Martin Aryee

Screening human lung cancer with predictive models of serum magnetic resonance spectroscopy metabolomics.

Schult TA, Lauer MJ, Berker Y, Cardoso MR, Vandergrift LA, Habbel P, Nowak J, Taupitz M, Aryee M, Mino-Kenudson MA, Christiani DC, Cheng LL.

Proc Natl Acad Sci U S A. 2021 12 21. 118(51). PMID: 34903652

Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq.

Malinin NL, Lee G, Lazzarotto CR, Li Y, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Iafrate AJ, Le LP, Aryee MJ, Joung JK, Tsai SQ.

Nat Protoc. 2021 12. 16(12):5592-5615. PMID: 34773119

Augmenting and directing long-range CRISPR-mediated activation in human cells.

Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK.

Nat Methods. 2021 09. 18(9):1075-1081. PMID: 34354266

Smart-RRBS for single-cell methylome and transcriptome analysis.

Gu H, Raman AT, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A.

Nat Protoc. 2021 08. 16(8):4004-4030. PMID: 34244697

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma.

Adane B, Alexe G, Seong BKA, Lu D, Hwang EE, Hnisz D, Lareau CA, Ross L, Lin S, Dela Cruz FS, Richardson M, Weintraub AS, Wang S, Iniguez AB, Dharia NV, Conway AS, Robichaud AL, Tanenbaum B, Krill-Burger JM, Vazquez F, Schenone M, Berman JN, Kung AL, Carr SA, Aryee MJ, Young RA, Crompton BD, Stegmaier K.

Cancer Cell. 2021 06 14. 39(6):827-844.e10. PMID: 34129824

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.

Shareef SJ, Bevill SM, Raman AT, Aryee MJ, van Galen P, Hovestadt V, Bernstein BE.

Nat Biotechnol. 2021 09. 39(9):1086-1094. PMID: 33958785

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.

Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B.

Biophys J. 2020 11 03. 119(9):1905-1916. PMID: 33086041

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE.

Cell. 2020 09 17. 182(6):1474-1489.e23. PMID: 32841603

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.

Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG.

Nat Biotechnol. 2021 04. 39(4):451-461. PMID: 32788668

Author Correction: Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.

Townes FW, Hicks SC, Aryee MJ, Irizarry RA.

Genome Biol. 2020 Jul 22. 21(1):179. PMID: 32698904