Publications

MASSACHUSETTS GENERAL HOSPITAL

HARVARD MEDICAL SCHOOL

2023

• Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K,Hochedlinger K. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat Cell Biol. 2023 Jul 17. doi: 10.1038/s41556-023-01191-z.Epub ahead of print. PMID: 37460697.
• Kfoury YS, Ji F, Jain E, Mazzola MC, Schiroli G, Papazian A, Mercier FE, Sykes DB, Kiem A, Randolph MA, Abdel-Wahab OI, Calvi LM, Sadreyev R, Scadden DT. The bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression. Blood Adv. 2023 Jul 14:bloodadvances.2022008268. doi: 10.1182/bloodadvances.2022008268. Epub ahead of print. PMID: 37450380.
• Guinn MT, Szuter ES, Yokose T, Ge J, Rosales IA, Chetal K, Sadreyev RI, Cuenca AG, Kreisel D, Sage PT, Russell PS, Madsen JC, Colvin RB, Alessandrini A. Intragraft B cell differentiation during the development of tolerance to kidney allografts is associated with a regulatory B cell signature revealed by single cell transcriptomics. Am J Transplant. 2023 Jun 8:S1600-6135(23)00524-5. doi: 10.1016/j.ajt.2023.05.036. Epub ahead of print. PMID: 37295719.
• Rojas RA, Kutateladze AA, Plummer L, Stamou M, Keefe DL Jr, Salnikov KB, Delaney A, Hall JE, Sadreyev R, Ji F, Fliers E, Gambosova K, Quinton R, Merino PM, Mericq V, Seminara SB, Crowley WF Jr, Balasubramanian R. Phenotypic continuum between Waardenburg syndrome and idiopathic hypogonadotropic hypogonadism in humans with SOX10 variants. Genet Med. 2023 Jun;25(6):100855. doi: 10.1016/j.gim.2023.100855. Erratum for: Genet Med. 2021 Apr;23(4):629-636. PMID: 37272927.
• Rhee C, Scadden EW, Wong LP, Schiroli G, Mazzola MC, Chea PL, Kato H, Hoyer FF, Mistry M, Lee BK, Kim J, Nahrendorf M, Mansour M, Sykes DB, Sadreyev R, Scadden DT. Limited plasticity of monocyte fate and function associated with epigenetic scripting at the level of progenitors. Blood. 2023 Jun 2:blood.2023020257. doi: 10.1182/blood.2023020257. Epub ahead of print. PMID: 37267513.
• Gopal RK, Vantaku VR, Panda A, Reimer B, Rath S, To TL, Fisch AS, Cetinbas M, Livneh M, Calcaterra MJ, Gigliotti BJ, Pierce KA, Clish CB, Dias-Santagata D, Sadow PM, Wirth LJ, Daniels GH, Sadreyev RI, Calvo SE, Parangi S, Mootha VK. Effectors enabling adaptation to mitochondrial complex I loss in Hurthle cell carcinoma. Cancer Discov. 2023 Jun 1:CD-22-0976. doi: 10.1158/2159-8290.CD-22-0976. Epub ahead of print. PMID: 37262067.
• Vyas CM, Sadreyev RI, Gatchel JR, Kang JH, Reynolds CF, Mischoulon D, Chang G, Hazra A, Manson JE, Blacker D, De Vivo I, Okereke OI. Pilot Study of Second-Generation DNA Methylation Epigenetic Markers in Relation to Cognitive and Neuropsychiatric Symptoms in Older Adults. J Alzheimers Dis. 2023;93(4):1563-1575. doi: 10.3233/JAD-230093. PMID: 37212116; PMCID: PMC10336852.
• Smith CJ, Rendina DN, Kingsbury MA, Malacon KE, Nguyen DM, Tran JJ, Devlin BA, Raju RM, Clark MJ, Burgett L, Zhang JH, Cetinbas M, Sadreyev RI, Chen K, Iyer MS, Bilbo SD. Microbial modulation via cross-fostering prevents the effects of pervasive environmental stressors on microglia and social behavior, but not the dopamine system. Mol Psychiatry. 2023 May 17. doi: 10.1038/s41380-023-02108-w. Epub ahead of print. PMID: 37198262.
• Bommakanti K, Seist R, Kukutla P, Cetinbas M, Batts S, Sadreyev RI, Stemmer- Rachamimov A, Brenner GJ, Stankovic KM. Comparative Transcriptomic Analysis of Archival Human Vestibular Schwannoma Tissue from Patients with and without Tinnitus. J Clin Med. 2023 Apr 1;12(7):2642. doi: 10.3390/jcm12072642. PMID: 37048724; PMCID: PMC10095534
• He S, Lei P, Kang W, Cheung P, Xu T, Mana M, Park CY, Wang H, Imada S, Russell JO, Wang J, Wang R, Zhou Z, Chetal K, Stas E, Mohad V, Bruun-Rasmussen P, Sadreyev RI, Hodin RA, Zhang Y, Breault DT, Camargo FD, Yilmaz √ñH, Fredberg JJ, Saeidi N. Stiffness Restricts the Stemness of the Intestinal Stem Cells and Skews Their Differentiation Toward Goblet Cells. Gastroenterology. 2023 Jun;164(7):1137-1151.e15. doi: 10.1053/j.gastro.2023.02.030. Epub 2023 Mar 4. PMID: 36871599; PMCID: PMC10200762.
• Yoon SH, Meyer MB, Arevalo C, Tekguc M, Zhang C, Wang JS, Castro Andrade CD, Strauss K, Sato T, Benkusky NA, Lee SM, Berdeaux R, Foretz M, Sundberg TB, Xavier RJ, Adelmann CH, Brooks DJ, Anselmo A, Sadreyev RI, Rosales IA, Fisher DE, Gupta N, Morizane R, Greka A, Pike JW, Mannstadt M, Wein MN. A parathyroid hormone/salt-inducible kinase signaling axis controls renal vitamin D activation and organismal calcium homeostasis. J Clin Invest. 2023 May 1;133(9):e163627. doi: 10.1172/JCI163627. PMID: 36862513; PMCID: PMC10145948.
• Janssen H, Kahles F, Liu D, Downey J, Koekkoek LL, Roudko V, D'Souza D, McAlpine CS, Halle L, Poller WC, Chan CT, He S, Mindur JE, Kiss MG, Singh S, Anzai A, Iwamoto Y, Kohler RH, Chetal K, Sadreyev RI, Weissleder R, Kim-Schulze S, Merad M, Nahrendorf M, Swirski FK. Monocytes re-enter the bone marrow during fasting and alter the host response to infection. Immunity. 2023 Apr 11;56(4):783-796.e7. doi: 10.1016/j.immuni.2023.01.024. Epub 2023 Feb 23. PMID: 36827982; PMCID: PMC10101885.
• Gnanaguru G, Tabor SJ, Bonilla GM, Sadreyev R, Yuda K, K√∂hl J, Connor KM. Microglia refine developing retinal astrocytic and vascular networks through the complement C3/C3aR axis. Development. 2023 Mar 1;150(5):dev201047. doi: 10.1242/dev.201047. Epub 2023 Mar 1. PMID: 36762625; PMCID: PMC10110418.
• Kenkel WM, Kingsbury MA, Reinhart JM, Cetinbas M, Sadreyev RI, Carter CS, Perkeybile AM. Lasting consequences on physiology and social behavior following cesarean delivery in prairie voles. Horm Behav. 2023 Apr;150:105314. doi: 10.1016/j.yhbeh.2023.105314. Epub 2023 Feb 1. PMID: 36731301; PMCID: PMC10023354.
• Asbjornsdottir B, Miranda-Ribera A, Fiorentino M, Konno T, Cetinbas M, Lan J, Sadreyev RI, Gudmundsson LS, Gottfredsson M, Lauth B, Birgisdottir BE, Fasano A. Prophylactic Effect of Bovine Colostrum on Intestinal Microbiota and Behavior in Wild-Type and Zonulin Transgenic Mice. Biomedicines. 2022 Dec 29;11(1):91. doi: 10.3390/biomedicines11010091. PMID: 36672598; PMCID: PMC9855927.
• Generoso SF, Neguembor MV, Hershberg EA, Sadreyev RI, Kurimoto K, Yabuta Y, Ricci R, Audergon P, Bauer M, Saitou M, Hochedlinger K, Beliveau BJ, Cosma MP, Lee JT, Payer B. Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming. Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2213810120. doi: 10.1073/pnas.2213810120. Epub 2023 Jan 20. PMID: 36669113; PMCID: PMC9942853.
• Su KW, Cetinbas M, Martin VM, Virkud YV, Seay H, Ndahayo R, Rosow R, Elkort M, Gupta B, Kramer E, Pronchick T, Reuter S, Sadreyev RI, Huang JL, Shreffler WG, Yuan Q. Early infancy dysbiosis in food protein-induced enterocolitis syndrome: A prospective cohort study. Allergy. 2023 Jun;78(6):1595-1604. doi: 10.1111/all.15644. Epub 2023 Jan 24. PMID: 36635218.
• Ji F, Van Rechem C, Whetstine JR, Sadreyev RI. Computational workflow for integrative analyses of DNA replication timing, epigenomic, and transcriptomic data. STAR Protoc. 2022 Nov 8;3(4):101827. doi: 10.1016/j.xpro.2022.101827. PMID: 36386876; PMCID: PMC9647704.
• Nakazawa H, Wong LP, Shelton L, Sadreyev R, Kaneki M. Farnesysltransferase Inhibitor Prevents Burn Injury-Induced Metabolome Changes in Muscle. Metabolites. 2022 Aug 27;12(9):800. doi: 10.3390/metabo12090800. PMID: 36144205; PMCID: PMC9506277.
• McAlpine CS, Kiss MG, Zuraikat FM, Cheek D, Schiroli G, Amatullah H, Huynh P, Bhatti MZ, Wong LP, Yates AG, Poller WC, Mindur JE, Chan CT, Janssen H, Downey J, Singh S, Sadreyev RI, Nahrendorf M, Jeffrey KL, Scadden DT, Naxerova K, St-Onge MP, Swirski FK. Sleep exerts lasting effects on hematopoietic stem cell function and diversity. J Exp Med. 2022 Nov 7;219(11):e20220081. doi: 10.1084/jem.20220081. Epub 2022 Sep 21. PMID: 36129517; PMCID: PMC9499822.
• Amatullah H, Fraschilla I, Digumarthi S, Huang J, Adiliaghdam F, Bonilla G, Wong LP, Rivard ME, Beauchamp C, Mercier V, Goyette P, Sadreyev RI, Anthony RM, Rioux JD, Jeffrey KL. Epigenetic reader SP140 loss of function drives Crohn's disease  due  to uncontrolled macrophage topoisomerases. Cell. 2022 Aug 18;185(17):3232-3247.e18. doi: 10.1016/j.cell.2022.06.048. Epub 2022 Aug 10. PMID: 35952671; PMCID: PMC9442451.
• Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, N√§√§r AM. An intranasal ASO therapeutic targeting SARS-CoV-2. Nat Commun. 2022 Aug 3;13(1):4503. doi: 10.1038/s41467-022-32216-0. PMID: 35922434; PMCID: PMC9349213.
• Rohde D, Vandoorne K, Lee IH, Grune J, Zhang S, McAlpine CS, Schloss MJ, Nayar R, Courties G, Frodermann V, Wojtkiewicz G, Honold L, Chen Q, Schmidt S,Iwamoto Y, Sun Y, Cremer S, Hoyer FF, Iborra-Egea O, Mu√±oz-Guijosa C, Ji F, Zhou B, Adams RH, Wythe JD, Hidalgo J, Watanabe H, Jung Y, van der Laan AM, Piek JJ,Kfoury Y, D√©sog√®re PA, Vinegoni C, Dutta P, Sadreyev RI, Caravan P, Bayes-Genis A, Libby P, Scadden DT, Lin CP, Naxerova K, Swirski FK, Nahrendorf M. Bone marrow endothelial dysfunction promotes myeloid cell expansion in cardiovascular disease. Nat Cardiovasc Res. 2022 Jan;1(1):28-44. doi: 10.1038/s44161-021-00002-8. Epub 2021 Dec 23. PMID: 35747128; PMCID: PMC9216333.
• Kim MH, Kim MY, Salloum S, Qian T, Wong LP, Xu M, Lee Y, Shroff SG, Sadreyev RI, Corey KE, Baumert TF, Hoshida Y, Chung RT. Atorvastatin favorably modulates a clinical hepatocellular carcinoma risk gene signature. Hepatol Commun. 2022 Sep;6(9):2581-2593. doi: 10.1002/hep4.1991. Epub 2022 Jun 16. PMID: 35712812; PMCID: PMC9426409.
• Poller WC, Downey J, Mooslechner AA, Khan N, Li L, Chan CT, McAlpine CS, Xu C, Kahles F, He S, Janssen H, Mindur JE, Singh S, Kiss MG, Alonso-Herranz L,Iwamoto Y, Kohler RH, Wong LP, Chetal K, Russo SJ, Sadreyev RI, Weissleder R,Nahrendorf M, Frenette PS, Divangahi M, Swirski FK. Brain motor and fear circuits regulate leukocytes during acute stress. Nature. 2022 Jul;607(7919):578-584. doi: 10.1038/s41586-022-04890-z. Epub 2022 May 30. PMID: 35636458; PMCID: PMC9798885.
• Ji F, Bonilla G, Krykbaev R, Ruvkun G, Tabach Y, Sadreyev RI. DEPCOD: a tool to detect and visualize co-evolution of protein domains. Nucleic Acids Res. 2022:gkac349. doi: 10.1093/nar/gkac349 .
• Franklin R, Guo Y, He S, Chen M, Ji F, Zhou X, Frankhouser D, Do BT, Chiem C, Jang M, Blanco MA, Vander Heiden MG, Rockne RC, Ninova M, Sykes DB, Hochedlinger K, Lu R, Sadreyev RI, Murn J, Volk A, Cheloufi S. Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity. Nat Commun. 2022 ;13(1):235 0.
• Adiliaghdam F, Amatullah H, Digumarthi S, Saunders TL, Rahman RU, Wong LP, Sadreyev R, Droit L, Paquette J, Goyette P, Rioux JD, Hodin R, Mihindukulasuriya KA, Handley SA, Jeffrey KL. Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Sci Immunol. 2022 ;7(70):eabn66 31.
• Sebastian C, Ferrer C, Serra M, Choi JE, Ducano N, Mira A, Shah MS, Stopka SA, Perciaccante AJ, Isella C, Moya-Rull D, Vara-Messler M, Giordano S, Maldi E, Desai N, Capen DE, Medico E, Cetinbas M, Sadreyev RI, Brown D, Rivera MN, Sapino A, Breault DT, Agar NYR, Mostoslavsky R. A non-dividing cell population with high pyruvate dehydrogenase kinase activity regulates metabolic heterogeneity and tumorigenesis in the intestine. Nat Commun. 2022 ;13(1):1
• Mealer RG, Williams SE, Noel M, Yang B, D'Souza AK, Nakata T, Graham DB, Creasey EA, Cetinbas M, Sadreyev RI, Scolnick EM, Woo CM, Smoller JW, Xavier RJ, Cummings RD. The schizophrenia-associated variant in SLC39A8 alters protein glycosylation in the mouse brain. Mol Psychiatry.  .
• Nakatani T, Lin J, Ji F, Ettinger A, Pontabry J, Tokoro M, Altamirano-Pacheco L, Fiorentino J, Mahammadov E, Hatano Y, Van Rechem C, Chakraborty D, Ruiz-Morales ER, Arguello Pascualli PY, Scialdone A, Yamagata K, Whetstine JR, Sadreyev RI, Torres-Padilla ME. DNA replication fork speed underlies cell fate changes and promotes reprogramming. Nat Genet. 2022 ;54(3):318 .
• Williams SE, Noel M, Lehoux S, Cetinbas M, Xavier RJ, Sadreyev RI, Scolnick EM, Smoller JW, Cummings RD, Mealer RG. Mammalian brain glycoproteins exhibit diminished glycan complexity compared to other tissues. Nat Commun. 2022 ;13( 75.
• Guo N, McDermott KD, Shih YT, Zanga H, Ghosh D, Herber C, Meara WR, Coleman J, Zagouras A, Wong LP, Sadreyev R, Gonçalves JT, Sahay A. Transcriptional regulation of neural stem cell expansion in the adult hippocampus. Elife. 2022;11 195.
• Sohn J, Milosevic J, Brouse T, Aziz N, Elkhoury J, Wang S, Hauschild A, van Gastel N, Cetinbas M, Tufa SF, Keene DR, Sadreyev RI, Pu WT, Sykes DB. A new murine model of Barth syndrome neutropenia links TAFAZZIN deficiency to increased ER stress-induced apoptosis. Blood Adv. 2022 ;6(8):2 2577.
• Mori T, Verma R, Nakamoto-Matsubara R, Siu KT, Panaroni C, Fulzele KS, Mukaihara K, Onyewadume C, Maebius A, Kato H, Wong LP, Sadreyev RI, Scadden DT, Raje NS. Low NCOR2 levels in multiple myeloma patients drive multidrug resistance via MYC upregulation. Blood Cancer J. 2021 ;1 ):194.
• Matilainen O, Ribeiro ARS, Verbeeren J, Cetinbas M, Sood H, Sadreyev RI, Garcia SMDA. Loss of muscleblind splicing factor shortens Caenorhabditis elegans lifespan by reducing the activity of p38 MAPK/PMK-1 and transcription factors ATF-7 and Nrf/SKN-1. Genetics. 2021 ;219( yab114.
• Mehrotra I, Serena G, Cetinbas M, Kenyon V, Martin VM, Harshman SG, Zomorrodi AR, Sadreyev RI, Fasano A, Leonard MM. Characterization of the blood microbiota in children with Celiac disease. Curr Res Microb Sci. 20 :100069.
• Hsieh FK, Ji F, Damle M, Sadreyev RI, Kingston RE. HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7. Life Sci Alliance. 2022 Jan;5(1). doi: 10.26508/lsa.202101127. Print 2022 Jan. PubMed PM 34663690.
• Van Rechem C, Ji F, Chakraborty D, Black JC, Sadreyev RI, Whetstine JR. Collective regulation of chromatin modifications predicts replication timing during cell cycle. Cell Rep. 2021 Oct 5;37(1):109799. doi: 10.1016/j.celrep.2021.109799. PubMed PMID: 34610305; PubMed Central PMCID C8530517.
• Kfoury YS, Ji F, Mazzola M, Sykes DB, Scherer AK, Anselmo A, Akiyama Y, Mercier F, Severe N, Kokkaliaris KD, Zhao T, Brouse T, Saez B, Seidl J, Papazian A, Ivanov P, Mansour MK, Sadreyev RI, Scadden DT. tiRNA signaling via stress-regulated vesicle transfer in the hematopoietic niche. Cell Stem Cell. 2021 Sep 15;. doi: 10.1016/j.stem.2021.08.014. [Epub ahead of print] PubMed PM 34551362.
• Kim MH, Salloum S, Wang JY, Wong LP, Regan J, Lefteri K, Manickas-Hill Z, Gao C, Li JZ, Sadreyev RI, Yu XG, Chung RT. Type I, II, and III Interferon Signatures Correspond to Coronavirus Disease 2019 Severity. J Infect Dis. 2021 Sep 1;224(5):777-782. doi: 10.1093/infdis/jiab288. PubMed PMID: 34467988; PubMed Central PMCID C8244575.
• Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K. Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes Dev. 2021 Sep 1;35(17-18):1209-1228. doi: 10.1101/gad.348678.121. Epub 2021 Aug 19. PubMed PMID: 34413137; PubMed Central PMCID C8415322.
• Stanley TL, Fourman LT, Wong LP, Sadreyev R, Billingsley JM, Feldpausch MN, Zheng I, Pan CS, Boutin A, Lee H, Corey KE,  Torriani M, Kleiner DE, Chung RT, Hadigan CM, Grinspoon SK. Growth Hormone Releasing Hormone Reduces Circulating Markers of Immune Activation in Parallel with Effects on Hepatic Immune Pathways in Individuals with HIV-infection and Nonalcoholic Fatty Liver Disease. Clin Infect Dis. 2021 Aug 16;73(4):621-630. doi: 10.1093/cid/ciab019. PubMed PMID: 33852720; PubMed Central PMCID C8366828.
• McAlpine CS, Park J, Griciuc A, Kim E, Choi SH, Iwamoto Y, Kiss MG, Christie KA, Vinegoni C, Poller WC, Mindur JE, Chan CT, He S, Janssen H, Wong LP, Downey J, Singh S, Anzai A, Kahles F, Jorfi M, Feruglio PF, Sadreyev RI, Weissleder R, Kleinstiver BP, Nahrendorf M, Tanzi RE, Swirski FK. Astrocytic interleukin-3 programs microglia and limits Alzheimer's disease. Nature. 2021 Jul;595(7869):701-706. doi: 10.1038/s41586-021-03734-6. Epub 2021 Jul 14. PubMed PM 34262178.
• Kukutla P, Ahmed SG, DuBreuil DM, Abdelnabi A, Cetinbas M, Fulci G, Aldikacti B, Stemmer-Rachamimov A, Plotkin SR, Wainger B, Sadreyev RI, Brenner GJ. Transcriptomic signature of painful human neurofibromatosis type 2 schwannomas. Ann Clin Transl Neurol. 2021 Jul;8(7):1508-1514. doi: 10.1002/acn3.51386. Epub 2021 May 30. PubMed PMID: 34053190; PubMed Central PMCID C8283170.
• Rojas RA, Kutateladze AA, Plummer L, Stamou M, Keefe DL Jr, Salnikov KB, Delaney A, Hall JE, Sadreyev R, Ji F, Fliers E, Gambosova K, Quinton R, Merino PM, Mericq V, Seminara SB, Crowley WF Jr, Balasubramanian R. Phenotypic continuum between Waardenburg syndrome and idiopathic hypogonadotropic hypogonadism in humans with SOX10 variants. Genet Med. 2021 Apr;23(4):629-636. doi: 10.1038/s41436-020-01051-3. Epub 2021 Jan 13. PubMed PMID: 33442024; PubMed Central PMCID C8335791.
• Kim MH, Salloum S, Wang JY, Wong LP, Regan J, Lefteri K, Manickas-Hill Z, Li JZ, Sadreyev RI, Yu XG, Chung RT. Type I, II, and III interferon signatures correspond to COVID-19 disease severity. medRxiv. 2021 Mar 12;. doi: 10.1101/2021.03.10.21253317. PubMed PMID: 33758894; PubMed Central PMCID C7987053.
• Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, Janneke van der Woude C, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2021 Mar;19(3):519-527.e5. doi: 10.1016/j.cgh.2020.03.013. Epub 2020 Mar 14. PubMed PMID: 32184182; NIHMSID: S1605506.
• Choi JE, Sebastian C, Ferrer CM, Lewis CA, Sade-Feldman M, LaSalle T, Gonye A, Lopez BGC, Abdelmoula WM, Regan MS, Cetinbas M, Pascual G, Wojtkiewicz GR, Silveira GG, Boon R, Ross KN, Tirosh I, Saladi SV, Ellisen LW, Sadreyev RI, Benitah SA, Agar NYR, Hacohen N, Mostoslavsky R. A unique subset of glycolytic tumour-propagating cells drives squamous cell carcinoma. Nat Metab. 2021 Feb;3(2):182-195. doi: 10.1038/s42255-021-00350-6. Epub 2021 Feb 22. PubMed PMID: 33619381; PubMed Central PMCI MC7954080.
• Xiao L, Salem JE, Clauss S, Hanley A, Bapat A, Hulsmans M, Iwamoto Y, Wojtkiewicz G, Cetinbas M, Schloss MJ, Tedeschi J, Lebrun-Vignes B, Lundby A, Sadreyev RI, Moslehi J, Nahrendorf M, Ellinor PT, Milan DJ. Ibrutinib-Mediated Atrial Fibrillation Attributable to Inhibition of C-Terminal Src Kinase. Circulation. 2020 Dec 22;142(25):2443-2455. doi: 10.1161/CIRCULATIONAHA.120.049210. Epub 2020 Oct 23. PubMed P  33092403.
• Wang L, Sinnott-Armstrong N, Wagschal A, Wark AR, Camporez JP, Perry RJ, Ji F, Sohn Y, Oh J, Wu S, Chery J, Moud BN, Saadat A, Dankel SN, Mellgren G, Tallapragada DSP, Strobel SM, Lee MJ, Tewhey R, Sabeti PC, Schaefer A, Petri A, Kauppinen S, Chung RT, Soukas A, Avruch J, Fried SK, Hauner H, Sadreyev RI, Shulman GI, Claussnitzer M, Näär AM. A MicroRNA Linking Human Positive Selection and Metabolic Disorders. Ce 020 Oct 13.
• Chan CT, Fenn AM, Harder NK, Mindur JE, McAlpine CS, Patel J, Valet C, Rattik S, Iwamoto Y, He S, Anzai A, Kahles F, Poller WC, Janssen H, Wong LP, Fernandez-Hernando C, Koolbergen DR, van der Laan AM, Yvan-Charvet L, Sadreyev RI, Nahrendorf M, Westerterp M, Tall AR, Gustafsson JA, Swirski FK. Liver X receptors are required for thymic resilience and T cell output. J Exp Med 2020  05; 217(10)
• Van Rechem C, Ji F, Mishra S, Chakraborty D, Murphy SE, Dillingham ME, Sadreyev RI, Whetstine JR. The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. Biochim Biophys Acta Gene Regul Mech 2020 Oct; 1 10):194624.
• Borren NZ, Plichta D, Joshi AD, Bonilla G, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis 2020 Sep 18; 2 ):1524-1532.
• Rahimi RA, Nepal K, Cetinbas M, Sadreyev RI, Luster AD. Distinct functions of tissue-resident and circulating memory Th2 cells in allergic airway disease. J Exp Med 20 ep 07; 217(9)
• deFilippi C, Toribio M, Wong LP, Sadreyev R, Grundberg I, Fitch KV, Zanni MV, Lo J, Sponseller CA, Sprecher E, Rashidi N, Thompson MA, Cagliero D, Aberg JA, Braun LR, Stanley TL, Lee H, Grinspoon SK. Differential Plasma Protein Regulation and Statin Effects in Human Immunodeficiency Virus (HIV)-Infected and Non-HIV-Infected Patients Utilizing a Proteomics Approach. J Infect Dis 2020 Aug 17 2(6):929-939.
• Sato T, Verma S, Andrade CDC, Omeara M, Campbell N, Wang JS, Cetinbas M, Lang A, Ausk BJ, Brooks DJ, Sadreyev RI, Kronenberg HM, Lagares D, Uda Y, Pajevic PD, Bouxsein ML, Gross TS, Wein MN. A FAK/HDAC5 signaling axis controls osteocyte mechanotransduction. Nat Commun 2020 0 ; 11(1):3282.
• Yildirim O, Izgu EC, Damle M, Chalei V, Ji F, Sadreyev RI, Szostak JW, Kingston RE. S-phase Enriched Non-coding RNAs Regulate Gene Expression and Cell Cycle Progression. Cell Rep 2020 May  31(6):107629.
• Sen P, Wilkie AR, Ji F, Yang Y, Taylor IJ, Velazquez-Palafox M, Vanni EAH, Pesola JM, Fernandez R, Chen H, Morsett LM, Abels ER, Piper M, Lane RJ, Hickman SE, Means TK, Rosenberg ES, Sadreyev RI, Li B, Coen DM, Fishman JA, El Khoury J. Linking indirect effects of cytomegalovirus in transplantation to modulation of monocyte innate immune function. Sci Adv 2020 Apr 17):eaax9856.
• Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases. Clin Gastroenterol Hep  2020 Mar 14.
• Kwak SS, Washicosky KJ, Brand E, von Maydell D, Aronson J, Kim S, Capen DE, Cetinbas M, Sadreyev R, Ning S, Bylykbashi E, Xia W, Wagner SL, Choi SH, Tanzi RE. Amyloid-β42/40 ratio drives tau pathology in 3D human neural cell culture models of Alzheimer's disease. Nat Commun 2020  3; 11(1):1377.
• Lee S, Micalizzi D, Truesdell SS, Bukhari SIA, Boukhali M, Lombardi-Story J, Kato Y, Choo MK, Dey-Guha I, Ji F, Nicholson BT, Myers DT, Mazzola MA, Raheja R, Langenbucher A, Haradhvala NJ, Lawrence MS, Gandhi R, Tiedje C, Diaz-Muñoz MD, Sweetser DA, Sadreyev R, Sykes D, Haas W, Haber DA, Maheswaran S, Vasudevan S. A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells. Genome Biol. 2020  10; 21(1):33.
• Clarke TL, Tang R, Chakraborty D, Van Rechem C, Ji F, Mishra S, Ma A, Kaniskan HÜ, Jin J, Lawrence MS, Sadreyev RI, Whetstine JR. Histone Lysine Methylation Dynamics Control DNA Copy-Number Amplification. Cancer Discov 2020 F 10(2):306-325.
• Yang F, Wang W, Cetinbas M, Sadreyev R, Blower M. Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation A 2020 Jan 02.
• Nishimori S, O'Meara MJ, Castro CD, Noda H, Cetinbas M, da Silva Martins J, Ayturk U, Brooks DJ, Bruce M, Nagata M, Ono W, Janton CJ, Bouxsein ML, Foretz M, Berdeaux R, Sadreyev RI, Gardella TJ, Jüppner H, Kronenberg HM, Wein MN. Salt-inducible kinases dictate parathyroid hormone 1 receptor action in bone development and remodeling. J. Clin. Invest. 2019 Dec 02;  12):5187-5203.
• Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell 2019 Nov 07; 5):622-638.e13.
• Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, Hock H, Hochedlinger K. Inducible histone K-to-M mutations are dynamic tools  to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat. Cell Biol. 2019 11 (11):1449-1461.
• Frodermann V, Rohde D, Courties G, Severe N, Schloss MJ, Amatullah H, McAlpine CS, Cremer S, Hoyer FF, Ji F, van Koeverden ID, Herisson F, Honold L, Masson GS, Zhang S, Grune J, Iwamoto Y, Schmidt SP, Wojtkiewicz GR, Lee IH, Gustafsson K, Pasterkamp G, de Jager SCA, Sadreyev RI, MacFadyen J, Libby P, Ridker P, Scadden DT, Naxerova K, Jeffrey KL, Swirski FK, Nahrendorf M. Exercise reduces inflammatory cell production and cardiovascular inflammation via instruction of hematopoietic progenitor cells. Nat. Med. 2019 11 (11):1761-1771.
• Kong X, Liu J, Cetinbas M, Sadreyev R, Koh M, Huang H, Adeseye A, He P, Zhu J, Russell H, Hobbie C, Onderdonk AB. New and Preliminary Evidence on Altered Oral and Gut Microbiota in Individuals with Autism Spectrum Disorder (ASD): Implications for ASD Diagnosis and Subtyping Based on Microbial Biomarkers. Nutrients 9 Sep 06; 11(9)
• Etchegaray JP, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross KN, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev RI, Ramaswamy S, Nechaev S, Whetstine JR, Roeder RG, Adelman K, Goren A, Mostoslavsky R. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. Mol. Cell 2019 08 22 (4):683-699.e7.
• Ciccone DN, Namiki Y, Chen C, Morshead KB, Wood AL, Johnston CM, Morris JW, Wang Y, Sadreyev R, Corcoran AE, Matthews AGW, Oettinger MA. The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF. J. Biol. m. 2019 Jul 08.
• Griciuc A, Patel S, Federico AN, Choi SH, Innes BJ, Oram MK, Cereghetti G, McGinty D, Anselmo A, Sadreyev RI, Hickman SE, El Khoury J, Colonna M, Tanzi RE. TREM2 Acts Downstream of CD33 in Modulating Microglial Pathology in Alzheimer's Disease.  on 2019 Jun 28.
• Ji F, Sadreyev RI. Single-Cell RNA-seq: Introduction to Bioinformatics Analysis. Curr Protoc Mol Biol 2 Jun; 127(1):e92.
• Mao K, Ji F, Breen P, Sewell A, Han M, Sadreyev R, Ruvkun G. Mitochondrial Dysfunction in C. elegans Activates Mitochondrial Relocalization and Nuclear Hormone Receptor-Dependent Detoxification Genes. Cell Metab. 2019 May 07; 5):1182-1191.e4.
• Freire R, Ingano L, Serena G, Cetinbas M, Anselmo A, Sapone A, Sadreyev RI, Fasano A, Senger S. Human gut derived-organoids provide model to study gluten response and effects of microbiota-derived molecules in celiac disease. Sci Rep 201 y 07; 9(1):7029.
• Sherill-Rofe D, Rahat D, Findlay S, Mellul A, Guberman I, Braun M, Bloch I, Lalezari A, Samiei A, Sadreyev R, Goldberg M, Orthwein A, Zick A, Tabach Y. Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes. Genome Res. 201 ; 29(3):439-448.
• Lochhead RB, Arvikar SL, Aversa JM, Sadreyev RI, Strle K, Steere AC. Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis. Cell. Microbiol. 201 b; 21(2):e12954.
• Lochhead RB, Ordoñez D, Arvikar SL, Aversa JM, Oh LS, Heyworth B, Sadreyev R, Steere AC, Strle K. Interferon-gamma production in Lyme arthritis synovial tissue promotes differentiation of fibroblast-like synoviocytes into immune effector cells. Cell. Microbiol. 201 b; 21(2):e12992.
• Miranda-Ribera A, Ennamorati M, Serena G, Cetinbas M, Lan J, Sadreyev RI, Jain N, Fasano A, Fiorentino M. Exploiting the Zonulin Mouse Model to Establish the Role of Primary Impaired Gut Barrier Function on Microbiota Composition and Immune Profiles. Front Im l 2019; 10:2233.
• Ji F, Sadreyev RI. RNA-seq: Basic Bioinformatics Analysis. Curr Protoc Mol Biol 8 10; 124(1):e68.
• Cetinbas M, Yu S, Sadreyev RI. Whole Genome Next-Generation Sequencing Mutation Identification in Pseudomonas aeruginosa. Curr Protoc Mol Biol 8 10; 124(1):e69.
• Savji N, Meijers WC, Bartz TM, Bhambhani V, Cushman M, Nayor M, Kizer JR, Sarma A, Blaha MJ, Gansevoort RT, Gardin JM, Hillege HL, Ji F, Kop WJ, Lau ES, Lee DS, Sadreyev R, van Gilst WH, Wang TJ, Zanni MV, Vasan RS, Allen NB, Psaty BM, van der Harst P, Levy D, Larson M, Shah SJ, de Boer RA, Gottdiener JS, Ho JE. The Association of Obesity and Cardiometabolic Traits With Incident HFpEF and HFrEF. JACC He Fail 2018 Jul 06.
• Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K. Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming. Cell S Cell 2018 Jul 04.
• Patra KC, Kato Y, Mizukami Y, Widholz S, Boukhali M, Revenco I, Grossman EA, Ji F, Sadreyev RI, Liss AS, Screaton RA, Sakamoto K, Ryan DP, Mino-Kenudson M, Castillo CF, Nomura DK, Haas W, Bardeesy N. Mutant GNAS drives pancreatic tumourigenesis by inducing PKA-mediated SIK suppression and reprogramming lipid metabolism. Nat. Cell Biol. 201 l; 20(7):811-822.
• Bar-Nur O, Gerli MFM, Di Stefano B, Almada AE, Galvin A, Coffey A, Huebner AJ, Feige P, Verheul C, Cheung P, Payzin-Dogru D, Paisant S, Anselmo A, Sadreyev RI, Ott HC, Tajbakhsh S, Rudnicki MA, Wagers AJ, Hochedlinger K. Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors. Stem Cell Reports 2018 May  10(5):1505-1521.
• Newman MA, Ji F, Fischer SEJ, Anselmo A, Sadreyev RI, Ruvkun G. The surveillance of pre-mRNA splicing is an early step in RNAi of endogenous genes. Genes Dev. 2018 May  32(9-10):670-681.
• Garcia EG, Iyer S, Loontiens S, Sadreyev RI, Speleman F, Langenau DM. Cell of origin dictates aggression and stem cell number in acute lymphoblastic leukemia.  emia 2018 Apr 18.
• Ferrer CM, Alders M, Postma AV, Park S, Klein MA, Cetinbas M, Pajkrt E, Glas A, van Koningsbruggen S, Christoffels VM, Mannens MMAM, Knegt L, Etchegaray JP, Sadreyev RI, Denu JM, Mostoslavsky G, van Maarle MC. An inactivating mutation in the histone deacetylase SIRT6 causes human perinatal lethality. Genes Dev. 2018 Ma ; 32(5-6):373-388.
• Senger S, Ingano L, Freire R, Anselmo A, Zhu W, Sadreyev R, Walker WA, Fasano A. Human Fetal-Derived Enterospheres Provide Insights on Intestinal Development and a Novel Model to Study Necrotizing Enterocolitis (NEC). Cell Mol Gastroenterol Hepat 018; 5(4):549-568.
• Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signal Cell 2017 Nov 30.
• Ardehali MB, Anselmo A, Cochrane JC, Kundu S, Sadreyev RI, Kingston RE. Polycomb Repressive Complex 2 Methylates Elongin A to Regulate Transcription. . Cell 2017 Nov 15.
• King KR, Aguirre AD, Ye YX, Sun Y, Roh JD, Ng RP, Kohler RH, Arlauckas SP, Iwamoto Y, Savol A, Sadreyev RI, Kelly M, Fitzgibbons TP, Fitzgerald KA, Mitchison T, Libby P, Nahrendorf M, Weissleder R. IRF3 and type I interferons fuel a fatal response to myocardial infarction. . Med. 2017 Nov 06.
• Del Rosario BC, Anselmo A, Wang PI, Sadreyev RI, Lee JT. Genetic Intersection of Tsix and Hedgehog Signaling during the Initiation of X-Chromosome Inactivation. Dev. Cell 2017 No ; 43(3):359-371.e6.
• Lobbardi R, Pinder J, Martinez-Pastor B, Theodorou M, Blackburn JS, Abraham BJ, Namiki Y, Mansour M, Abdelfattah NS, Molodtsov A, Alexe G, Toiber D, de Waard M, Jain E, Boukhali M, Lion M, Bhere D, Shah K, Gutierrez A, Stegmaier K,  Silverman LB, Sadreyev RI, Asara JM, Oettinger MA, Haas W, Look AT, Young RA, Mostoslavsky R, Dellaire G, Langenau DM. TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia. Cancer Discov 201 v; 7(11):1336-1353.
• Hata AN, Rowley S, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Ji F, Jung J, Light M, Lee JS, Debussche L, Sidhu S, Sadreyev RI, Watters J, Engelman JA. Synergistic activity and heterogeneous acquired resistance of combined MDM2 and MEK inhibition in KRAS mutant cancers cogene 2017 Aug 07.
• Dai N, Ji F, Wright J, Minichiello L, Sadreyev RI, Avruch J. IGF2 mRNA binding protein-2 is a tumor promoter that drives cancer proliferation through its client mRNAs IGF2 and HMGA life 2017 Jul 28; 6
• Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cel ature 2017 Jul 26.
• Chu HP, Froberg JE, Kesner B, Oh HJ, Ji F, Sadreyev R, Pinter SF, Lee JT. PAR-TERRA directs homologous sex chromosome pairing. Nat. Struct.  Biol. 2017 Jul 10.
• Walsh RM, Shen EY, Bagot RC, Anselmo A, Jiang Y, Javidfar B, Wojtkiewicz GJ, Cloutier J, Chen JW, Sadreyev R, Nestler EJ, Akbarian S, Hochedlinger K. Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice. Nat Commu 7 May 09; 8:15142.
• Pym E, Sasidharan N, Thompson-Peer KL, Simon DJ, Anselmo A, Sadreyev R, Hall Q, Nurrish S, Kaplan JM. Shank is a dose-dependent regulator of Cav1 calcium current and CREB target expressio ife 2017 May 06; 6
• Hulsmans M, Clauss S, Xiao L, Aguirre AD, King KR, Hanley A, Hucker WJ, Wülfers EM, Seemann G, Courties G, Iwamoto Y, Sun Y, Savol AJ, Sager HB, Lavine KJ, Fishbein GA, Capen DE, Da Silva N, Miquerol L, Wakimoto H, Seidman CE, Sadreyev RI, Naxerova K, Mitchell RN, Brown D, Libby P, Weissleder R, Swirski FK, Kohl P, Vinegoni C, Milan DJ, Ellinor PT, Nahrendorf M. Macrophages Facilitate Electrical Conduction in the Heart. Cell 2017 Apr  69(3):510-522.e20.
• Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.   Dev. 2017 Mar 29.
• Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cel m Cell 2017 Mar 29.
• Lau MS, Schwartz MG, Kundu S, Savol AJ, Wang PI, Marr SK, Grau DJ, Schorderet P, Sadreyev RI, Tabin CJ, Kingston RE. Mutation of a nucleosome compaction region disrupts Polycomb-mediated axial patterning. Science 2017 Mar  55(6329):1081-1084.
• Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Mol. Cell 2017 F ; 65(3):432-446.e5.
• Strle K, Sulka KB, Pianta A, Crowley JT, Arvikar SL, Anselmo A, Sadreyev R, Steere AC. TH17 Cytokine Responses in Lyme Disease Correlate with Borreliaburgdorferi Antibodies During Early Infection in Patients with Erythema Migrans and with Autoantibodies Late in the Illness in Patients with Antibiotic-Refractory Lyme Arthritis. Clin. I . Dis. 2017 Jan 11.
• Lehrbach NJ, Ji F, Sadreyev R. Next-Generation Sequencing for Identification of EMS-Induced Mutations in Caenorhabditis elegans. Curr Protoc Mol Biol 2017 Ja  117:7.29.1-7.29.12.
• Fusco DN, Pratt H, Kandilas S, Cheon SS, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O'Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Fro crobiol 2017; 8:240.
• Savol AJ, Wang PI, Jeon Y, Colognori D, Yildirim E, Pinter SF, Payer B, Lee JT, Sadreyev RI. Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. PLoS  017; 12(8):e0182568.
• Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA. Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants. Microbi 016 Dec 30; 4(1):68.
• Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M. Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs. Mol. Cell 2016 15; 64(6):1088-1101.
• McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. BMC Biol 6 Dec 07; 14(1):105.
• Moore JC, Tang Q, Yordán NT, Garcia EG, Lobbardi R, Ramakrishnan A, Marvin DL, Anselmo A, Sadreyev RI, Langenau DM. Single-cell imaging of normal and malignant cell engraftment into optically clear prkdc-null SCID zebrafish. J. Exp. Med. 2016 N ; 213(12):2575-2589.
• Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM. SIKs control osteocyte responses to parathyroid hormone. Nat Com 016 Oct 19; 7:13176.
• Sykes DB, Kfoury YS, Mercier FE, Wawer MJ, Law JM, Haynes MK, Lewis TA, Schajnovitz A, Jain E, Lee D, Meyer H, Pierce KA, Tolliday NJ, Waller A, Ferrara SJ, Eheim AL, Stoeckigt D, Maxcy KL, Cobert JM, Bachand J, Szekely BA, Mukherjee S, Sklar LA, Kotz JD, Clish CB, Sadreyev RI, Clemons PA, Janzer A, Schreiber SL, Scadden DT. Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Le a. Cell 2016 Sep 14.
• Moore JC, Mulligan TS, Torres Yordán N, Castranova D, Pham VN, Tang Q, Lobbardi R, Anselmo A, Liwski RS, Berman JN, Sadreyev RI, Weinstein BM, Langenau DM. T cell immune deficiency in zap70 mutant zebrafish. Mo ll. Biol. 2016 Sep 6.
• Sarkar A, Huebner AJ, Sulahian R, Anselmo A, Xu X, Flattery K, Desai N, Sebastian C, Yram MA, Arnold K, Rivera M, Mostoslavsky R, Bronson R, Bass AJ, Sadreyev R, Shivdasani RA, Hochedlinger K. Sox2 Suppresses Gastric Tumorigenesis in   Cell Rep 2016 Aug 3.
• Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R, Borowsky ML, Eggan K, Zon L, Galloway JL, Kingston RE. CAT7 and cat7l long non-coding RNAs Tune Polycomb Repressive Complex 1 Function During Human and Zebrafish Development.  ol. Chem. 2016 Jul 12.
• Deaton AM, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE. Enhancer regions show high histone H3.3 turnover that changes during differenti . Elife 2016 Jun 15; 5
• Kugel S, Sebastián C, Fitamant J, Ross KN, Saha SK, Jain E, Gladden A, Arora KS, Kato Y, Rivera MN, Ramaswamy S, Sadreyev RI, Goren A, Deshpande V, Bardeesy N, Mostoslavsky R. SIRT6 Suppresses Pancreatic Cancer through Control  n28b. Cell 2016 May 11.
• Moore FE, Garcia EG, Lobbardi R, Jain E, Tang Q, Cortes M, Molodtsov A, Kasheta M, Luo CC, Mylvaganam R, Yoder JA, Blackburn JS, Sadreyev RI, Ceol CJ, North TE, Langenau DM. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafi . Exp. Med. 2016 May 2.
• Bukhari SI, Truesdell SS, Lee S, Kollu S, Classon A, Boukhali M, Jain E, Mortensen RD, Yanagiya A, Sadreyev RI, Haas W, Vasudevan S. A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence. Mol. Ce 16 Mar 3; 61(5):760-73.
• Hata AN, Niederst MJ, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Mulvey HE, Maruvka YE, Ji F, Bhang HE, Siravegna G, Hu H, Raoof S, Lockerman E, Kalsy A, Lee D, Keating CL, Ruddy DA, Damon LJ, Crystal AS, Costa C, Piotrowska Z, Bardelli A, Iafrate AJ, Sadreyev RI, Stegmeier F, Getz G, Sequist LV, Faber AC, Engelman JA. Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition. Nat.  2016 Mar; 22(3):262-9.
• Nishikawa JL, Boeszoermenyi A, Vale-Silva LA, Torelli R, Posteraro B, Sohn YJ, Ji F, Gelev V, Sanglard D, Sanguinetti M, Sadreyev RI, Mukherjee G, Bhyravabhotla J, Buhrlage SJ, Gray NS, Wagner G, Näär AM, Arthanari H. Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction. Nature 2 eb 25; 530(7591):485-9.
• Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ. Chromatin topology is coupled to Polycomb group protein subnuclear organizatio t Commun 2016; 7:10291.
• Varmeh S, Borre PV, Gunda V, Brauner E, Holm T, Wang Y, Sadreyev RI, Parangi S. Genome-wide analysis of differentially expressed miRNA in PLX4720-resistant and parental human thyroid cancer cel es. Surgery 2015 Oct 5.
• Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV. Using homology relations within a database markedly boosts protein sequence similarity search. Proc. Natl. Acad. Sci. U.S.A.  Jun 2; 112(22):7003-8.
• Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genet 015 Jun; 200(2):537-49.
• Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y. PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. Nu  Acids Res. 2015 May 9.
• Guo S, Ergun A, Lu L, Walker WA, Ganguli K. Secreted Metabolites of Bifidobacterium infantis and Lactobacillus acidophilus Protect Immature Human Enterocytes from IL-1?-Induced Inflammation: A Transcription Profiling Analysis. P NE 2015; 10(4):e0124549.
• Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets. Ce 14 Nov 6; 159(4):869-83.
• West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol. Ce 14 Sep 4; 55(5):791-802.
• Broering TJ, Alavattam KG, Sadreyev RI, Ichijima Y, Kato Y, Hasegawa K, Camerini-Otero RD, Lee JT, Andreassen PR, Namekawa SH. BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis. J. Cell Bio 14 Jun 9; 205(5):663-75.
• Sadreyev RI. Informatics for molecular biologists. Curr Protoc Biol 2014; 106:19.0.1-2.
• Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax c x. Elife 2014; 3:e02833.
• Sadreyev RI, Yildirim E, Pinter SF, Lee JT. Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci. Proc. Natl. Acad. Sci. U.S.A.  Apr 23; 110(17):6949-54.
• Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT. Xist RNA is a potent suppressor of hematologic cancer in mice. Ce 13 Feb 14; 152(4):727-42.
• Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome  2012 Oct; 22(10):1864-76.
• Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem  2012 Jul 6; 11(1):75-90.
• Yildirim E, Sadreyev RI, Pinter SF, Lee JT. X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat. Struct. Mol l. 2012 Jan; 19(1):56-61.
• Spencer RJ, del Rosario BC, Pinter SF, Lessing D, Sadreyev RI, Lee JT. A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. Gen  2011 Oct; 189(2):441-54.
• Sun S, Fukue Y, Nolen L, Sadreyev R, Lee JT. Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expressi ranscription ; 1(1):46-56.
• Sadreyev RI, Feramisco JD, Tsao H, Grishin NV. Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways. Bioinformat 009 Nov 15; 25(22):2891-6.
• Feramisco JD, Sadreyev RI, Murray ML, Grishin NV, Tsao H. Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database. J. Invest. Derma 2009 Nov; 129(11):2628-36.
• Wang Y, Sadreyev RI, Grishin NV. PROCAIN server for remote protein sequence similarity search. Bioinformat 009 Aug 15; 25(16):2076-7.
• Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res. 2009 J 7(Web Server issue):W90-4.
• Sadreyev RI, Kim BH, Grishin NV. Discrete-continuous duality of protein structure space. Curr. Opin. Struc ol. 2009 Jun; 19(3):321-8.
• Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucleic Acids  2009 Jun; 37(11):3522-30.
• Sadreyev RI, Shi S, Baker D, Grishin NV. Structure similarity measure with penalty for close non-equivalent residues. Bioinformati 09 May 15; 25(10):1259-63.
• Sadreyev RI, Wang Y, Grishin NV. Considering scores between unrelated proteins in the search database improves profile comparison. B oinformatics 2009; 10:399.
• Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. P ns 2009; 77 Suppl 9:89-99.
• Sadreyev RI, Grishin NV. Accurate statistical model of comparison between multiple sequence alignments. Nucleic Ac es. 2008 Apr; 36(7):2240-8.
• Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for remote homology inference. Nucleic Acids Res. 2007 J 5(Web Server issue):W653-8.
• Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV. A comprehensive system for evaluation of remote sequence similarity detection. Bioinformatics 2007; 8:314.
• Krishna SS, Sadreyev RI, Grishin NV. A tale of two ferredoxins: sequence similarity and structural differenc MC Struct. Biol. 2006; 6:8.
• Sadreyev RI, Grishin NV. Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and fol MC Struct. Biol. 2006; 6:6.
• Kim BH, Sadreyev R, Grishin NV. COG4849 is a novel family of nucleotidyltransferases.  l. Recognit. ; 18(5):422-5.
• Sadreyev RI, Grishin NV. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. BMC B ormatics 2004 Aug 5; 5:106.
• Sadreyev RI, Grishin NV. Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinfor s 2004 Apr 12; 20(6):818-28.
• Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Prot ci. 2003 Oct; 12(10):2262-72.
• Mittelman D, Sadreyev R, Grishin N. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinfo cs 2003 Aug 12; 19(12):1531-9
• Pei J, Sadreyev R, Grishin NV. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioi atics 2003 Feb 12; 19(3):427-8
• Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. M iol. 2003 Feb 7; 326(1):317-36.
• Kinch LN, Wrabl JO, Krishna SS, Majumdar I, Sadreyev RI, Qi Y, Pei J, Cheng H, Grishin NV. CASP5 assessment of fold recognition target predictions teins 2003; 53 Suppl 6:395-409.
• Sadreyev RI, Panchin YV. Effects of glutamate agonists on the isolated neurons from the locomotor network of the mollusc Clione limacina. Ne port 2002 Dec 3; 13(17):2235-9.
• Sadreyev RI, Panchin YV. The role of putative glutamatergic neurons and their connections in the locomotor central pattern generator of the mollusk, Clione limacina. Comp. Biochem. Physiol., Part A Mol. Integ ysiol. 2000 Jun; 126(2):193-202.
• Arshavsky YI, Deliagina TG, Orlovsky GN, Panchin YV, Popova LB, Sadreyev RI. Analysis of the central pattern generator for swimming in the mollusk Clione. Ann. N.  ad. Sci. 1998 Nov 16; 860:51-69.
• Panchin YV, Sadreyev RI. Effects of acetylcholine and glutamate on isolated neurons of locomotory network of Clione. Neuroreport 1997 Sep

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