Publications
We asked that our work be acknowledged in publications and presentations supported by BiNGS. Please also consider including our bioinformaticians in the authors list in cases where they contributed significantly.
Please acknowledge us with the following statement:
“The development of the Bioinformatics for Next Generation Sequencing (BiNGS) shared resource facility is partially supported by the NCI P30 (P30CA196521) Cancer Center support grant, the ISMMS Skin Biology and Disease Resource-based Center NIAMS P30 support grant (AR079200), and the Black Family Stem Cell Institute. This work was also supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai and supported by the Clinical and Translational Science Awards (CTSA) grant UL1TR004419 from the National Center for Advancing Translational Sciences. Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD026880. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”
Hung M, Lo HF, Beckmann AG, et al. Cadherin-dependent adhesion is required for muscle stem cell niche anchorage and maintenance. Development. 2024 Mar 8:dev.202387. doi: 10.1242/dev.202387
Mendelson K, Martin TC, Nguyen CB, et al. Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation. JCI Insight. 2024 Feb 6:e166611. doi: 10.1172/jci.insight.166611
Chakraborty S, Coleman C, Manoj P, et al. De novo and histologically transformed small cell lung cancer is sensitive to lurbinectedin treatment through the modulation of EMT and NOTCH signaling pathways. Clin Cancer Res. 2023 Jun 29:CCR-23-0471. doi: 10.1158/1078-0432.CCR-23-0471
Efe G, Dunbar KJ, Sugiura K, et al. p53 gain-of-function mutation induces metastasis via Brd4-dependent Csf-1 expression. Cancer Discov. 2023 Sep 7. doi: 10.1158/2159-8290.CD-23-0601
Filipescu, D., Carcamo, S., Agarwal, A. et al. MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. Nat Cell Biol (2023). https://doi.org/10.1038/s41556-023-01208-7
Kotini AG, Carcamo S, Cruz-Rodriguez N, et al. Patient-Derived iPSCs Faithfully Represent the Genetic Diversity and Cellular Architecture of Human Acute Myeloid Leukemia. Blood Cancer Discov. 2023 Apr 17:OF1-OF18. doi: 10.1158/2643-3230.BCD-22-0167
Mohammed Ismail W, Mazzone A, Ghiraldini FG, et al. MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming. Commun Biol. 2023 Feb 23;6(1):215. doi: 10.1038/s42003-023-04571-1
Proteau S, Krossa I, Husser C, et al. LKB1-SIK2 loss drives uveal melanoma proliferation and hypersensitivity to SLC8A1 and ROS inhibition. EMBO Mol Med. 2023 Nov 15:e17719. doi: 10.15252/emmm.202317719
Rialdi A, Duffy M, Scopton AP, et al. WNTinib is a multi-kinase inhibitor with specificity against β-catenin mutant hepatocellular carcinoma. Nat Cancer. 2023 Aug 3. doi: 10.1038/s43018-023-00609-9
Sen U, Coleman C, Sen T. Stearoyl coenzyme A desaturase-1: multitasker in cancer, metabolism, and ferroptosis. Trends Cancer. 2023 Apr 5:S2405-8033(23)00032-8. doi: 10.1016/j.trecan.2023.03.003
Singh DK, Carcamo S, Farias EF, et al. 5-Azacytidine- and retinoic-acid-induced reprogramming of DCCs into dormancy suppresses metastasis via restored TGF-β-SMAD4 signaling. Cell Rep. 2023 May 29:112560. doi: 10.1016/j.celrep.2023.112560
Tamari M, Del Bel KL, Ver Heul AM, et al. Sensory neurons promote immune homeostasis in the lung. Cell. 2023 Dec 13:S0092-8674(23)01313-2. doi: 10.1016/j.cell.2023.11.027
Thrane K, Winge MCG, Wang H, et al. Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. J Invest Dermatol. 2023 May 2:S0022-202X(23)02040-7. doi: 10.1016/j.jid.2023.02.040
Torre D, Fstkchyan YS, Ho JSY, et al. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell. 2023 November 22. doi: 10.1016/j.molcel.2023.10.036
Carcamo, S., Nguyen, B.C., Grossi, E. et al. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Reports 39, 1, 110637 (2022). https://doi.org/10.1016/j.celrep.2022.110637
Esposito, D., Pant, I., Shen, Y. et al. ROCK1 mechano-signaling dependency of human malignancies driven by TEAD/YAP activation. Nat Commun 13, 703 (2022). https://doi.org/10.1038/s41467-022-28319-3
Schoenfeld DA, Zhou R, Zairis S, et al. Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma. Mol Cancer Res. 2022 Aug 5;20(8):1193-1207. https://doi.org/10.1158/1541-7786.mcr-21-1039
Sun D, Singh DK, Carcamo S, et al. MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells. Sci Adv. 2022 Dec 2;8(48):eabo0876. doi: 10.1126/sciadv.abo0876
Wang, P., Karakose, E., et al. Disrupting the DREAM complex enables proliferation of adult human pancreatic beta cells. The Journal of Clinical Investigation (2022). https://doi.org/10.1172/JCI157086
Zhou, R.W., Xu, J., Martin, T.C. et al. A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nat Commun 13, 6041 (2022). https://doi.org/10.1038/s41467-022-33377-8
Kang C, Rostoker R, Ben-Shumel S, et al. TMEM176B Regulates AKT/mTOR Signaling and Tumor Growth in Triple-Negative Breast Cancer. Cells. 2021; 10(12):3430. https://doi.org/10.3390/cells10123430
Khalil BD, Sanchez R, Rahman T, et al. An NR2F1-specific agonist suppresses metastasis by inducing cancer cell dormancy. J Exp Med. 2021; 219(1):e20210836. https://doi.org/10.1084/jem.20210836
Group, P.T.C., Calabrese, C., Davidson, N.R., et al. (2020). Genomic basis for RNA alterations in cancer. Nature 578, 129-136. https://doi.org/10.1038/s41586-020-1970-0
Han, B.Y., Seah, M.K.Y., Brooks, I.R., et al. (2020). Global translation during early development depends on the essential transcription factor PRDM10. Nat Commun 11, 3603. https://doi.org/10.1038/s41467-020-17304-3
Mzoughi, S., Fong, J.Y., Papadopoli, D., et al. (2020b). PRDM15 is a key regulator of metabolism critical to sustain B-cell lymphomagenesis. Nat Commun 11, 3520. https://doi.org/10.1038/s41467-020-17064-0
Chung, V.Y., Tan, T.Z., Ye, J., et al. (2019). The role of GRHL2 and epigenetic remodeling in epithelial-mesenchymal plasticity in ovarian cancer cells. Commun Biol 2, 272. https://doi.org/10.1038/s42003-019-0506-3
Demircioglu, D., Cukuroglu, E., Kindermans, M., et al. (2019). A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell 178, 1465-1477 e1417. https://doi.org/10.1016/j.cell.2019.08.018
Fong, J.Y., Pignata, L., Goy, P.A., et al. (2019). Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation. Cancer Cell 36, 194-209 e199. https://doi.org/10.1016/j.ccell.2019.07.003
Pobbati, A.V., Mejuch, T., Chakraborty, S., et al. (2019). Identification of Quinolinols as Activators of TEAD-Dependent Transcription. ACS Chem Biol 14, 2909-2921. https://doi.org/10.1021/acschembio.9b00786
Qadeer, Z.A., Valle-Garcia, D., Hasson, D., et al. (2019). ATRX In-Frame Fusion Neuroblastoma Is Sensitive to EZH2 Inhibition via Modulation of Neuronal Gene Signatures. Cancer Cell 36, 512-527 e519. https://doi.org/10.1016/j.ccell.2019.09.002
Seah, M.K.Y., Wang, Y., Goy, P.A., et al. (2019). The KRAB-zinc-finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons. Development 146. https://doi.org/10.1242/dev.170266
Steinbach, N., Hasson, D., Mathur, D., et al. (2019). PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. Nucleic Acids Res 47, 5573-5586. https://doi.org/10.1093/nar/gkz272
Wang, S., Zhang, C., Hasson, D., et al. (2019). Epigenetic Compensation Promotes Liver Regeneration. Dev Cell 50, 43-56 e46. https://doi.org/10.1016/j.devcel.2019.05.034
Yu, J.X., Craig, A.J., Duffy, M.E., et al. (2019). Phenotype-Based Screens with Conformation-Specific Inhibitors Reveal p38 Gamma and Delta as Targets for HCC Polypharmacology. Mol Cancer Ther 18, 1506-1519. https://dx.doi.org/10.1158%2F1535-7163.MCT-18-0571
Alonso, A., Bernstein, E., and Hasson, D. (2018). Histone Native Chromatin Immunoprecipitation. Methods Mol Biol 1832, 77-104. https://doi.org/10.1007/978-1-4939-8663-7_5
Georgilis, A., Klotz, S., Hanley, C.J., et al. (2018). PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells. Cancer Cell 34, 85-102 e109. https://doi.org/10.1016/j.ccell.2018.06.007
Strub, T., Ghiraldini, F.G., Carcamo, S., et al. (2018). SIRT6 haploinsufficiency induces BRAF(V600E) melanoma cell resistance to MAPK inhibitors via IGF signalling. Nat Commun 9, 3440. https://doi.org/10.1038/s41467-018-05966-z
Tabaglio, T., Low, D.H., Teo, W.K.L., et al. (2018). MBNL1 alternative splicing isoforms play opposing roles in cancer. Life Sci Alliance 1, e201800157. https://dx.doi.org/10.26508%2Flsa.201800157