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Items: 39

1.

TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas.

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.

Oncoimmunology. 2018 Mar 19;7(7):e1442999. doi: 10.1080/2162402X.2018.1442999. eCollection 2018.

2.

Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures.

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.

Nat Commun. 2018 Apr 30;9(1):1725. doi: 10.1038/s41467-018-04129-4.

3.

Genetic Mechanisms of Immune Evasion in Colorectal Cancer.

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.

Cancer Discov. 2018 Jun;8(6):730-749. doi: 10.1158/2159-8290.CD-17-1327. Epub 2018 Mar 6.

4.

Inherited DNA-Repair Defects in Colorectal Cancer.

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.

Am J Hum Genet. 2018 Mar 1;102(3):401-414. doi: 10.1016/j.ajhg.2018.01.018. Epub 2018 Feb 22.

5.

Effect of tissue frozen on quantitative optical properties using optical coherence tomography.

Li JH, Chen J, Mu XJ, Shao QL, Zhou YQ, Yan LJ.

Appl Opt. 2017 Oct 20;56(30):8335-8339. doi: 10.1364/AO.56.008335.

PMID:
29091612
6.

Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance.

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, Gόmez 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.

Sci Transl Med. 2017 Aug 9;9(402). pii: eaai7993. doi: 10.1126/scitranslmed.aai7993. Erratum in: Sci Transl Med. 2019 Feb 13;11(479):.

7.

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

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.

Cell Rep. 2016 Oct 18;17(4):1206. doi: 10.1016/j.celrep.2016.10.009. No abstract available.

8.

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

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.

Cell Rep. 2016 Apr 26;15(4):857-865. doi: 10.1016/j.celrep.2016.03.075. Epub 2016 Apr 14. Erratum in: Cell Rep. 2016 Oct 18;17 (4):1206.

9.

Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib Combination Treatment for BRAF Inhibitor-Refractory Metastatic Melanoma: A Phase 2 Clinical Trial.

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 Jr, 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.

JAMA Oncol. 2016 Aug 1;2(8):1056-64. doi: 10.1001/jamaoncol.2016.0509.

10.

An integrated map of structural variation in 2,504 human genomes.

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.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

11.

Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

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.

Nat Commun. 2015 Sep 8;6:8389. doi: 10.1038/ncomms9389. No abstract available.

PMID:
26346554
12.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

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.

Nat Commun. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256. Erratum in: Nat Commun. 2015;6:8389.

13.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.

Genome Biol. 2014;15(10):480.

14.

Insulin-producing acinar cells in adult human pancreas.

Yu L, Luo JX, Wei JL, Mu XJ, Ren XX, Yang Z, Peng YT, Zhao HL.

Pancreas. 2014 May;43(4):592-6.

PMID:
24713842
15.

Eight-year survival of AIDS patients treated with Chinese herbal medicine.

Zhao HL, Sun CZ, Jiang WP, Dai ZK, Shi WX, Yang KK, Mu XJ, Zhang XX, Sui Y.

Am J Chin Med. 2014;42(2):261-74. doi: 10.1142/S0192415X14500177.

PMID:
24707861
16.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

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, Gümüş 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.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

17.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

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.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

18.

[Diagnosis and treatment of lumbar disc herniation by discography and percutaneous transforaminal endoscopic surgery].

Bai YB, Xu L, Xi JC, Mu XJ.

Zhonghua Yi Xue Za Zhi. 2012 Dec 18;92(47):3350-3. Chinese.

PMID:
23328597
19.

Signal-on architecture for electrochemical aptasensors based on multiple ion channels.

Li LD, Mu XJ, Peng Y, Chen ZB, Guo L, Jiang L.

Anal Chem. 2012 Dec 18;84(24):10554-9. doi: 10.1021/ac302351n. Epub 2012 Nov 26.

PMID:
23130990
20.

Architecture of the human regulatory network derived from ENCODE data.

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.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

21.

The GENCODE pseudogene resource.

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.

Genome Biol. 2012 Sep 26;13(9):R51. doi: 10.1186/gb-2012-13-9-r51.

22.

A systematic survey of loss-of-function variants in human protein-coding genes.

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.

Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Erratum in: Science. 2012 Apr 20;336(6079):296.

23.

Genomics and privacy: implications of the new reality of closed data for the field.

Greenbaum D, Sboner A, Mu XJ, Gerstein M.

PLoS Comput Biol. 2011 Dec;7(12):e1002278. doi: 10.1371/journal.pcbi.1002278. Epub 2011 Dec 1. Review.

24.

The real cost of sequencing: higher than you think!

Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB.

Genome Biol. 2011 Aug 25;12(8):125. doi: 10.1186/gb-2011-12-8-125.

25.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.

Nucleic Acids Res. 2011 Sep 1;39(16):7058-76. doi: 10.1093/nar/gkr342. Epub 2011 May 19.

26.

Mapping copy number variation by population-scale genome sequencing.

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.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

27.

The structure and roles of sterile flowers in Viburnum macrocephalum f. keteleeri (Adoxaceae).

Jin B, Wang L, Wang J, Teng NJ, He XD, Mu XJ, Wang YL.

Plant Biol (Stuttg). 2010 Nov;12(6):853-62. doi: 10.1111/j.1438-8677.2009.00298.x.

PMID:
21040300
28.

[Spatial distribution characteristics of organic carbon in the soil-plant systems in the Yellow River estuary tidal flat wetland].

Dong HF, Yu JB, Sun ZG, Mu XJ, Chen XB, Mao PL, Wu CF, Guan B.

Huan Jing Ke Xue. 2010 Jun;31(6):1594-9. Chinese.

PMID:
20698278
29.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.

Nat Biotechnol. 2010 Jan;28(1):47-55. doi: 10.1038/nbt.1600. Epub 2009 Dec 27.

30.

Polymorphisms within promoter of Japanese flounder (Paralichthys olivaceus) ovary cytochrome P450-c19 (CYP19a) gene associated with reproductive traits.

He F, Wen HS, Dong SL, Shi B, Chen CF, Wang LS, Yao J, Mu XJ, Zhou YG.

Fish Physiol Biochem. 2009 Aug;35(3):333-40. doi: 10.1007/s10695-008-9237-y. Epub 2008 Jun 7.

PMID:
19578940
31.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.

Genome Biol. 2009 Feb 23;10(2):R23. doi: 10.1186/gb-2009-10-2-r23.

32.

Association of reproductive performance with SNPs of FOXL2 gene by SSCP in Japanese flounder (Paralichthys olivaceus).

Shi B, Wen HS, He F, Dong SL, Ma S, Chen CF, Wang LS, Yao J, Mu XJ, Zhou YG.

Comp Biochem Physiol B Biochem Mol Biol. 2009 May;153(1):1-7. doi: 10.1016/j.cbpb.2008.10.007. Epub 2008 Oct 29.

PMID:
19007901
33.

Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication.

Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P, Robek MD.

J Biol Chem. 2008 Oct 31;283(44):30079-89. doi: 10.1074/jbc.M804296200. Epub 2008 Aug 29.

34.

Identification of estrogen receptor alpha gene polymorphisms by SSCP and its effect on reproductive traits in Japanese flounder (Paralichthys olivaceus).

He F, Wen HS, Dong SL, Wang LS, Chen CF, Shi B, Mu XJ, Yao J, Zhou YG.

Comp Biochem Physiol B Biochem Mol Biol. 2008 Jul;150(3):278-83. doi: 10.1016/j.cbpb.2008.03.013. Epub 2008 Mar 28.

PMID:
18450491
35.
36.

Manganese(III) acetate promoted regioselective phosphonation of heteroaryl compounds.

Mu XJ, Zou JP, Qian QF, Zhang W.

Org Lett. 2006 Nov 9;8(23):5291-3.

PMID:
17078700
37.

Plant regeneration from in vitro-cultured seedling leaf protoplasts of Actinidia eriantha Benth.

Zhang YJ, Qian YQ, Mu XJ, Cai QG, Zhou YL, Wei XP.

Plant Cell Rep. 1998 Jul;17(10):819-821. doi: 10.1007/s002990050490.

PMID:
30736599
38.

[Effect of expression of exogenous PDGF-A chain on growth and transformation of CHO cells].

Yeh HJ, Jin JJ, Wang YX, Zhou JQ, Lin XH, Mu XJ, Li WY.

Shi Yan Sheng Wu Xue Bao. 1989 Dec;22(4):455-65. Chinese.

PMID:
2626897
39.

[Expression of exogenous platelet-derived growth factor B chain gene in CHO cells].

Yeh HJ, Jin JJ, Hsu L, Mu XJ, Li WY.

Shi Yan Sheng Wu Xue Bao. 1989 Sep;22(3):313-23. Chinese.

PMID:
2686321

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