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Molecular characterization of renal cell carcinoma tumors from a phase III anti-angiogenic adjuvant therapy trial. Nat Commun. 2022 10 10; 13(1):5959.
Motzer RJ, Martini JF, Mu XJ, Staehler M, George DJ, Valota O, Lin X, Pandha HS, Ching KA, Ravaud A. PMID: 36216827; PMCID: PMC9550765.
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PubMed Mentions:
2 Fields:
Translation:
Humans
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Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial. Nat Med. 2021 12; 27(12):2200-2211.
Powles T, Sridhar SS, Loriot Y, Bellmunt J, Mu XJ, Ching KA, Pu J, Sternberg CN, Petrylak DP, Tambaro R, Dourthe LM, Alvarez-Fernandez C, Aarts M, di Pietro A, Grivas P, Davis CB. PMID: 34893775.
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PubMed Mentions:
16 Fields:
Translation:
Humans
-
HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol. 2022 01; 23(1):172-184.
Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JL, Carrington M. PMID: 34895481; PMCID: PMC8742225.
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PubMed Mentions:
17 Fields:
Translation:
Humans
-
Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes. Cell Rep. 2021 12 07; 37(10):110089.
Markenscoff-Papadimitriou E, Binyameen F, Whalen S, Price J, Lim K, Ypsilanti AR, Catta-Preta R, Pai EL, Mu X, Xu D, Pollard KS, Nord AS, State MW, Rubenstein JL. PMID: 34879283; PMCID: PMC9512081.
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PubMed Mentions:
14 Fields:
Translation:
AnimalsCells
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Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor. Cancer Cell. 2021 10 11; 39(10):1404-1421.e11.
Freeman-Cook K, Hoffman RL, Miller N, Almaden J, Chionis J, Zhang Q, Eisele K, Liu C, Zhang C, Huser N, Nguyen L, Costa-Jones C, Niessen S, Carelli J, Lapek J, Weinrich SL, Wei P, McMillan E, Wilson E, Wang TS, McTigue M, Ferre RA, He YA, Ninkovic S, Behenna D, Tran KT, Sutton S, Nagata A, Ornelas MA, Kephart SE, Zehnder LR, Murray B, Xu M, Solowiej JE, Visswanathan R, Boras B, Looper D, Lee N, Bienkowska JR, Zhu Z, Kan Z, Ding Y, Mu XJ, Oderup C, Salek-Ardakani S, White MA, VanArsdale T, Dann SG. PMID: 34520734.
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PubMed Mentions:
32 Fields:
Translation:
Humans
-
Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer. Prostate Cancer Prostatic Dis. 2021 09; 24(3):786-793.
Armstrong AJ, Li X, Tucker M, Li S, Mu XJ, Eng KW, Sboner A, Rubin M, Gerstein M. PMID: 33568750; PMCID: PMC8384621.
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PubMed Mentions:
4 Fields:
Translation:
Humans
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Avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma: biomarker analysis of the phase 3 JAVELIN Renal 101 trial. Nat Med. 2020 11; 26(11):1733-1741.
Motzer RJ, Robbins PB, Powles T, Albiges L, Haanen JB, Larkin J, Mu XJ, Ching KA, Uemura M, Pal SK, Alekseev B, Gravis G, Campbell MT, Penkov K, Lee JL, Hariharan S, Wang X, Zhang W, Wang J, Chudnovsky A, di Pietro A, Donahue AC, Choueiri TK. PMID: 32895571; PMCID: PMC8493486.
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PubMed Mentions:
138 Fields:
Translation:
HumansCellsCTClinical Trials
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Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. Nat Commun. 2020 07 20; 11(1):3644.
Zaidi SH, Harrison TA, Phipps AI, Steinfelder R, Trinh QM, Qu C, Banbury BL, Georgeson P, Grasso CS, Giannakis M, Adams JB, Alwers E, Amitay EL, Barfield RT, Berndt SI, Borozan I, Brenner H, Brezina S, Buchanan DD, Cao Y, Chan AT, Chang-Claude J, Connolly CM, Drew DA, Farris AB, Figueiredo JC, French AJ, Fuchs CS, Garraway LA, Gruber S, Guinter MA, Hamilton SR, Harlid S, Heisler LE, Hidaka A, Hopper JL, Huang WY, Huyghe JR, Jenkins MA, Krzyzanowski PM, Lemire M, Lin Y, Luo X, Mardis ER, McPherson JD, Miller JK, Moreno V, Mu XJ, Nishihara R, Papadopoulos N, Pasternack D, Quist MJ, Rafikova A, Reid EEG, Shinbrot E, Shirts BH, Stein LD, Teney CD, Timms L, Um CY, Van Guelpen B, Van Tassel M, Wang X, Wheeler DA, Yung CK, Hsu L, Ogino S, Gsur A, Newcomb PA, Gallinger S, Hoffmeister M, Campbell PT, Thibodeau SN, Sun W, Hudson TJ, Peters U. PMID: 32686686; PMCID: PMC7371703.
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PubMed Mentions:
36 Fields:
Translation:
Humans
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Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. BMC Bioinformatics. 2020 Mar 20; 21(1):119.
Smith AM, Walsh JR, Long J, Davis CB, Henstock P, Hodge MR, Maciejewski M, Mu XJ, Ra S, Zhao S, Ziemek D, Fisher CK. PMID: 32197580; PMCID: PMC7085143.
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PubMed Mentions:
22 Fields:
Translation:
Humans
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First-in-Human Study of Utomilumab, a 4-1BB/CD137 Agonist, in Combination with Rituximab in Patients with Follicular and Other CD20+ Non-Hodgkin Lymphomas. Clin Cancer Res. 2020 06 01; 26(11):2524-2534.
Gopal AK, Levy R, Houot R, Patel SP, Popplewell L, Jacobson C, Mu XJ, Deng S, Ching KA, Chen Y, Davis CB, Huang B, Fly KD, Thall A, Woolfson A, Bartlett NL. PMID: 32144134.
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PubMed Mentions:
27 Fields:
Translation:
HumansCTClinical Trials
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Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures. Nat Commun. 2018 04 30; 9(1):1725.
Kan Z, Ding Y, Kim J, Jung HH, Chung W, Lal S, Cho S, Fernandez-Banet J, Lee SK, Kim SW, Lee JE, Choi YL, Deng S, Kim JY, Ahn JS, Sha Y, Mu XJ, Nam JY, Im YH, Lee S, Park WY, Nam SJ, Park YH. PMID: 29713003; PMCID: PMC5928087.
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PubMed Mentions:
61 Fields:
Translation:
HumansCells
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TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas. Oncoimmunology. 2018; 7(7):e1442999.
Hamada T, Soong TR, Masugi Y, Kosumi K, Nowak JA, da Silva A, Mu XJ, Twombly TS, Koh H, Yang J, Song M, Liu L, Gu M, Shi Y, Nosho K, Morikawa T, Inamura K, Shukla SA, Wu CJ, Garraway LA, Zhang X, Wu K, Meyerhardt JA, Chan AT, Glickman JN, Rodig SJ, Freeman GJ, Fuchs CS, Nishihara R, Giannakis M, Ogino S. PMID: 29900052; PMCID: PMC5993482.
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PubMed Mentions:
34 Fields:
-
Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov. 2018 06; 8(6):730-749.
Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. PMID: 29510987; PMCID: PMC5984687.
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PubMed Mentions:
226 Fields:
Translation:
HumansCells
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Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018 03 01; 102(3):401-414.
AlDubayan SH, Giannakis M, Moore ND, Han GC, Reardon B, Hamada T, Mu XJ, Nishihara R, Qian Z, Liu L, Yurgelun MB, Syngal S, Garraway LA, Ogino S, Fuchs CS, Van Allen EM. PMID: 29478780; PMCID: PMC5985280.
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PubMed Mentions:
45 Fields:
Translation:
HumansCells
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Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. Sci Transl Med. 2017 Aug 09; 9(402).
Giltnane JM, Hutchinson KE, Stricker TP, Formisano L, Young CD, Estrada MV, Nixon MJ, Du L, Sanchez V, Ericsson PG, Kuba MG, Sanders ME, Mu XJ, Van Allen EM, Wagle N, Mayer IA, Abramson V, G?mez H, Rizzo M, Toy W, Chandarlapaty S, Mayer EL, Christiansen J, Murphy D, Fitzgerald K, Wang K, Ross JS, Miller VA, Stephens PJ, Yelensky R, Garraway L, Shyr Y, Meszoely I, Balko JM, Arteaga CL. PMID: 28794284; PMCID: PMC5723145.
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PubMed Mentions:
63 Fields:
Translation:
HumansCells
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 10 18; 17(4):1206.
Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. PMID: 27760322; PMCID: PMC5638785.
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PubMed Mentions:
120 Fields:
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Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib Combination Treatment for BRAF Inhibitor-Refractory Metastatic Melanoma: A Phase 2 Clinical Trial. JAMA Oncol. 2016 Aug 01; 2(8):1056-64.
Chen G, McQuade JL, Panka DJ, Hudgens CW, Amin-Mansour A, Mu XJ, Bahl S, Jané-Valbuena J, Wani KM, Reuben A, Creasy CA, Jiang H, Cooper ZA, Roszik J, Bassett RL, Joon AY, Simpson LM, Mouton RD, Glitza IC, Patel SP, Hwu WJ, Amaria RN, Diab A, Hwu P, Lazar AJ, Wargo JA, Garraway LA, Tetzlaff MT, Sullivan RJ, Kim KB, Davies MA. PMID: 27124486; PMCID: PMC4982774.
View in:
PubMed Mentions:
16 Fields:
Translation:
HumansCellsCTClinical Trials
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 Apr 26; 15(4):857-865.
Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. PMID: 27149842; PMCID: PMC4850357.
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PubMed Mentions:
363 Fields:
-
Pyruvate to Lactate Metabolic Changes during Neurodevelopment Measured Dynamically Using Hyperpolarized 13C Imaging in Juvenile Murine Brain. Dev Neurosci. 2016; 38(1):34-40.
Chen Y, Kim H, Bok R, Sukumar S, Mu X, Sheldon RA, Barkovich AJ, Ferriero DM, Xu D. PMID: 26550989; PMCID: PMC4732911.
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PubMed Mentions:
11 Fields:
Translation:
HumansAnimalsCells
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An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 01; 526(7571):75-81.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. PMID: 26432246; PMCID: PMC4617611.
View in:
PubMed Mentions:
983 Fields:
Translation:
HumansCells
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Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015 Sep 08; 6:8389.
Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. PMID: 26346554.
View in:
PubMed Mentions:
1 Fields:
-
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015 Jun 01; 6:7256.
Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. PMID: 26028266; PMCID: PMC4451611.
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PubMed Mentions:
52 Fields:
Translation:
HumansCells
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FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol. 2014; 15(10):480.
Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M. PMID: 25273974; PMCID: PMC4203974.
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PubMed Mentions:
176 Fields:
Translation:
Humans
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Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 04; 342(6154):1235587.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. PMID: 24092746; PMCID: PMC3947637.
View in:
PubMed Mentions:
220 Fields:
Translation:
HumansCells
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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013 May; 23(5):749-61.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. PMID: 23478400; PMCID: PMC3638132.
View in:
PubMed Mentions:
126 Fields:
Translation:
Humans
-
The GENCODE pseudogene resource. Genome Biol. 2012 Sep 26; 13(9):R51.
Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. PMID: 22951037; PMCID: PMC3491395.
View in:
PubMed Mentions:
174 Fields:
Translation:
HumansAnimalsCells
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Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100.
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. PMID: 22955619; PMCID: PMC4154057.
View in:
PubMed Mentions:
785 Fields:
Translation:
HumansCells
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A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17; 335(6070):823-8.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. PMID: 22344438; PMCID: PMC3299548.
View in:
PubMed Mentions:
647 Fields:
Translation:
Humans
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Genomics and privacy: implications of the new reality of closed data for the field. PLoS Comput Biol. 2011 Dec; 7(12):e1002278.
Greenbaum D, Sboner A, Mu XJ, Gerstein M. PMID: 22144881; PMCID: PMC3228779.
View in:
PubMed Mentions:
30 Fields:
Translation:
Humans
-
The real cost of sequencing: higher than you think! Genome Biol. 2011 Aug 25; 12(8):125.
Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. PMID: 21867570; PMCID: PMC3245608.
View in:
PubMed Mentions:
134 Fields:
Translation:
Humans
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Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res. 2011 Sep 01; 39(16):7058-76.
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. PMID: 21596777; PMCID: PMC3167619.
View in:
PubMed Mentions:
45 Fields:
Translation:
HumansCells
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Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 03; 470(7332):59-65.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. PMID: 21293372; PMCID: PMC3077050.
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PubMed Mentions:
595 Fields:
Translation:
Humans
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Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol. 2010 Jan; 28(1):47-55.
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. PMID: 20037582; PMCID: PMC2951730.
View in:
PubMed Mentions:
107 Fields:
Translation:
HumansAnimals
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PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009 Feb 23; 10(2):R23.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PMID: 19236709; PMCID: PMC2688268.
View in:
PubMed Mentions:
112 Fields:
Translation:
Cells
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Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. J Biol Chem. 2008 Oct 31; 283(44):30079-89.
Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P, Robek MD. PMID: 18757365; PMCID: PMC2662072.
View in:
PubMed Mentions:
42 Fields:
Translation:
HumansCells