2026
CUT&RUN
Pham K, Rodriquez V, Tokcan E, Kraushaar D. A side-by-side comparison of commercial CUT&RUN kits. J Biomol Tech. 2026 6;37(1):4-17. doi: 10.7171/001c.154138. PMID: 42088458; PMCID: PMC13138781.
Murdaugh RL, Eberl BR, Richard RU, Campos-Hensley EI, Nnyagu AN, Elam WA, Tsao AN, Tremblay JR, Ma R, Dei-Ampeh AK, Pham K, Kraushaar DC, Yu K, Olson CM, Serin-Harmanci A, Deneen B, Anastas JN. H3 dopaminylation and CaMKII modulate diffuse midline glioma response to CDK9 inhibition. bioRxiv [Preprint]. 2026 Apr 10:2026.04.07.714507. doi: 10.64898/2026.04.07.714507. PMID: 41993356; PMCID: PMC13082024.
Richard RU, Bagnetto C, Murdaugh RL, Eberl BR, Jiao AL, Kebede AF, Zee BM, Harrington MM, Filbin MG, Serin-Harmanci A, Shi Y, Anastas JN. SAGA/ATAC complexes sustain aberrant chromatin regulation and promote tumorigenesis in diffuse midline glioma. bioRxiv [Preprint]. 2026 Jan 23:2026.01.22.701194. doi: 10.64898/2026.01.22.701194. PMID: 41648478; PMCID: PMC12871717.
Sequencing
Rosas IO, McDowell-Sanchez AK, Sanchez S, Cala-Garcia JD, Waich Cohen AR, Ruiz-Echartea E, Ochsner SA, Kraushaar DC, Celada LJ, Sun D, Polverino F, Coarfa C, McKenna NJ, Tsoyi K. Macropinocytosis inhibition attenuates pro-fibrotic responses in lung fibroblasts and pulmonary fibrosis models. J Clin Invest. 2026 Apr 30:e197651. doi: 10.1172/JCI197651. Epub ahead of print. PMID: 42066052
Yu X, Sarabia S, Urbicain M, Somvanshi S, Patel R, Rao P, Tran TM, Yeh YP, Chang KS, Lo YT, Epps J, Scorsone KA, Chiu HS, Hollingsworth EF, Perez CR, Najaf Panah MJ, Zorman B, Muscal J, Finegold MJ, Goss JA, Alaggio R, Roy A, Fisher KE, Heczey A, Woodfield S, Vasudevan S, Patel K, Chen TW, Lopez-Terrada D, Sumazin P. Asynchronous transitions from high-risk hepatoblastoma to carcinoma. J Hepatol. 2026 Feb 28:S0168-8278(26)00117-0. doi: 10.1016/j.jhep.2026.02.023. Epub ahead of print. PMID: 41771380.
Smith AJ, Schrank Z, Guan N, Pedroza DA, Calderon S, Yuan X, Zhao N, Gabriel Z, Gao Y, Rivas C, Liu F, Serody JS, Perou CM, Earp HS, Rosen JM. MERTK inhibition cooperates with immunomodulatory cyclophosphamide to induce CXCL9+ monocyte-macrophage programming and durable anti-tumor immunity in triple negative breast cancer. bioRxiv [Preprint]. 2026 Feb 6:2026.02.04.703648. doi: 10.64898/2026.02.04.703648. PMID: 41676642; PMCID: PMC12889580
Bu W, Lee T, Anurag M, Ding Y, Xu R, He L, Bu AZ, Nagi C, Gutierrez C, Hilsenbeck S, Cheng C, Zhang B, Huang S, Xu J, Osborne CK, Sreekumar A, Chang E, Creighton CJ, Zhang X, Li Y. Rat somatic genome editing enables ER+ breast cancer modeling. bioRxiv [Preprint]. 2025 Sep 18:2025.09.15.675961. doi: 10.1101/2025.09.15.675961. PMID: 41000773; PMCID: PMC12458290.
Amanya SB, Murthy A, Bisht N, Bullock ZN, Ernste KJ, Vasquez-Perez J, Liu W, Trivedi A, Oyewole-Said D, Paul A, Umokoro L, Akhanov V, Samuel M, Shi Z, Nguyen MH, Huang S, Jeong M, Iakova P, Jain KA, Pham K, Kraushaar DC, Konduri V, Decker WK. Overlapping MHC class I/II Epitopes Program cDC1-like Differentiation of Monocyte-Derived Dendritic Cells via mTORC1 Signaling Inhibition. bioRxiv [Preprint]. 2026 Apr 8:2026.04.06.716309. doi: 10.64898/2026.04.06.716309. PMID: 41993385; PMCID: PMC13082029.
2025
Lei JT, Dobrolecki LE, Huang C, Srinivasan RR, Vasaikar SV, Lewis AN, Sallas C, Zhao N, Cao J, Landua JD, Moon CI, Liao Y, Hilsenbeck SG, Osborne CK, Rimawi MF, Ellis MJ, Petrosyan V, Wen B, Li K, Saltzman AB, Jain A, Malovannaya A, Wulf GM, Marangoni E, Li S, Kraushaar DC, Wang T, Damodaran S, Zheng X, Meric-Bernstam F, Echeverria GV, Anurag M, Chen X, Welm BE, Welm AL, Zhang B, Lewis MT (2025). Patient-Derived Xenografts of Triple-Negative Breast Cancer Enable Deconvolution and Prediction of Chemotherapy Responses. bioRxiv [Preprint]. 2025 Jan 8:2024.12.09.627518. DOI: 10.1101/2024.12.09.627518, PMID: 39713418.
Li CH, Sharma S, Heczey AA, Woods ML, Steffin DHM, Louis CU, Grilley BJ, Thakkar SG, Wu M, Wang T, Rooney CM, Brenner MK, Heslop HE, 2025. Long-term outcomes of GD2-directed CAR-T cell therapy in patients with neuroblastoma. Nat Med. 2025;31(4):1125-9. Epub 20250217. PMC11042400.
Somes LK, Lei JT, Yi X, Chamorro DF, Shafer P, Gad AZ, Dobrolecki LE, Madaras E, Ahmed N, Lewis MT, Zhang B, Hoyos V., (2025). ZP4: A novel target for CAR-T cell therapy in triple negative breast cancer. Mol Ther. 2025 Apr 2;33(4):1621-1641. doi: 10.1016/j.ymthe.2025.02.029. Epub 2025 Feb 20, PMID: 39980195
2024
Dong, M.P.; Dharmaraj, N.; Kaminagakura, E.; Xue, J.; Leach, D.G.; Hartgerink, J.D.; Zhang, M.; Hanks, H.-J.; Ye, Y.; Aouizerat, B.E.; et al. Stimulator of Interferon Genes Pathway Activation through the Controlled Release of STINGel Mediates Analgesia and Anti-Cancer Effects in Oral Squamous Cell Carcinoma. Biomedicines 2024, 12, 920. https://doi.org/10.3390/ biomedicines12040920.
Adkins-Threats M, Arimura S, Huang YZ, Divenko M, To S, Mao H, Zeng Y, Hwang JY, Burclaff JR, Jain S, Mills JC. Metabolic regulator ERRγ governs gastric stem cell differentiation into acid-secreting parietal cells. Cell Stem Cell. 2024 May 7: S1934-5909(24)00143-7. doi: 10.1016/j.stem.2024.04.016. PMID: 38733994
Bollepogu Raja KK, Yeung K, Shim YK, Mardon G. Integrative genomic analyses reveal putative cell type-specific targets of the Drosophila ets transcription factor Pointed. BMC Genomics. 2024 Jan 23;25(1):103. doi: 10.1186/s12864-024-10017-7. PMID: 38262913; PMCID: PMC10807358.
Carvalho, C.D., Tukeman, G., Delgado, C.Z., Ambekar, Y.S., Mekonnen, T.T., Singh, M., Rodriguez, V., Ricco, E., Kraushaar, D.C., Aglyamov, S., Scarcelli, G., Larin, K, Finnell, R.H., Cabrera M.R. Dolutegravir induces FOLR1 expression during brain organoid development. Frontiers in Molecular Neuroscience, 2024, 17: doi: 10.3389/fnmol.2024.1394058.
Ding X, Wu Y, Rodriguez V, Ricco E, Okoh JT, Liu Y, Kraushaar DC, Rasband MN. Age-dependent regulation of axoglial interactions and behavior by oligodendrocyte AnkyrinG. bioRxiv [Preprint]. 2024 Apr 2:2024.04.01.587609. doi: 10.1101/2024.04.01.587609. PMID: 38617359; PMCID: PMC11014615.
Maneix L, Iakova P, Lee CG, Moree SE, Lu X, Datar GK, Hill CT, Spooner E, King JCK, Sykes DB, Saez B, Di Stefano B, Chen X, Krause DS, Sahin E, Tsai FTF, Goodell MA, Berk BC, Scadden DT, Catic A. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat Cell Biol. 2024 Apr;26(4):593-603. doi: 10.1038/s41556-024-01387-x. Epub 2024 Mar 29. PMID: 38553595; PMCID: PMC11021199.
Souto, E. P., Gong, P., Landua, J. D., Srinivasan, R. R., Ganesan, A., Dobrolecki, L. E., Purdy, S. C., Pan, X., Zeosky, M., Chung, A., Yi, S. S., Ford, H. L., & Lewis, M. T. (2024). Lineage tracing and single-cell RNA sequencing reveal a common transcriptional state in breast cancer tumor-initiating cells characterized by IFN/STAT1 activity. Cancer Research; DOI: 10.1158/0008-5472.CAN-23-4022, PMC11997551
Sederman C, Yang CH, Cortes-Sanchez E, Di Sera T, Huang X, Scherer SD, Zhao L, Chu Z, White ER, Atkinson A, Wagstaff J, Varley KE, Lewis MT, Qiao Y, Welm BE, Welm AL, Marth GT, (2024). A precision oncology-focused deep learning framework for personalized selection of cancer therapy. bioRxiv [Preprint]. 2024 Dec 16:2024.12.12.628190. doi: 10.1101/2024.12.12.628190. PMID: 39763776
Adeniyi-Ipadeola GO, Hankins JD, Kambal A, Zeng X-L, Patil K, Poplaski V, Bomidi C, Nguyen-Phuc H, Grimm SL, Coarfa C, Stossi F, Crawford SE, Blutt SE, Speer AL, Estes MK, Ramani S. Infant and adult human intestinal enteroids are morphologically and functionally distinct. mBio. 2024 Aug 14;15(8):e0131624. doi: 10.1128/mbio.01316-24. Epub 2024 Jul 2. PMID: 38953637; PMCID: PMC11323560.
Zhao D, Ravikumar V, Leach TJ, Kraushaar D, Lauder E, Li L, Sun Y, Oravecz-Wilson K, Keller ET, Chen F, Maneix L, Jenq RR, Britton R, King KY, Santibanez AE, Creighton CJ, Rao A, Reddy P (2024). Inflammation-induced epigenetic imprinting regulates intestinal stem cells. Cell Stem Cell. 2024 Oct 3;31(10):1447-1464.e6. doi: 10.1016/j.stem.2024.08.006. Epub 2024 Sep 3. PMID: 39232559; PMCID: PMC11963838.
Kami Reddy KR, Piyarathna DWB, Park JH, Putluri V, Amara CS, Kamal AHM, Xu J, Kraushaar D, Huang S, Jung SY, Eberlin LS, Johnson JR, Kittles RA, Ballester LY, Parsawar K, Siddiqui MM, Gao J, Langer Gramer A, Bollag RJ, Terris MK, Lotan Y, Creighton CJ, Lerner SP, Sreekumar A, Kaipparettu BA, Putluri N (2024). Mitochondrial reprogramming by activating OXPHOS via glutamine metabolism in African American patients with bladder cancer. JCI Insight. 2024 Sep 10;9(17): e172336. doi: 10.1172/jci.insight.172336. PMID: 39253977; PMCID: PMC11385078.
Anvar Z, Jochum MD, Chakchouk I, Sharif M, Demond H, To AK, Kraushaar DC, Wan YW, Andrews S, Kelsey G, Veyver IB (2024). Maternal loss-of-function of Nlrp2 results in failure of epigenetic reprogramming in mouse oocytes. Res Sq [Preprint]. 2024 Jun 4: rs.3.rs-4457414. doi: 10.21203/rs.3.rs-4457414/v1. PMID: 38883732; PMCID: PMC11177987.
Tindall RR, Yang Y, Hernandez I, Qin A, Li J, Zhang Y, Gomez TH, Younes M, Shen Q, Bailey-Lundberg JM, Zhao Z, Kraushaar D, Castro P, Cao Y, Zheng WJ, Ko TC. Aging- and alcohol-associated spatial transcriptomic signature in mouse acute pancreatitis reveals heterogeneity of inflammation and potential pathogenic factors. J Mol Med (Berl). 2024 Aug;102(8):1051-1061. doi: 10.1007/s00109-024-02460-6. Epub 2024 Jun 28. PMID: 38940937; PMCID: PMC11269349.
2023
RNA-seq
Shaiken, T. E., Grimm, S. L., Siam, M., Williams, A., Rezaeian, A. H., Kraushaar, D., Ricco, E., Robertson, M. J., Coarfa, C., Jain, A., Malovannaya, A., Stossi, F., Opekun, A. R., Price, A. P., & Dubrulle, J. (2023). Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience, 26(2), 105965. https://doi.org/10.1016/j.isci.2023.105965. PMID: 36824274
Szwarc, M. M., Hai, L., Maurya, V. K., Rajapakshe, K., Perera, D., Ittmann, M. M., Mo, Q., Lin, Y., Bettini, M. L., Coarfa, C., & Lydon, J. P. (2022). Histopathologic and transcriptomic phenotypes of a conditional RANKL transgenic mouse thymus. Cytokine, 160, 156022. https://doi.org/10.1016/j.cyto.2022.156022. PMID: 36099756.
Watanabe, N., Mo, F., Zheng, R., Ma, R., Bray, V. C., van Leeuwen, D. G., Sritabal-Ramirez, J., Hu, H., Wang, S., Mehta, B., Srinivasan, M., Scherer, L. D., Zhang, H., Thakkar, S. G., Hill, L. C., Heslop, H. E., Cheng, C., Brenner, M. K., & Mamonkin, M. (2023). Feasibility and preclinical efficacy of CD7-unedited CD7 CAR T cells for T cell malignancies. Molecular therapy: the journal of the American Society of Gene Therapy, 31(1), 24–34. https://doi.org/10.1016/j.ymthe.2022.09.003 PMID: 36086817.
Chambers, C., Cermakova, K., Chan, Y. S., Kurtz, K., Wohlan, K., Lewis, A. H., Wang, C., Pham, A., Dejmek, M., Sala, M., Loeza Cabrera, M., Aguilar, R., Nencka, R., Lacorazza, H. D., Rau, R. E., & Hodges, H. C. (2023). SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia. Cancer research, 83(7), 983–996. https://doi.org/10.1158/0008-5472.CAN-22-2129 PMID: 36662812.
Gou, X., Kim, B. J., Anurag, M., Lei, J. T., Young, M. N., Holt, M. V., Fandino, D., Vollert, C. T., Singh, P., Alzubi, M. A., Malovannaya, A., Dobrolecki, L. E., Lewis, M. T., Li, S., Foulds, C. E., & Ellis, M. J. (2023). Kinome reprogramming is a targetable vulnerability in ESR1 fusion-driven breast cancer. Cancer research, CAN-22-3484. Advance online publication. https://doi.org/10.1158/0008-5472.CAN-22-3484. PMID: 37071495
Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep. 2023 Aug 29;42(8):112821. doi: 10.1016/j.celrep.2023.112821. Epub 2023 Jul 18. PMID: 37467106.
Cobos FA, Panah MJN, Epps J, Long X, Man TK, Chiu HS, Chomsky E, Kiner E, Krueger MJ, di Bernardo D, Voloch L, Molenaar J, van Hooff SR, Westermann F, Jansky S, Redell ML, Mestdagh P, Sumazin P. Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes. Genome Biol. 2023 Aug 1;24(1):177. doi: 10.1186/s13059-023-03016-6. PMID: 37528411; PMCID: PMC10394903
Whole genome bisulfite sequencing
Li Z, Chang TC, Junco JJ, Devidas M, Li Y, Yang W, Huang X, Hedges DJ, Cheng Z, Shago M, Carroll AJ, Heerema NA, Gastier-Foster J, Wood BL, Borowitz MJ, Sanclemente L, Raetz EA, Hunger SP, Feingold E, Rosser TC, Sherman SL, Loh ML, Mullighan CG, Yu J, Wu G, Lupo PJ, Rabin KR, Yang JJ. Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia. Blood. 2023 Jul 13;142(2):172-184. doi: 10.1182/blood.2023019765. PMID: 37001051; PMCID: PMC10352600.
2022
10x VISIUM
Stur, E., Corvigno, S., Xu, M., Chen, K., Tan, Y., Lee, S., Liu, J., Ricco, E., Kraushaar, D., Castro, P., Zhang, J., and Sood, A. K. (2022). Spatially resolved transcriptomics of high-grade serous ovarian carcinoma. iScience 25, 103923. PMID: 35252817.
Nanostring
Sumazin P, Peters TL, Sarabia, SF, Kim HR, Hollingsworth EF, Alvarez KR, Perez C, Sayeed H, Pozza A, Ranganathan S, Rangaswami AA, Goss JA, Vasudevan SA, Heczey A, Roy A, Alaggio R, Finegold MJ, López-Terrada DH, (2022). Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive hepatocellular neoplasms in children and adolescents. Journal of Hepatology, https://doi.org/10.1101/2021.07.15.445600.
De Paiva, C. S., Trujillo-Vargas, C. M., Schaefer, L., Yu, Z., Britton, R. A., and Pflugfelder, S. C. (2021). Differentially Expressed Gene Pathways in the Conjunctiva of Sjogren Syndrome Keratoconjunctivitis Sicca. Front Immunol 12, 702755. PMID: 34349764
Trujillo-Vargas, C. M., Mauk, K. E., Hernandez, H., de Souza, R. G., Yu, Z., Galletti, J. G., Dietrich, J., Paulsen, F., and de Paiva, C. S. (2022). Immune phenotype of the CD4(+) T cells in the aged lymphoid organs and lacrimal glands. Geroscience. PMID: 35279788.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., Guimaraes de Souza, R., Yu, Z., and Pflugfelder, S. C. (2022). IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease with Aging in RXRalpha Mutant Mouse. Front Med (Lausanne) 9, 849990. PMID: 3540243.
RNA-seq
Piyarathna,B., Coarfa, C., and Weigel, N. L. (2022). Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities. Scientific Report 12, 5351. PMID: 35354884.
Karolak, J. A., Deutsch G, Gambin T., Szafranski P., Popek E., and Stankiewicz, P. (2022). Transcriptome and Immunohistochemical Analyses in TBX4- and FGF10-Deficient Lungs Imply TMEM100 as a Mediator of Human Lung Development. Amer Jour of Respiratory Cell & Molec Biol, V66-6. PMID: 35648090.
Zhou, J., Hamdan, H., Yalamanchili, H. K., Pang, K., Pohodich, A. E., Lopez, J., Shao, Y., Oses-Prieto, J. A., Li, L., Kim, W., Durham, M. A., Bajikar, S. S., Palmer, D. J., Ng, P., Thompson, M. L., Bebin, E. M., Muller, A. J., Kuechler, A., Kampmeier, A., Haack, T. B., Burlingame, A. L., Liu, Z., Rasband, M. N., and Zoghbi, H. Y. (2022). Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders. Proc Natl Acad Sci U S A 119. PMID: 35074918, PMCID: PMC8794850.
Steimle, J. D., Grisanti Canozo, F. J., Park, M., Kadow, Z. A., Samee, M. A. H., and Martin, J. F. (2022). Decoding the PITX2 controlled genetic network in atrial fibrillation. JCI Insight. PMID: 35471998.
Singh, S, Lee, N, Pedroza, D, Bado, I, Zhang, L, Aguirre, S, Hamor, C, Shen, Y, Xu, Y, Hu, J, Gao, Y, , Zhao, N, Chen, S-H, Wan, Y-W, Liu, Z, Chang, JT, Hollern, D, Perou, CM, Zhang, X. H-F, and Rosen, JM. Chemotherapy coupled to macrophage inhibition induces T-cell and B-cell infiltration and durable regression in triple-negative breast cancer, Cancer Res, (2022) Apr 20:canres.3714. doi: 10.1158/0008-5472.CAN-21-3714. Online ahead of print. PMID: 35442423.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., and Pflugfelder, S. C. (2022). Single-cell transcriptional profiling of murine conjunctival immune cells reveals distinct populations expressing homeostatic and regulatory genes. Mucosal Immunol. PMID: 35361907.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., Guimaraes de Souza, R., Yu, Z., and Pflugfelder, S. C. (2022). IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease with Aging in RXRalpha Mutant Mouse. Front Med (Lausanne) 9, 849990. PMID: 3540243.