Xinmeng Jasmine Mu, Ph.D.

Email: xmu@broadinstitute.org

Address: 301 Binney St., 5th floor

Cambridge MA 02142

*: Co-first authorship

Khurana E*, Fu Y*, Colonna V*, Mu XJ*, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A et al. (2013) Integrative annotation of variants from 1,092 humans: application to cancer genomics. Science, 342, 1235587.

Montgometry SB, Goode D, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewsk KJ, Smith KS, Anaya V, Richardson, R, Davis J, The 1000 Genomes Pilot Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein MB, Makova KD, Marchini J, McVean G and Lunter G. (2013) The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Research, 23, 749-761.

The 1000 Genomes Project Consortium. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56-65.

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, Cheng 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 J, 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 and Snyder M. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.

The ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.

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 and Gerstein MB. (2012) The GENCODE pseudogene resource. Genome Biology, 13, R51.

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, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB and Tyler-Smith C. (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335, 823-828.

Greenbaum D, Sboner A, Mu XJ and Gerstein MB. (2011) Genomics & Privacy: Implications of the New Reality of Closed Data for the Field. Plos Computational Biology, 7, e1002278.

Sboner A, Mu XJ, Greenbaum D, Auerbach RK andGerstein MB. (2011) The real cost of sequencing: higher than you think! Genome Biology, 12, 125.

Mu XJ, Zhi L, Kong Y, Lam HY and Gerstein MB. (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research, 39, 7058-7076.

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, Stutz 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, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA and Korbel JO. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.

The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.

Lam HY*, Mu XJ*, Stutz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO* and Gerstein MB. (2010) Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology, 28, 47-55.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M and Gerstein MB. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology, 10, R23.

Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P and Robek MD. (2008) Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. Journal of Biological Chemistry, 283, 30079-30089.

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