Xin Mu, MD, MS
SRA 2
Radiology
School of Medicine

Publications (37)

Top publication keywords:
TransposasesGenome, HumanINDEL MutationCyclin-Dependent Kinase 6Cyclin-Dependent Kinase 4GenomicsHLA-A3 AntigenMolecular Sequence AnnotationGenetic VariationBiomarkers, TumorCyclin-Dependent Kinase 2Chromosome BreakpointsEuchromatinPseudogenesDNA, Intergenic

• Integrative Analyses of Tumor and Peripheral Biomarkers in the Treatment of Advanced Renal Cell Carcinoma.
  Cancer discovery 2024 Choueiri TK, Donahue AC, Braun DA, Rini BI, Powles T, Haanen JBAG, Larkin J, Mu XJ, Pu J, Teresi RE, di Pietro A, Robbins PB, Motzer RJ
• Estimate of fetal brain temperature using proton resonance frequency thermometry during 3 Tesla fetal magnetic resonance imaging.
  Quantitative imaging in medicine and surgery 2023 Ellison J, Kim K, Li Y, Mu X, Glenn O, Ozhinsky E, Peyvandi S, Xu D
• Molecular characterization of renal cell carcinoma tumors from a phase III anti-angiogenic adjuvant therapy trial.
  Nature communications 2022 Motzer RJ, Martini JF, Mu XJ, Staehler M, George DJ, Valota O, Lin X, Pandha HS, Ching KA, Ravaud A
• Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial.
  Nature medicine 2021 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
• HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study.
  The Lancet. Oncology 2021 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

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• Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes.
  Cell reports 2021 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
• Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor.
  Cancer cell 2021 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…
• Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer.
  Prostate cancer and prostatic diseases 2021 Armstrong AJ, Li X, Tucker M, Li S, Mu XJ, Eng KW, Sboner A, Rubin M, Gerstein M
• Avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma: biomarker analysis of the phase 3 JAVELIN Renal 101 trial.
  Nature medicine 2020 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, …
• Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival.
  Nature communications 2020 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…
• Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data.
  BMC bioinformatics 2020 Smith AM, Walsh JR, Long J, Davis CB, Henstock P, Hodge MR, Maciejewski M, Mu XJ, Ra S, Zhao S, Ziemek D, Fisher CK
• 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.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 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
• Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures.
  Nature communications 2018 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
• TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas.
  Oncoimmunology 2018 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…
• Genetic Mechanisms of Immune Evasion in Colorectal Cancer.
  Cancer discovery 2018 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…
• Inherited DNA-Repair Defects in Colorectal Cancer.
  American journal of human genetics 2018 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
• Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance.
  Science translational medicine 2017 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, …
• Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
  Cell reports 2016 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, …
• Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib Combination Treatment for BRAF Inhibitor-Refractory Metastatic Melanoma: A Phase 2 Clinical Trial.
  JAMA oncology 2016 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…
• Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
  Cell reports 2016 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, …
• Pyruvate to Lactate Metabolic Changes during Neurodevelopment Measured Dynamically Using Hyperpolarized 13C Imaging in Juvenile Murine Brain.
  Developmental neuroscience 2015 Chen Y, Kim H, Bok R, Sukumar S, Mu X, Sheldon RA, Barkovich AJ, Ferriero DM, Xu D
• An integrated map of structural variation in 2,504 human genomes.
  Nature 2015 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, …
• Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
  Nature communications 2015 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
• Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
  Nature communications 2015 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
• FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
  Genome biology 2014 Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M
• Integrative annotation of variants from 1092 humans: application to cancer genomics.
  Science (New York, N.Y.) 2013 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, …
• The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
  Genome research 2013 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, …
• The GENCODE pseudogene resource.
  Genome biology 2012 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
• Architecture of the human regulatory network derived from ENCODE data.
  Nature 2012 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, …
• A systematic survey of loss-of-function variants in human protein-coding genes.
  Science (New York, N.Y.) 2012 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, …
• Genomics and privacy: implications of the new reality of closed data for the field.
  PLoS computational biology 2011 Greenbaum D, Sboner A, Mu XJ, Gerstein M
• The real cost of sequencing: higher than you think!
  Genome biology 2011 Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB
• Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.
  Nucleic acids research 2011 Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB
• Mapping copy number variation by population-scale genome sequencing.
  Nature 2011 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, …
• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
  Nature biotechnology 2009 Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB
• PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
  Genome biology 2009 Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB
• Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication.
  The Journal of biological chemistry 2008 Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P, Robek MD