Sam Kuan

Title(s)	SRA 3, Cellular and Molecular Medicine
School	Vc-health Sciences-schools
Address	9500 Gilman Drive # La Jolla CA 92093
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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. to make corrections and additions.

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Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature. 2023 Dec; 624(7991):378-389. Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, Lin L, Yang Q, Lee S, Li B, Kuan S, Liu H, Zhou J, Pinto-Duarte A, Lucero J, Osteen J, Nunn M, Smith KA, Tasic B, Yao Z, Zeng H, Wang Z, Shang J, Behrens MM, Ecker JR, Wang A, Preissl S, Ren B. PMID: 38092917; PMCID: PMC10719105.

View in: PubMed Mentions: 8 Fields:
Sci Science
Translation:Humans Animals Cells
An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 2021 10; 598(7879):129-136. Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. PMID: 34616068; PMCID: PMC8494637.

View in: PubMed Mentions: 76 Fields:
Sci Science
Translation:Humans Animals Cells
A compendium of promoter-centered long-range chromatin interactions in the human genome. Nat Genet. 2019 10; 51(10):1442-1449. Jung I, Schmitt A, Diao Y, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr CL, Li B, Kuan S, Kim D, Ren B. PMID: 31501517; PMCID: PMC6778519.

View in: PubMed Mentions: 166 Fields:
Gen Genetics
Translation:Humans Cells
Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci. 2018 Jul; 21(7):1015. Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. PMID: 29497140.

View in: PubMed Mentions: 2 Fields:
Neu Neurology
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci. 2018 03; 21(3):432-439. Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. PMID: 29434377; PMCID: PMC5862073.

View in: PubMed Mentions: 153 Fields:
Neu Neurology
Translation:Animals Cells
Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature. 2016 09 22; 537(7621):548-552. Dahl JA, Jung I, Aanes H, Greggains GD, Manaf A, Lerdrup M, Li G, Kuan S, Li B, Lee AY, Preissl S, Jermstad I, Haugen MH, Suganthan R, Bjørås M, Hansen K, Dalen KT, Fedorcsak P, Ren B, Klungland A. PMID: 27626377; PMCID: PMC6283663.

View in: PubMed Mentions: 267 Fields:
Sci Science
Translation:Humans Animals Cells
EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling. Mol Cell. 2015 Oct 15; 60(2):307-18. Liu F, Hon GC, Villa GR, Turner KM, Ikegami S, Yang H, Ye Z, Li B, Kuan S, Lee AY, Zanca C, Wei B, Lucey G, Jenkins D, Zhang W, Barr CL, Furnari FB, Cloughesy TF, Yong WH, Gahman TC, Shiau AK, Cavenee WK, Ren B, Mischel PS. PMID: 26455392; PMCID: PMC4609298.

View in: PubMed Mentions: 103 Fields:
Cel Cell Biology Mol Molecular Biology
Translation:Humans Animals Cells
Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015 Feb 19; 518(7539):350-354. Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. PMID: 25693566; PMCID: PMC4449149.

View in: PubMed Mentions: 121 Fields:
Sci Science
Translation:Humans Cells
A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. PMID: 25409824; PMCID: PMC4266106.

View in: PubMed Mentions: 886 Fields:
Sci Science
Translation:Humans Animals Cells
5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell. 2014 Oct 23; 56(2):286-297. Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, Ren B. PMID: 25263596; PMCID: PMC4319980.

View in: PubMed Mentions: 192 Fields:
Cel Cell Biology Mol Molecular Biology
Translation:Animals Cells
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013 May 23; 153(5):1134-48. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. PMID: 23664764; PMCID: PMC3786220.

View in: PubMed Mentions: 430 Fields:
Cel Cell Biology
Translation:Humans Animals Cells
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. PMID: 22889292; PMCID: PMC3491367.

View in: PubMed Mentions: 288 Fields:
Gen Genetics
Translation:Humans Animals
A map of the cis-regulatory sequences in the mouse genome. Nature. 2012 Aug 02; 488(7409):116-20. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. PMID: 22763441; PMCID: PMC4041622.

View in: PubMed Mentions: 837 Fields:
Sci Science
Translation:Animals Cells
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012 Feb; 22(2):246-58. Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. PMID: 22156296; PMCID: PMC3266032.

View in: PubMed Mentions: 297 Fields:
Gen Genetics
Translation:Humans Cells
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 2011 Oct; 21(10):1393-409. Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B. PMID: 21876557; PMCID: PMC3193447.

View in: PubMed Mentions: 55 Fields:
Cel Cell Biology
Translation:Humans Cells
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res. 2011 Aug; 39(14):6056-68. Galante PA, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FC, Gerber AL, Nicolás MF, Salim AC, Silva AP, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RG, Oliveira TY, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA, Vasconcelos AT, Ren B, Zago MA, Strausberg RL, Simpson AJ, de Souza SJ, Camargo AA. PMID: 21493686; PMCID: PMC3152357.

View in: PubMed Mentions: 10 Fields:
Bio Biochemistry
Translation:Humans Cells
An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3. Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. PMID: 21131980; PMCID: PMC3017233.

View in: PubMed Mentions: 223 Fields:
Mol Molecular Biology
Translation:Animals Cells
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol. 2010; 11(11):R114. Zhao Q, Kirkness EF, Caballero OL, Galante PA, Parmigiani RB, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos AT, Ren B, de Souza SJ, Camargo AA, Simpson AJ, Strausberg RL. PMID: 21108794; PMCID: PMC3156953.

View in: PubMed Mentions: 19 Fields:
Gen Genetics
Translation:Humans Cells
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010 May 07; 6(5):479-91. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. PMID: 20452322; PMCID: PMC2867844.

View in: PubMed Mentions: 456 Fields:
Cel Cell Biology
Translation:Humans Cells