Publications | Page 27 | Englander Institute for Precision Medicine

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2020

Nienhold R, Ciani Y, Koelzer VH, Tzankov A, Haslbauer JD, Menter T, Schwab N, Henkel M, Frank A, Zsikla V et al.. 2020. Two distinct immunopathological profiles in autopsy lungs of COVID-19.. Nat Commun. 11(1):5086.

Chu C-S, Hellmuth JC, Singh R, Ying H-Y, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. 2020. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage.. Mol Cell. 80(5):845-861.e10.

Dooley BJ, Verma A, Ding R, Yang H, Muthukumar T, Lubetzky M, Shankaranarayanan D, Elemento O, Suthanthiran M. 2020. Urinary Cell Transcriptome Profiling and Identification of ITM2A, SLAMF6, and IKZF3 as Biomarkers of Acute Rejection in Human Kidney Allografts.. Transplant Direct. 6(8):e588.

Verma A, Muthukumar T, Yang H, Lubetzky M, Cassidy MF, Lee JR, Dadhania DM, Snopkowski C, Shankaranarayanan D, Salvatore SP et al.. 2020. Urinary cell transcriptomics and acute rejection in human kidney allografts.. JCI Insight. 5(4)

Karaoğlanoğlu F, Ricketts C, Ebren E, Rasekh MEslami, Hajirasouliha I, Alkan C. 2020. VALOR2: characterization of large-scale structural variants using linked-reads.. Genome Biol. 21(1):72.

Faquih T, van Smeden M, Luo J, le Cessie S, Kastenmüller G, Krumsiek J, Noordam R, van Heemst D, Rosendaal FR, Vlieg Avan Hylcka et al.. 2020. A Workflow for Missing Values Imputation of Untargeted Metabolomics Data.. Metabolites. 10(12)

2019

De Giorgi U, Procopio G, Giannarelli D, Sabbatini R, Bearz A, Buti S, Basso U, Mitterer M, Ortega C, Bidoli P et al.. 2019. Association of Systemic Inflammation Index and Body Mass Index with Survival in Patients with Renal Cell Cancer Treated with Nivolumab.. Clin Cancer Res. 25(13):3839-3846.

Toosi H, Moeini A, Hajirasouliha I. 2019. BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples.. BMC Bioinformatics. 20(Suppl 11):282.

Madhukar NS, Khade PK, Huang L, Gayvert K, Galletti G, Stogniew M, Allen JE, Giannakakou P, Elemento O. 2019. A Bayesian machine learning approach for drug target identification using diverse data types.. Nat Commun. 10(1):5221.

Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA. 2019. BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.. Genome Res. 29(8):1352-1362.

de Wit R, de Bono J, Sternberg CN, Fizazi K, Tombal B, Wülfing C, Kramer G, Eymard J-C, Bamias A, Carles J et al.. 2019. Cabazitaxel versus Abiraterone or Enzalutamide in Metastatic Prostate Cancer.. N Engl J Med. 381(26):2506-2518.

Fernandez EM, Eng K, Beg S, Beltran H, Faltas BM, Mosquera JMiguel, Nanus DM, Pisapia DJ, Rao RA, Robinson BD et al.. 2019. Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution.. JCO Precis Oncol. 3

Quell JD, Römisch-Margl W, Haid M, Krumsiek J, Skurk T, Halama A, Stephan N, Adamski J, Hauner H, Mook-Kanamori D et al.. 2019. Characterization of Bulk Phosphatidylcholine Compositions in Human Plasma Using Side-Chain Resolving Lipidomics.. Metabolites. 9(6)

Lee RS, Zhang L, Berger A, Lawrence MG, Song J, Niranjan B, Davies RG, Lister NL, Sandhu SK, Rubin MA et al.. 2019. Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target.. Neoplasia. 21(4):389-400.

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y et al.. 2019. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.. Cancer Cell. 35(4):603-617.e8.

Conteduca V, Oromendia C, Eng KW, Bareja R, Sigouros M, Molina A, Faltas BM, Sboner A, Mosquera JMiguel, Elemento O et al.. 2019. Clinical features of neuroendocrine prostate cancer.. Eur J Cancer. 121:7-18.

Laimighofer M, Lickert R, Fuerst R, Theis FJ, Winkler C, Bonifacio E, Ziegler A-G, Krumsiek J. 2019. Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity - indications of immune cell activation.. Sci Rep. 9(1):6250.

Vikova V, Jourdan M, Robert N, Requirand G, Boireau S, Bruyer A, Vincent L, Cartron G, Klein B, Elemento O et al.. 2019. Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance.. Theranostics. 9(2):540-553.

Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LAD, Hickman C et al.. 2019. Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization.. NPJ Digit Med. 2:21.

Courtiol P, Maussion C, Moarii M, Pronier E, Pilcer S, Sefta M, Manceron P, Toldo S, Zaslavskiy M, Le Stang N et al.. 2019. Deep learning-based classification of mesothelioma improves prediction of patient outcome.. Nat Med. 25(10):1519-1525.

Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L et al.. 2019. Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer.. Sci Transl Med. 11(484)

Skvortsova K, Masle-Farquhar E, Luu P-L, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y et al.. 2019. DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns.. Cancer Cell. 35(2):297-314.e8.

Gayvert K, Elemento O. 2019. Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity.. Methods Mol Biol. 1903:179-184.

Matejka K, Stückler F, Salomon M, Ensenauer R, Reischl E, Hoerburger L, Grallert H, Kastenmüller G, Peters A, Daniel H et al.. 2019. Dynamic modelling of an ACADS genotype in fatty acid oxidation - Application of cellular models for the analysis of common genetic variants.. PLoS One. 14(5):e0216110.

Grive KJ, Hu Y, Shu E, Grimson A, Elemento O, Grenier JK, Cohen PE. 2019. Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.. PLoS Genet. 15(3):e1007810.