Xiaojing Wang

π-HuB: the proteomic navigator of the human body.

He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y; π-HuB Consortium.

Nature, 636(8042):322-331, 2024.

Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors.

Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O’Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X.

Science, 381(6662):eabn4180, 2023.

Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology.

Ji S, Feng L, Fu Z, Wu G, Wu Y, Lin Y, Lu D, Song Y, Cui P, Yang Z, Sang C, Song G, Cai S, Li Y, Lin H, Zhang S, Wang X, Qiu S, Zhang X, Hua G, Li J, Zhou J, Dai Z, Wang X, Ding L, Wang P, Gao D, Zhang B, Rodriguez H, Fan J, Clevers H, Zhou H, Sun Y, Gao Q.

Sci Transl Med. 15(706):eadg3358, 2023.

Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma.

Dong L, Lu D, Chen R, Lin Y, Zhu H, Zhang Z, Cai S, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q, Gao D, Zhou H, Fan J.

Cancer Cell., 40(1):70-87, 2022

Multimodule characterization of immune subgroups in intrahepatic cholangiocarcinoma reveals distinct therapeutic vulnerabilities.

Lin J, Dai Y, Sang C, Song G, Xiang B, Zhang M, Dong L, Xia X, Ma J, Shen X, Ji S, Zhang S, Wang M, Fang H, Zhang X, Wang X, Zhang B, Zhou J, Fan J, Zhou H, Gao D, Gao Q.

J Immunother Cancer, 10(7):e004892, 2022

Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities.

Vasaikar S^#, Huang C^#, Wang X^#, Petyuk VA^#, Savage SR^#, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD^@, Liebler DC^@, Liu T^@, Zhang B^@, Clinical Proteomic Tumor Analysis Consortium.

Cell, 177(4):1035-1049, 2019 (# first authors; @ corresponding authors)

PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations.

Wen B, Wang X, Zhang B.

Genome Res, 29(3):485-493, 2019

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma.

Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, Ma L, Wang X, Zhou J, Liu Y, Boja E, Robles AI, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D, Zhou H, Fan J.

Cell, 179(2):561-577, 2019

Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity.

Wang X, Codreanu SG, Wen B, Li K, Chambers M, Liebler DC, Zhang B.

Mol Cell Proteomics, 17(3):422-430, 2018

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA.

Genome Biol, 19(1):12, 2018

Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity.

Wang J^#, Mouradov D^#, Wang X^#, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B^@, Sieber OM^@.

Gastroenterology, 153(4):1082-1095, 2017 (# first authors; @ corresponding authors)

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.

Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B^@, Li Y^@, Li J^@.

J Proteome Res, 16(2):421-432, 2017 (@ corresponding authors)

Methods, tools and current perspectives in proteogenomics.

Ruggles KV^#, Krug K^#, Wang X^#, Clauser KR, Wang J, Payne SH, Fenyö D^@, Zhang B^@, Mani DR^@.

Mol Cell Proteomics, 16(6):959-981, 2017 (# first authors; @ corresponding authors)

Comprehensive and sensitive proteogenomics data analysis strategy based on complementary multi-stage database search.

Madar IH^#, Lee W^#, Wang X^#, Ko SI, Kim H, Mun DG, Zhang B^@, Paek E^@, Lee SW^@.

Int J Mass Spectrom, doi: 10.1016/j.ijms.2017.08.015, 2017 (# first authors; @ corresponding authors)

Protein Modification by Endogenously Generated Lipid Electrophiles: Mitochondria as the Source and Target.

Beavers WN, Rose KL, Galligan JJ, Mitchener MM, Rouzer CA, Tallman KA, Lamberson CR, Wang X, Hill S, Ivanova PT, Brown HA, Zhang B, Porter NA, Marnett LJ.

ACS Chem Biol, doi: 10.1021/acschembio.7b00480, 2017

proBAMsuite, a bioinformatics framework for genome-based representation and analysis of proteomics data.

Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B.

Mol Cell Proteomics, 15:1164-1175, 2016

Proteogenomics connects somatic mutations to signalling in breast cancer.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.

Nature, 534:55-62, 2016

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res, 15:691-706, 2016

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.

Wen B, Xu S, Zhou R, Zhang B, Wang X, Liu X, Xu X, Liu S.

BMC Bioinformatics, 17(1):244, 2016

Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC.

Sci Data, 2:150022, 2015

Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data.

Sun H, Chen C, Lian B, Zhang M, Wang X, Zhang B, Li Y, Yang P, Xie L.

J Proteome Res, 14(4):1678-86, 2015

Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.

Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C.

Sci Rep, 5:10940, 2015

Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa.

Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL.

J Proteome Res, 14(12):5318-26, 2015

Activation of the Endogenous Renin-Angiotensin-Aldosterone System or Aldosterone Administration Increases Urinary Exosomal Sodium Channel Excretion.

Qi Y, Wang X, Rose KL, MacDonald WH, Zhang B, Schey KL, Luther JM.

J Am Soc Nephrol, 2015

Proteogenomic characterization of human colon and rectal cancer.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; the National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC).

Nature, 513:382-387, 2014

NFAT transcriptional activity is associated with metastatic capacity in colon cancer.

Tripathi MK, Deane NG, Zhu J, An H, Mima S, Wang X, Padmanabhan S, Shi Z, Prodduturi N, Ciombor KK, Chen X, Washington MK, Zhang B^@, Beauchamp RD^@. (@ co-corresponding authors)

Cancer Res, 74:6947-6957, 2014

Integrating genomic, transcriptomic and interactome data to improve peptide and protein identification in shotgun proteomics

Wang X, Zhang B.

J Proteome Res, 13:2715-2723, 2014

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data.

Wang X, Liu Q, Zhang B.

Proteomics, 14:2676-2687, 2014

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ.

Cancer Res, 74:387-397, 2014

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.

Wang X, Zhang B.

Bioinformatics, 29:3235-3237, 2013

Protein identification using customized protein sequence databases derived from RNA-Seq data.

Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B.

J Proteome Res, 11(2):1009-17, 2012

Genetic dissection of the Gpnmb network in the eye.

Lu H, Wang X, Pullen M, Guan H, Chen H, Sahu S, Zhang B, Chen H, Williams RW, Gelsert EE, Lu L, Jablonski MM.

Invest Ophthalmol Vis Sci, 2011