Publications

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# Co-first authors; * Corresponding authors

Boulay G#, Broye L#, Dong R#, Iyer S, Sanalkumar R, Xing YH, Buisson R, Rengarajan S, Naigles B, Duc B, Volorio A, Awad M, Renella R, Chebib I, Nielsen P, Choy E, Cote G, Zou L, Letovanec I, Stamenkovic I, Rivera NM*, Riggi N*. EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in desmoplastic small round cell tumors. Nat. Commun., 2024, 15, 7460.
Takahashi M#, Chong BH, Zhang S, Yang TY, Matthew JL, Harry S, Maynard M, Hilbert B, White DR, Murrey EH, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali A, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen QM, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher ED, Maheswaran S, Haber AD, Boland MG, Sade-Feldman M, Jenkins WR, Hata NA, Bardeesy MN, Suvà LM, Martin RB, Liau BB, Ott JC, Rivera NM, Lawrence SM*, Bar-PeledDrug L*. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell, 2024, doi: 10.1101/2023.10.20.563287.

Xing YH#, Dong R#, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera NM*. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat. Biotechnol., 2023: 1-13.
Sanalkumar R#, Dong R#, Xing YH, Lee L, Iyer S, Letovanec I, Rosa S, Chebib I, Nielsen P, Renella R, Cote G, Choy E, Aryee M, Stegmayer K, Stamenkovic I, Rivera NM*, Riggi N*. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. Sci. Adv., 2023, 9(13): eabo3789.

Yasuhara T, Xing YH, Bauer N, Lee L, Dong R, Yadav T, Soberman R, Rivera M, Zou L, Condensates induced by transcription inhibition localize active chromatin to nucleoli. Mol. Cell, 2022, 82(15): 2738-2753.
Möller E, Praz V, Rajendran S, Dong R, Cauderay A, Xing YH, Lee L, Fusco C, Broye L, Cironi L, Iyer S, Rengarajan S, Awad M, Naigles B, Letovanec I, Ormas N, Finzi G, Rosa S, Sessa F, Chebib I, Nielsen G, Digklia A, Spentzos D, Cote G, Choy E, Aryee M, Stamenkovic I, Boulay G, Rivera M, Riggi N. EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma. Nat. Commun., 2022, 13(1): 1-18.

Dong R, Yuan GC*, SpatialDWLS: accurate deconvolution of spatial transcriptomic data. Genome Biol., 2021, 22(1): 1-10.
Dries R#, Zhu Q#, Dong R, Eng CH, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George R, Pierson N, Cai L, Yuan GC*. Giotto, a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol., 2021, 22(1): 1-31.

Dong R, Yuan GC*, GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinform., 2020 21: 1-7.

Dong R, Ma XK, Chen LL and Yang L*. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline. Methods Mol. Biol., 2019. vol 1870.
Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L*. CIRCexplorer3: A CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics, 2019, 17(5): 511-521.
Akerberg B#, Gu F#, Dusen N, Zhang X, Dong R, Li K, Zhang B, Zhou B, Sethi I, Ma Q, Wasson L, Wen T, Liu J, Dong K, Conlon F, Zhou J, Yuan GC, Zhou P, Pu W*. A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. Nat. Commun., 2019, 10(1): 1-16.
Tsoucas D*, Dong R, Chen H, Zhu Q, Guo G, Yuan GC*. Accurate estimation of cell-type composition from gene expression data. Nat. Commun., 2019, 10(1): 2975.

Dong R#, Ma XK#, Li GW, Yang L*. CIRCpedia v2: An Updated Database for Comprehensive CircRNA Annotation and Expression Comparison. Genomics Proteomics Bioinformatics, 2018, 16(4), 226-233.

Dong R#, Ma XK#, Chen LL*, Yang L*. Increased complexity of circRNA expression during species evolution. RNA Biol., 2017, 14(8):1064-1074.
Xing YH#, Yao RW#, Zhang Y#, Guo CJ, Jiang S, Xu G, Dong R, Yang L and Chen LL*. SLERT Regulates DDX21 Rings Associated with Pol I Transcription. Cell, 2017, 169(4): 664-678.
Zhong C#, Xie Z#, Yin Q#, Dong R, Yang S, Wu Y, Yang L and Li J*. Parthenogenetic haploid embryonic stem cells efficiently support mouse generation by oocyte injection. Cell Res., 2016, 26(1):131-4.
Zhang XO#, Dong R#, Zhang Y#, Zhang JL, Luo Z, Zhang J, Chen LL* and Yang L*. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res., 2016, 26(9):1277-87.
Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL and Yang L*. CircRNA-derived pseudogenes. Cell Res., 2016, 26(6):747-50.
Zhong C#, Yin Q#, Xie Z#, Bai M#, Dong R#, Tang W, Xing YH, Zhang H, Yang S, Chen LL, Bartolomei MS, Ferguson-Smith A, Li D, Yang L*, Wu Y* and Li J*. CRISPR-Cas9-Mediated Genetic Screening in Mice with Haploid Embryonic Stem Cells Carrying a Guide RNA Library. Cell Stem Cell, 2015, 17(2):221-32.
Chen T#, Xiang JF#, Zhu S#, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L* and Chen LL*. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res., 2015, 25(4):459-76.