Key papers highlighted Lab members underlined
*equal authorship

Markus H, Zhao J, Contente-Cuomo T, Raupach E, Odenheimer-Bergman A, Connor S, McDonald BR, Hutchins E, McGilvery M, de la Maza MC, Van Keuren Jensen K, Pirrotte P, Goel A, Becerra C, Von Hoff DD, Celinski SA, Hingorani P, Murtaza M.
Sub-nucleosomal organization in urine cell-free DNA
Pre-print online at bioRxiv (doi:10.1101/696633)

McDonald BRContente-Cuomo T, Sammut SJ, Odenheimer-Bergman A, Ernst B, Perdigones N, Chin SF, Farooq M, Mejia R, Cronin PA, Anderson KS, Kosiorek HE, Northfelt DW, McCullough AE, Patel BK, Weitzel JN, Slavin TP, Caldas C, Pockaj BA, Murtaza M 
Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer. 
Pre-print online at bioRxiv (doi:10.1101/425470)

In Press
Lorch G, Sivaprakasam K, Zismann V, Perdigones N, Contente-Cuomo T, Nazareno A, Facista S, Wong S, Liang WS, Amman JM, Sinicropi-Yao SL, Koenig MJ, Perle KL, Whitsett TG, Murtaza M, Trent J, Carbone DP, Hendricks WPD.
Identification of frequent activating HER2 mutations in primary canine pulmonary adenocarcinoma.
Pre-print online on bioRxiv (doi: 10.1101/528182)

In Press
De Mattos-Arruda L, Sammut SJ, Ross E, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda O, Chin SF, Ali R, Cope W, Tiezzi D, Contente-Cuomo T, Mayor R, Arias A, Reshef D, Martinez E, Peg V, Ramon y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C. 
The genomic and immune landscapes of lethal metastatic breast cancer.
Cell Reports (2019 May, PMID: 31141692)

CRUK blog
Farooq M, Murtaza M.
Circulating tumor DNA analysis and opportunities for personalized cancer medicine.
Companion and Complementary Diagnostics: From Biomarker Discovery to Clinical Implementation (2019 May, doi: 10.1016/B978-0-12-813539-6.00011-0)

Book Chapter
Hurth C, Contente-Cuomo T, Murtaza M, Zenhausern F.
Influence of a single nucleotide polymorphism and DNA hybridization on the drying patterns of micro droplets.
Journal of Nanomedicine (2018 Jun)

Tsui DWY*, Murtaza M*, Wong ASC, Rueda OM, Smith CG, Chandrananda D, Soo RA, Lim HL, Goh BC, Caldas C, Forshew T, Gale D, Liu W, Morris J, Marass F, Eisen T, Chin TM, Rosenfeld N.
Dynamics of multiple resistance mechanisms in plasma DNA during EGFR-targeted therapies in non-small cell lung cancer.
EMBO Molecular Medicine (2018 Jun, PMID: 29848757

Markus H, Contente-Cuomo T, Farooq M, Liang WS, Borad MJ, Sivakumar S, Gollins S, Tran NL, Dhruv HD, Berens M, Bryce A, Sekulic A, Ribas A, Trent J, LoRusso PM, Murtaza M.
Evaluation of pre-analytical factors affecting plasma DNA analysis. 
Scientific Reports (2018 May, doi:10.1038/s41598-018-25810-0)

TGen press release
Perdigones NMurtaza M
Capturing tumor heterogeneity and clonal evolution in solid cancers using circulating tumor analysis. 
Pharmacology and Therapeutics (2017 Feb, PMID: 28167216)

Tsui DWY, Murtaza M
Applications of circulating DNA analysis in personalized medicine.
Cancer Genetics and Genomics for Personalized Medicine (In Press, ISBN: 9789814669870)

Book Chapter
Hendricks WPD, Sekulic A, Bryce AH, Murtaza M, Ramos P, Trent JM. 
Cancer Genomics and Evolution.
Holland-Frei Cancer Medicine (ISBN: 9781118934692)

Book Chapter
Murtaza M, Caldas C. 
Nucleosome mapping in plasma DNA predicts cancer gene expression. 
Nature Genetics (2016 Sep, PMID: 27681289)

News and Views
Murtaza M*, Dawson SJ*, Provenzano E, Grant J, Chin SF, Tsui DWY, Marass F, Gale D, Ali HR, Shah P, Contente-Cuomo T, Farahani H, Shumansky K, Kingsbury Z, Humphray S, Bentley D, Shah SP, Wallis M, Rosenfeld N, Caldas C. 
Multifocal clonal evolution characterized using circulating tumor DNA in a case of metastatic breast cancer. 
Nature Communications (2015 Nov, PMID: 26530965)

TGen press release
Mayo press release and video
JAMA Lab Reports
Genome Web

Schwarz RF, Ng CK, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD.
Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
PLoS Medicine (2015 Feb, PMID: 25710373)

Beaufort CM, Helmijr JC, Piskorz AM, Hoogstraat M, Ruigrok-Ritstier K, Besselink N, Murtaza M, van IJcken WF, Heine AA, Smid M, Koudijs MJ, Brenton JD, Berns EM, Helleman J.
Ovarian cancer cell line panel (OCCP): clinical importance of in vitro morphological subtypes.
PLoS One (2014 Sep, PMID: 25230021)

Weaver JM, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CA, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PA, Rosenfeld N, Tavaré S, Fitzgerald RC; OCCAMS Consortium.
Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.
Nature Genetics (2014 Aug, PMID: 24952744)

Gossage L, Murtaza M, Slatter AF, Lichtenstein CP, Warren A, Haynes B, Marass F, Roberts I, Shanahan SJ, Claas A, Dunham A, May AP, Rosenfeld N, Forshew T, Eisen T.
Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma.
Genes, Chromosomes and Cancer (2014 Jan, PMID: 24166983)

Murtaza M*, Dawson SJ*, Tsui DWY*, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong ASC, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N. 
Noninvasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. 
Nature (2013 May, PMID: 23563269)

Nature Medicine Community Corner
Genome Web
CRUK Press Release
Cambridge Press Release
Genome Web
Dawson SJ, Tsui D, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N. 
Circulating Tumor DNA to Monitor Metastatic Breast Cancer. 
New England Journal of Medicine (2013 Mar, PMID: 23484797)

NEJM Editorial
Nature News
Science Translational Medicine Editor's Choice
Nature Reviews Clinical Oncology Highlight
Lancet Oncology News
Genome Web
Forshew T*, Murtaza M*, Parkinson C*, Gale D*, Tsui DWY*, Kaper F, Dawson SJ, Piskorz AM, Jimenez-Linan M, Bentley D, Hadfield J, May AP, Caldas C, Brenton JD, Rosenfeld N. 
Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. 
Science Translational Medicine (2012 May, PMID: 22649089

Genome Web