. & Margulies E. (2012) PLoS Genetics. 8, 8, e1002871.

Delving into somatic variation in sporadic melanoma

Walia V., Mu E. W., Lin J. C. & Samuels Y. (2012) Pigment Cell and Melanoma Research. 25, 2, p. 155-170

2011

Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma

Prickett T., Wei X., Cardenas-Navia I., Teer J., Lin J., Walia V., Gartner J., Jiang J., Cherukuri P., Molinolo A., Davies M., Gershenwald J., Stemke-Hale K., Rosenberg S., Margulies E. & Samuels Y. (2011) Nature Genetics. 43, 11, p. 1119-1126

Mutations of the PIK3CA gene in human cancers

Samuels Y., Velculescu V., Kinzler K. W. & Vogelstein B. (2011) 02 Mar 2004,

Mutational inactivation of STAG2 causes aneuploidy in human cancer

Solomon D., Kim T., Diaz-Martinez L., Fair J., Elkahloun A., Harris B., Toretsky J., Rosenberg S., Shukla N., Ladanyi M., Samuels Y., James C., Yu H., Kim J. & Waldman T. (2011) Science. 333, 6045, p. 1039-1043

Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma

Wei X., Moncada-Pazos A., Cal S., Soria-Valles C., Gartner J., Rudloff U., Lin J., Rosenberg S., Lopez-Otin C. & Samuels Y. (2011) Human Mutation. 32, 6, p. E2148-E2175

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

Wei X., Walia V., Lin J., Teer J., Prickett T., Gartner J., Davis S., Stemke-Hale K., Davies M., Gershenwald J., Robinson W., Robinson S., Rosenberg S. & Samuels Y. (2011) Nature Genetics. 43, 5, p. 442-446

Oncogenic Mutations of PIK3CA in Human Cancers

Samuels Y. & Waldman T. (2011) PHOSPHOINOSITIDE 3-KINASE IN HEALTH AND DISEASE, VOL 2 . p. 21-41 (trueCurrent Topics in Microbiology and Immunology).

2010

Mutational and functional analysis reveals ADAMTS18 metalloproteinase as a novel driver in melanoma

Wei X., Prickett T., Viloria C., Molinolo A., Lin J., Cardenas-Navia I., Cruz P., Rosenberg S., Davies M., Gershenwald J., Lopez-Otin C. & Samuels Y. (2010) Molecular Cancer Research. 8, 11, p. 1513-1525

Novel somatic mutations in heterotrimeric G proteins in melanoma

Cardenas-Navia L., Cruz P., Lin J., Rosenberg S. & Samuels Y. (2010) Cancer Biology & Therapy. 10, 1, p. 33-37

IDH1R132 mutation identified in one human melanoma metastasis, but not correlated with metastases to the brain

Lopez G., Reitman Z., Solomon D., Waldman T., Bigner D., McLendon R., Rosenberg S., Samuels Y. & Yan H. (2010) Biochemical and Biophysical Research Communications. 398, 3, p. 585-587

Erratum: Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation (Proceedings of the National Academy of Sciences of the United States of America (2010) 107 (2598-2603) DOI: 10.1073/pnas.0914018107)

Ericson K., Gan C., Cheong I., Rago C., Samuels Y., Velculescu V. E., Kinzler K. W., Huso D. L., Vogelstein B. & Papadopoulos N. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107, 14, p. 6551

A growing family: Adding mutated Erbb4 as a novel cancer target

Rudloff U. & Samuels Y. (2010) Cell Cycle. 9, 8, p. 1487-1503

Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation

Ericson K., Gan C., Cheong I., Rago C., Samuels Y., Velculescu V., Kinzler K., Huso D., Vogelstein B. & Papadopoulos N. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107, 6, p. 2598-2603

TYRO3-mediated regulation of MITF: A novel target in melanoma?

Rudloff U. & Samuels Y. (2010) Pigment Cell and Melanoma Research. 23, 1, p. 9-11

2009

Protective roles of matrix metalloproteinases: From mouse models to human cancer

Lopez-Otin C., Palavalli L. H. & Samuels Y. (2009) Cell Cycle. 8, 22, p. 3657-3662

Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4

Prickett T., Agrawal N., Wei X., Yates K., Lin J., Wunderlich J., Cronin J., Cruz P., Rosenberg S. & Samuels Y. (2009) Nature Genetics. 41, 10, p. 1127-1132

Frequent mutations in the MITF pathway in melanoma

Cronin J., Wunderlich J., Loftus S., Prickett T., Wei X., Ridd K., Vemula S., Burrell A., Agrawal N., Lin J., Banister C., Buckhaults P., Rosenberg S., Bastian B., Pavan W. & Samuels Y. (2009) Pigment Cell & Melanoma Research. 22, 4, p. 435-444

Lack of inherited mutations of PTPRD in familial melanoma and melanoma-astrocytoma syndrome

Solomon D., Kim J., Yang X., Tucker M., Goldstein A., Samuels Y. & Waldman T. (2009) Pigment Cell and Melanoma Research. 22, 4, p. 489-491

Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma

Palavalli L., Prickett T., Wunderlich J., Wei X., Burrell A., Porter-Gill P., Davis S., Wang C., Cronin J., Agrawal N., Lin J., Westbroek W., Hoogstraten-Miller S., Molinolo A., Fetsch P., Filie A., O'Connell M., Banister C., Howard J., Buckhaults P., Weeraratna A., Brody L., Rosenberg S. & Samuels Y. (2009) Nature Genetics. 41, 5, p. 518-520

2008

Mutational inactivation of PTPRD in glioblastoma multiforme and malignant melanoma

Solomon D., Kim J., Cronin J., Sibenaller Z., Ryken T., Rosenberg S., Ressom H., Jean W., Bigner D., Yan H., Samuels Y. & Waldman T. (2008) Cancer Research. 68, 24, p. 10300-10306

2007

The structure of a human p110 alpha/p85 alpha complex elucidates the effects of oncogenic PI3K alpha mutations

Huang C., Mandelker D., Schmidt-Kittler O., Samuels Y., Velculescu V., Kinzler K., Vogelstein B., Gabelli S. & Amzel L. (2007) Science. 318, 5857, p. 1744-1748

Serial assessment of human tumor burdens in mice by the analysis of circulating DNA

Rago C., Huso D., Diehl F., Karim B., Liu G., Papadopoulos N., Samuels Y., Velculescu V., Vogelstein B., Kinzler K. & Diaz L. (2007) Cancer Research. 67, 19, p. 9364-9370

2006

iASPP preferentially binds p53 proline-rich region and modulates apoptotic function of codon 72-polymorphic p53

Bergamaschi D., Samuels Y., Sullivan A., Zvelebil M., Breyssens H., Bisso A., Del Sal S. G., Syed N., Smith P., Gasco M., Crook T. & Lu X. (2006) Nature Genetics. 38, 10, p. 1133-1141

Sequence mutations and amplification of PIK3CA and AKT2 genes in purified ovarian serous neoplasms

Nakayama K., Nakayama N., Kurman R., Cope L., Pohl G., Samuels Y., Velculescu V., Wang T. & Shih L. (2006) Cancer Biology & Therapy. 5, 7, p. 779-785

Oncogenic PI3K and its role in cancer

Samuels Y. & Ericson K. (2006) Current Opinion in Oncology. 18, 1, p. 77-82

2005

Colorectal cancer: Mutations in a signalling pathway

Parsons D., Wang T., Samuels Y., Bardelli A., Cummins J., DeLong L., Silliman N., Ptak J., Szabo S., Willson J., Markowitz S., Kinzler K., Vogelstein B., Lengauer C. & Velculescu V. (2005) Nature. 436, 7052, p. 792

Mutant PIK3CA promotes cell growth and invasion of human cancer cells

Samuels Y., Diaz L., Schmidt-Kittler O., Cummins J., DeLong L., Cheong I., Rago C., Huso D., Lengauer C., Kinzler K., Vogelstein B. & Velculescu V. (2005) Cancer Cell. 7, 6, p. 561-573

Mdm2 and mdmX prevent ASPP1 and ASPP2 from stimulating p53 without targeting p53 for degradation

Bergamaschi D., Samuels Y., Zhong S. & Lu X. (2005) Oncogene. 24, 23, p. 3836-3841

Inhibiting phosphoinositide 3-kinases

Samuels Y., Zhu J. & Lengauer C. (2005) Cancer Biology and Therapy. 4, 5, p. 546-547

Erratum: The PIK3CA gene is mutated with high frequency in human breast cancers (Cancer Biology and Therapy (2004) 3 (772-775))

Lin L., Bachman K. E., Ellis M., Ben H. P., Bachman K. E., Argani P., Samuels Y., Silliman N., Ptak J., Szabo S., Konishi H., Karakas B., Blair B. G., Lin C., Peters B. A., Velculescu V. E. & Park B. H. (2005) Cancer Biology and Therapy. 4, 2, p. 133

2004

Oncogenic mutations of PIK3CA in human cancers

Samuels Y. & Velculescu V. (2004) Cell Cycle. 3, 10, p. 1221-1224

The PIK3CA gene is mutated with high frequency in human breast cancers

Bachman K., Argani P., Samuels Y., Silliman N., Ptak J., Szabo S., Konishi H., Karakas B., Blair B., Lin C., Peters B., Velculescu V. & Park B. (2004) Cancer Biology and Therapy. 3, 8, p. 772-775

High Frequency of Mutations of the PIK3CA Gene in Human Cancers

Samuels Y., Wang Z., Bardelli A., Silliman N., Ptak J., Szabo S., Yan H., Gazdar A., Powell D., Riggins G., Willson J., Markowitz S., Kinzler K., Vogelstein B. & Velculescu V. (2004) Science. 304, 5670, p. 554

ASPP1 and ASPP2: Common Activators of p53 Family Members

Bergamaschi D., Samuels Y., Jin B., Duraisingham S., Crook T. & Lu X. (2004) Molecular and Cellular Biology. 24, 3, p. 1341-1350

2003

iASPP oncoprotein is a key inhibitor of p53 conserved from worm to human

Bergamaschi D., Samuels Y., O'Neil N., Trigiante G., Crook T., Hsieh J., O'Connor D., Zhong S., Campargue I., Tomlinson M., Kuwabara P. & Lu X. (2003) Nature Genetics. 33, 2, p. 162-167

1999

Prevalence of anti-hepatitis A antibodies, hepatitis B viral markers, and anti-hepatitis C antibodies among immigrants from the former USSR who arrived in Israel during 1990-1991

Almog R., Low M., Cohen D., Robin G., Ashkenazi S., Bercovier H., Gdalevich M., Samuels Y., Ashkenazi I., Shemer J., Eldad A. & Green M. S. (1999) Infection. 27, 3, p. 212-217

1998

Co-stimulation-dependent activation of a JNK-kinase in T lymphocytes

Avraham A., Jung S., Samuels Y., Seger R. & Ben-Neriah Y. (1998) European Journal of Immunology. 28, 8, p. 2320-2330