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Debashis Sahoo

TitleAssistant Professor
InstitutionUniversity of California San Diego
DepartmentPediatrics
Address9500 Gilman Drive #0984
La Jolla CA 92093
Phone858-246-1803
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    Collapse Research 
    Collapse Research Activities and Funding
    Application of Boolean Networks to discover stem and progenitor cells
    NIH/NCI R00CA151673Jul 1, 2014 - Aug 31, 2017
    Role: Principal Investigator
    Application of Boolean Networks to discover stem and progenitor cells
    NIH/NCI K99CA151673Jul 1, 2011 - Jun 30, 2014
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH. Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma. Nat Commun. 2018 Nov 02; 9(1):4651. PMID: 30389946.
      View in: PubMed
    2. Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH. Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma. Nat Commun. 2018 Oct 08; 9(1):4121. PMID: 30297829.
      View in: PubMed
    3. Chan CKF, Gulati GS, Sinha R, Tompkins JV, Lopez M, Carter AC, Ransom RC, Reinisch A, Wearda T, Murphy M, Brewer RE, Koepke LS, Marecic O, Manjunath A, Seo EY, Leavitt T, Lu WJ, Nguyen A, Conley SD, Salhotra A, Ambrosi TH, Borrelli MR, Siebel T, Chan K, Schallmoser K, Seita J, Sahoo D, Goodnough H, Bishop J, Gardner M, Majeti R, Wan DC, Goodman S, Weissman IL, Chang HY, Longaker MT. Identification of the Human Skeletal Stem Cell. Cell. 2018 Sep 20; 175(1):43-56.e21. PMID: 30241615.
      View in: PubMed
    4. Aznar N, Ear J, Dunkel Y, Sun N, Satterfield K, He F, Kalogriopoulos NA, Lopez-Sanchez I, Ghassemian M, Sahoo D, Kufareva I, Ghosh P. Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple. Sci Signal. 2018 Feb 27; 11(519). PMID: 29487190.
      View in: PubMed
    5. Sahoo D, Wei W, Auman H, Hurtado-Coll A, Carroll PR, Fazli L, Gleave ME, Lin DW, Nelson PS, Simko J, Thompson IM, Leach RJ, Troyer DA, True LD, McKenney JK, Feng Z, Brooks JD. Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. Oncotarget. 2018 Jan 19; 9(5):6550-6561. PMID: 29464091.
      View in: PubMed
    6. Medal RM, Im AM, Yamamoto Y, Lakhdari O, Blackwell TS, Hoffman HM, Sahoo D, Prince LS. The innate immune response in fetal lung mesenchymal cells targets VEGFR2 expression and activity. Am J Physiol Lung Cell Mol Physiol. 2017 Jun 01; 312(6):L861-L872. PMID: 28336813.
      View in: PubMed
    7. Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, van Weele LJ, Heiser D, Sim S, Lam J, Quake S, Clarke MF. A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell. 2017 02 02; 20(2):247-260.e5. PMID: 28041896.
      View in: PubMed
    8. Ngo M, Han A, Lakatos A, Sahoo D, Hachey SJ, Weiskopf K, Beck AH, Weissman IL, Boiko AD. Antibody Therapy Targeting CD47 and CD271 Effectively Suppresses Melanoma Metastasis in Patient-Derived Xenografts. Cell Rep. 2016 08 09; 16(6):1701-1716. PMID: 27477289.
      View in: PubMed
    9. Dalerba P, Sahoo D, Clarke MF. CDX2 as a Prognostic Biomarker in Colon Cancer. N Engl J Med. 2016 06 02; 374(22):2184. PMID: 27248627.
      View in: PubMed
    10. Krampitz GW, George BM, Willingham SB, Volkmer JP, Weiskopf K, Jahchan N, Newman AM, Sahoo D, Zemek AJ, Yanovsky RL, Nguyen JK, Schnorr PJ, Mazur PK, Sage J, Longacre TA, Visser BC, Poultsides GA, Norton JA, Weissman IL. Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors. Proc Natl Acad Sci U S A. 2016 Apr 19; 113(16):4464-9. PMID: 27035983; PMCID: PMC4843455 [Available on 10/19/16].
    11. Rennert RC, Achrol AS, Januszyk M, Kahn SA, Liu TT, Liu Y, Sahoo D, Rodrigues M, Maan ZN, Wong VW, Cheshier SH, Chang SD, Steinberg GK, Harsh GR, Gurtner GC. Multiple Subsets of Brain Tumor Initiating Cells Coexist in Glioblastoma. Stem Cells. 2016 06; 34(6):1702-7. PMID: 26991945.
      View in: PubMed
    12. Chen JY, Miyanishi M, Wang SK, Yamazaki S, Sinha R, Kao KS, Seita J, Sahoo D, Nakauchi H, Weissman IL. Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche. Nature. 2016 Feb 11; 530(7589):223-7. PMID: 26863982; PMCID: PMC4854608.
    13. Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF. CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med. 2016 Jan 21; 374(3):211-22. PMID: 26789870; PMCID: PMC4784450.
    14. Skelton RJ, Brady B, Khoja S, Sahoo D, Engel J, Arasaratnam D, Saleh KK, Abilez OJ, Zhao P, Stanley EG, Elefanty AG, Kwon M, Elliott DA, Ardehali R. CD13 and ROR2 Permit Isolation of Highly Enriched Cardiac Mesoderm from Differentiating Human Embryonic Stem Cells. Stem Cell Reports. 2016 Jan 12; 6(1):95-108. PMID: 26771355; PMCID: PMC4720015.
    15. Cheah MT, Chen JY, Sahoo D, Contreras-Trujillo H, Volkmer AK, Scheeren FA, Volkmer JP, Weissman IL. CD14-expressing cancer cells establish the inflammatory and proliferative tumor microenvironment in bladder cancer. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4725-30. PMID: 25825750; PMCID: PMC4403197.
    16. Chan CK, Seo EY, Chen JY, Lo D, McArdle A, Sinha R, Tevlin R, Seita J, Vincent-Tompkins J, Wearda T, Lu WJ, Senarath-Yapa K, Chung MT, Marecic O, Tran M, Yan KS, Upton R, Walmsley GG, Lee AS, Sahoo D, Kuo CJ, Weissman IL, Longaker MT. Identification and specification of the mouse skeletal stem cell. Cell. 2015 Jan 15; 160(1-2):285-98. PMID: 25594184; PMCID: PMC4297645.
    17. Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G, Kalisky T, Rothenberg ME, Quake SR, Clarke MF. A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nat Cell Biol. 2014 Dec; 16(12):1238-48. PMID: 25362351.
      View in: PubMed
    18. Pan Y, Volkmer JP, Mach KE, Rouse RV, Liu JJ, Sahoo D, Chang TC, Metzner TJ, Kang L, van de Rijn M, Skinner EC, Gambhir SS, Weissman IL, Liao JC. Endoscopic molecular imaging of human bladder cancer using a CD47 antibody. Sci Transl Med. 2014 Oct 29; 6(260):260ra148. PMID: 25355698.
      View in: PubMed
    19. Shin K, Lim A, Zhao C, Sahoo D, Pan Y, Spiekerkoetter E, Liao JC, Beachy PA. Hedgehog signaling restrains bladder cancer progression by eliciting stromal production of urothelial differentiation factors. Cancer Cell. 2014 Oct 13; 26(4):521-33. PMID: 25314078.
      View in: PubMed
    20. Dimov IK, Lu R, Lee EP, Seita J, Sahoo D, Park SM, Weissman IL, Lee LP. Discriminating cellular heterogeneity using microwell-based RNA cytometry. Nat Commun. 2014 Mar 25; 5:3451. PMID: 24667995; PMCID: PMC4075946.
    21. Voskoboynik A, Newman AM, Corey DM, Sahoo D, Pushkarev D, Neff NF, Passarelli B, Koh W, Ishizuka KJ, Palmeri KJ, Dimov IK, Keasar C, Fan HC, Mantalas GL, Sinha R, Penland L, Quake SR, Weissman IL. Identification of a colonial chordate histocompatibility gene. Science. 2013 Jul 26; 341(6144):384-7. PMID: 23888037; PMCID: PMC3810301.
    22. Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White RA, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife. 2013 Jul 02; 2:e00569. PMID: 23840927; PMCID: PMC3699833.
    23. Wu B, Sahoo D, Brooks JD. Comprehensive gene expression changes associated with mouse postnatal kidney development. J Urol. 2013 Jun; 189(6):2385-90. PMID: 23220383.
      View in: PubMed
    24. Rinkevich Y, Mori T, Sahoo D, Xu PX, Bermingham JR, Weissman IL. Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs, and their vasculature. Nat Cell Biol. 2012 Dec; 14(12):1251-60. PMID: 23143399; PMCID: PMC3685475.
    25. Sahoo D. The power of boolean implication networks. Front Physiol. 2012; 3:276. PMID: 22934030; PMCID: PMC3429050.
    26. Seita J, Sahoo D, Rossi DJ, Bhattacharya D, Serwold T, Inlay MA, Ehrlich LI, Fathman JW, Dill DL, Weissman IL. Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS One. 2012; 7(7):e40321. PMID: 22815738; PMCID: PMC3399844.
    27. Lewis PW, Sahoo D, Geng C, Bell M, Lipsick JS, Botchan MR. Drosophila lin-52 acts in opposition to repressive components of the Myb-MuvB/dREAM complex. Mol Cell Biol. 2012 Aug; 32(16):3218-27. PMID: 22688510; PMCID: PMC3434544.
    28. Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, Naik TJ, Storm TA, Mosley AR, Edris B, Schmid SM, Sun CK, Chua MS, Murillo O, Rajendran P, Cha AC, Chin RK, Kim D, Adorno M, Raveh T, Tseng D, Jaiswal S, Enger PØ, Steinberg GK, Li G, So SK, Majeti R, Harsh GR, van de Rijn M, Teng NN, Sunwoo JB, Alizadeh AA, Clarke MF, Weissman IL. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors. Proc Natl Acad Sci U S A. 2012 Apr 24; 109(17):6662-7. PMID: 22451913; PMCID: PMC3340046.
    29. Volkmer JP, Sahoo D, Chin RK, Ho PL, Tang C, Kurtova AV, Willingham SB, Pazhanisamy SK, Contreras-Trujillo H, Storm TA, Lotan Y, Beck AH, Chung BI, Alizadeh AA, Godoy G, Lerner SP, van de Rijn M, Shortliffe LD, Weissman IL, Chan KS. Three differentiation states risk-stratify bladder cancer into distinct subtypes. Proc Natl Acad Sci U S A. 2012 Feb 07; 109(6):2078-83. PMID: 22308455; PMCID: PMC3277552.
    30. Pang WW, Price EA, Sahoo D, Beerman I, Maloney WJ, Rossi DJ, Schrier SL, Weissman IL. Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age. Proc Natl Acad Sci U S A. 2011 Dec 13; 108(50):20012-7. PMID: 22123971; PMCID: PMC3250139.
    31. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol. 2011 Nov 13; 29(12):1120-7. PMID: 22081019; PMCID: PMC3237928.
    32. Tang C, Lee AS, Volkmer JP, Sahoo D, Nag D, Mosley AR, Inlay MA, Ardehali R, Chavez SL, Pera RR, Behr B, Wu JC, Weissman IL, Drukker M. An antibody against SSEA-5 glycan on human pluripotent stem cells enables removal of teratoma-forming cells. Nat Biotechnol. 2011 Aug 14; 29(9):829-34. PMID: 21841799; PMCID: PMC3537836.
    33. Ooi AG, Sahoo D, Adorno M, Wang Y, Weissman IL, Park CY. MicroRNA-125b expands hematopoietic stem cells and enriches for the lymphoid-balanced and lymphoid-biased subsets. Proc Natl Acad Sci U S A. 2010 Dec 14; 107(50):21505-10. PMID: 21118986; PMCID: PMC3003003.
    34. Sahoo D, Seita J, Bhattacharya D, Inlay MA, Weissman IL, Plevritis SK, Dill DL. MiDReG: a method of mining developmentally regulated genes using Boolean implications. Proc Natl Acad Sci U S A. 2010 Mar 30; 107(13):5732-7. PMID: 20231483; PMCID: PMC2851930.
    35. Inlay MA, Bhattacharya D, Sahoo D, Serwold T, Seita J, Karsunky H, Plevritis SK, Dill DL, Weissman IL. Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. Genes Dev. 2009 Oct 15; 23(20):2376-81. PMID: 19833765; PMCID: PMC2764492.
    36. Bhamre S, Sahoo D, Tibshirani R, Dill DL, Brooks JD. Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate. 2009 Feb 01; 69(2):181-90. PMID: 18973173; PMCID: PMC2612096.
    37. Sahoo D, Dill DL, Gentles AJ, Tibshirani R, Plevritis SK. Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol. 2008 Oct 30; 9(10):R157. PMID: 18973690.
      View in: PubMed
    38. Shachaf CM, Gentles AJ, Elchuri S, Sahoo D, Soen Y, Sharpe O, Perez OD, Chang M, Mitchel D, Robinson WH, Dill D, Nolan GP, Plevritis SK, Felsher DW. Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Res. 2008 Jul 01; 68(13):5132-42. PMID: 18593912; PMCID: PMC4191850.
    39. Wu CH, Sahoo D, Arvanitis C, Bradon N, Dill DL, Felsher DW. Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet. 2008 Jun 06; 4(6):e1000090. PMID: 18535662; PMCID: PMC2390767.