Martin Aryee

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment.

Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CF, Liss AS, Ting DT, Jacks T, Regev A.

Nat Genet. 2022 08. 54(8):1178-1191. PMID: 35902743

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery.

Siegenfeld AP, Roseman SA, Roh H, Lue NZ, Wagen CC, Zhou E, Johnstone SE, Aryee MJ, Liau BB.

Nat Commun. 2022 07 20. 13(1):4199. PMID: 35859152

Author Correction: 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. 2022 Jul. 19(7):899. PMID: 35761069

Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer.

Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT.

Cancer Discov. 2022 06 02. 12(6):1462-1481. PMID: 35320348

EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma.

Möller E, Praz V, Rajendran S, Dong R, Cauderay A, Xing YH, Lee L, Fusco C, Broye LC, Cironi L, Iyer S, Rengarajan S, Awad ME, Naigles B, Letovanec I, Ormas N, Finzi G, La Rosa S, Sessa F, Chebib I, Petur Nielsen G, Digklia A, Spentzos D, Cote GM, Choy E, Aryee M, Stamenkovic I, Boulay G, Rivera MN, Riggi N.

Nat Commun. 2022 04 27. 13(1):2267. PMID: 35477713

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.

Ludwig LS, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, Muus C, Fiorini C, Olive ME, Vockley CM, Munschauer M, Hunter A, Ogura H, Yamamoto T, Inada H, Nakagawa S, Ohzono S, Subramanian V, Chiarle R, Glader B, Carr SA, Aryee MJ, Kundaje A, Orkin SH, Regev A, McCavit TL, Kanno H, Sankaran VG.

Blood. 2022 04 21. 139(16):2534-2546. PMID: 35030251

CRISPR-Cas9 treatment partially restores amyloid-ß 42/40 in human fibroblasts with the Alzheimer's disease PSEN1 M146L mutation.

Konstantinidis E, Molisak A, Perrin F, Streubel-Gallasch L, Fayad S, Kim DY, Petri K, Aryee MJ, Aguilar X, György B, Giedraitis V, Joung JK, Pattanayak V, Essand M, Erlandsson A, Berezovska O, Ingelsson M.

Mol Ther Nucleic Acids. 2022 Jun 14. 28:450-461. PMID: 35505961

Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma.

Lietz CE, Newman ET, Kelly AD, Xiang DH, Zhang Z, Luscko CA, Lozano-Calderon SA, Ebb DH, Raskin KA, Cote GM, Choy E, Nielsen GP, Haibe-Kains B, Aryee MJ, Spentzos D.

Commun Biol. 2022 03 08. 5(1):213. PMID: 35260776

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