Publications

  1. Chang TC, Chen W, Qu C, Cheng Z, Hedges D, Elsayed A, Pounds SB, Shago M, Rabin KR, Raetz EA, Devidas M, Cheng C, Angiolillo A, Baviskar P, Borowitz M, Burke MJ, Carroll A, Carroll WL, Chen IM, Harvey R, Heerema N, Iacobucci I, Wang JR, Jeha S, Larsen E, Mattano L, Maloney K, Pui CH, Ramirez NC, Salzer W, Willman C, Winick N, Wood B, Hunger SP, Wu G, Mullighan CG, Loh ML. Genomic Determinants of Outcome in Acute Lymphoblastic Leukemia. J Clin Oncol. 2024 Oct 10; 42 (29):3491-3503 Epub 2024 Aug 09
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  2. Zanti M, O'Mahony DG, Parsons MT, Dorling L, Dennis J, Boddicker NJ, Chen W, Hu C, Naven M, Yiangou K, Ahearn TU, Ambrosone CB, Andrulis IL, Antoniou AC, Auer PL, Baynes C, Bodelon C, Bogdanova NV, Bojesen SE, Bolla MK, Brantley KD, Camp NJ, Campbell A, Castelao JE, Cessna MH, Chang-Claude J, Chen F, Chenevix-Trench G, Conroy DM, Czene K, De Nicolo A, Domchek SM, Dork T, Dunning AM, Eliassen AH, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, Garcia-Closas M, Glendon G, Gonzalez-Neira A, Grassmann F, Hadjisavvas A, Haiman CA, Hamann U, Hart SN, Hartman MBA, Ho WK, Hodge JM, Hoppe R, Howell SJ, Jakubowska A, Khusnutdinova EK, Ko YD, Kraft P, Kristensen VN, Lacey JV, Li J, Lim GH, Lindstrom S, Lophatananon A, Luccarini C, Mannermaa A, Martinez ME, Mavroudis D, Milne RL, Muir K, Nathanson KL, Nunez-Torres R, Obi N, Olson JE, Palmer JR, Panayiotidis MI, Patel AV, Pharoah PDP, Polley EC, Rashid MU, Ruddy KJ, Saloustros E, Sawyer EJ, Schmidt MK, Southey MC, Tan VK, Teo SH, Teras LR, Torres D, Trentham-Dietz A, Truong T, Vachon CM, Wang Q, Weitzel JN, Yadav S, Yao S, Zirpoli GR, Cline MS, Devilee P, Tavtigian SV, Goldgar DE, Couch FJ, Easton DF, Spurdle AB, Michailidou K, NBCS Collaborators//kConFab Investigators. Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification. medRxiv. 2024 Sep 4 Epub 2024 Sept 04
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  3. Yamada K, Menon JA, Kim Y, Cheng C, Chen W, Shih JA, Villasenor-Altamirano AB, Chen X, Tamura T, Merriam LT, Kim EY, Weissman AJ, Immunology of Cardiac Arrest Network (I-CAN). Protocol for immunophenotyping out-of-hospital cardiac arrest patients. STAR Protoc. 2024 Mar 15; 5 (1):102874 Epub 2024 Feb 03
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  4. Escherich CS, Chen W, Li Y, Yang W, Nishii R, Li Z, Raetz EA, Devidas M, Wu G, Nichols KE, Inaba H, Pui CH, Jeha S, Camitta BM, Larsen EC, Hunger SP, Loh ML, Yang JJ. Germline Genetic NBN Variation and Predisposition to B-cell Acute Lymphoblastic Leukemia in Children. Blood. 2024 Mar 6 Epub 2024 Mar 06
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  5. Chen C, Qin N, Wang M, Dong Q, Tithi SS, Hui Y, Chen W, Wu G, Kennetz D, Edmonson MN, Rusch MC, Thrasher A, Easton J, Mulder HL, Song N, Plonski NM, Shelton K, Im C, Ehrhardt MJ, Nichols KE, Leisenring WM, Stratton KL, Howell R, Yasui Y, Bhatia S, Armstrong GT, Ness KK, Hudson MM, Zhang J, Wang H, Srivastava DK, Robison LL, Wang Z. Cancer germline predisposing variants and late mortality from subsequent malignant neoplasms among long-term childhood cancer survivors: a report from the St Jude Lifetime Cohort and the Childhood Cancer Survivor Study. Lancet Oncol. 2023 Oct; 24 (10):1147-1156
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  6. Gao Q, Ryan SL, Iacobucci I, Ghate PS, Cranston RE, Schwab C, Elsayed AH, Shi L, Pounds S, Lei S, Baviskar P, Pei D, Cheng C, Bashton M, Sinclair P, Bentley DR, Ross MT, Kingsbury Z, James T, Roberts KG, Devidas M, Fan Y, Chen W, Chang TC, Wu G, Carroll A, Heerema N, Valentine V, Valentine M, Yang W, Yang JJ, Moorman AV, Harrison CJ, Mullighan CG. The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Blood. 2023 Aug 24; 142 (8):711-723
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  7. Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells. 2023 Jul 30; 12 (15) Epub 2023 July 30
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  8. Tamura T, Cheng C, Chen W, Merriam LT, Athar H, Kim YH, Manandhar R, Amir Sheikh MD, Pinilla-Vera M, Varon J, Hou PC, Lawler PR, Oldham WM, Seethala RR, Tesfaigzi Y, Weissman AJ, Baron RM, Ichinose F, Berg KM, Bohula EA, Morrow DA, Chen X, Kim EY, Immunology of Cardiac Arrest Network (I-CAN). Single-cell transcriptomics reveal a hyperacute cytokine and immune checkpoint axis after cardiac arrest in patients with poor neurological outcome. Med. 2023 Jul 14; 4 (7):432-456.e6 Epub 2023 May 30
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  9. Fang J, Singh S, Cheng C, Natarajan S, Sheppard H, Abu-Zaid A, Durbin AD, Lee HW, Wu Q, Steele J, Connelly JP, Jin H, Chen W, Fan Y, Pruett-Miller SM, Rehg JE, Koo SC, Santiago T, Emmons J, Cairo S, Wang R, Glazer ES, Murphy AJ, Chen T, Davidoff AM, Armengol C, Easton J, Chen X, Yang J. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun. 2023 Jul 6; 14 (1):4003 Epub 2023 July 06
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  10. Escherich C, Chen W, Miyamoto S, Namikawa Y, Yang W, Teachey DT, Li Z, Raetz EA, Larsen E, Devidas M, Martin PL, Bowman WP, Wu G, Pui CH, Hunger SP, Loh ML, Takagi M, Yang JJ. Identification of TCF3 germline variants in pediatric B-cell acute lymphoblastic leukemia. Blood Adv. 2023 May 23; 7 (10):2177-2180
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  11. Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K, Tithi SS, Goldin LR, Rotunno M, Caporaso N, Vogt A, Flamish D, Wyatt K, Liu J, Tucker M, Hahn CN, Brown AL, Scott HS, Mullighan C, Nichols KE, Metzger ML, McMaster ML, Yang JJ, Rampersaud E. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood. 2023 Mar 16; 141 (11):1293-1307
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  12. Sharma R, Oak N, Chen W, Gogal R, Kirschner M, Beier F, Schnieders MJ, Spies M, Nichols KE, Wlodarski M. Germline landscape of RPA1, RPA2 and RPA3 variants in pediatric malignancies: identification of RPA1 as a novel cancer predisposition candidate gene. Front Oncol. 2023; 13:1229507 Epub 2023 Oct 06
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  13. Chen W, Coombes BJ, Larson NB. Recent advances and challenges of rare variant association analysis in the biobank sequencing era. Front Genet. 2022; 13:1014947 Epub 2022 Oct 06
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  14. Chen W, Wang S, Tithi SS, Ellison DW, Schaid DJ, Wu G. A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes. Nat Commun. 2022 May 11; 13 (1):2592
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  15. Rampersaud E, Kang G, Palmer LE, Rashkin SR, Wang S, Bi W, Alberts NM, Anghelescu D, Barton M, Birch K, Boulos N, Brandow AM, Brooke RJ, Chang TC, Chen W, Cheng Y, Ding J, Easton J, Hodges JR, Kanne CK, Levy S, Mulder H, Patel AP, Puri L, Rosencrance C, Rusch M, Sapkota Y, Sioson E, Sharma A, Tang X, Thrasher A, Wang W, Yao Y, Yasui Y, Yergeau D, Hankins JS, Sheehan VA, Downing JR, Estepp JH, Zhang J, DeBaun M, Wu G, Weiss MJ. A polygenic score for acute vaso-occlusive pain in pediatric sickle cell disease. Blood Adv. 2021 Jul 27; 5 (14):2839-2851
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  16. Gonzalez-Pena V, Natarajan S, Xia Y, Klein D, Carter R, Pang Y, Shaner B, Annu K, Putnam D, Chen W, Connelly J, Pruett-Miller S, Chen X, Easton J, Gawad C. Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A. 2021 Jun 15; 118 (24)
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  17. Jeffers JR, Pinto EM, Rehg JE, Clay MR, Wang J, Neale G, Heath RJ, Lozano G, Lalli E, Figueiredo BC, Pappo AS, Rodriguez-Galindo C, Chen W, Pounds S, Ribeiro RC, Zambetti GP. The Common Germline TP53-R337H Mutation Is Hypomorphic and Confers Incomplete Penetrance and Late Tumor Onset in a Mouse Model. Cancer Res. 2021 May 1; 81 (9):2442-2456 Epub 2021 Feb 26
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  18. Placek K, Benatar M, Wuu J, Rampersaud E, Hennessy L, Van Deerlin VM, Grossman M, Irwin DJ, Elman L, McCluskey L, Quinn C, Granit V, Statland JM, Burns TM, Ravits J, Swenson A, Katz J, Pioro EP, Jackson C, Caress J, So Y, Maiser S, Walk D, Lee EB, Trojanowski JQ, Cook P, Gee J, Sha J, Naj AC, Rademakers R, Chen W, Wu G, Paul Taylor J, McMillan CT, CReATe Consortium. Machine learning suggests polygenic risk for cognitive dysfunction in amyotrophic lateral sclerosis. EMBO Mol Med. 2021 Jan 11; 13 (1):e12595 Epub 2020 Dec 03
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  19. Pinto EM, Figueiredo BC, Chen W, Galvao HCR, Formiga MN, Fragoso MCBV, Ashton-Prolla P, Ribeiro EMSF, Felix G, Costa TEB, Savage SA, Yeager M, Palmero EI, Volc S, Salvador H, Fuster-Soler JL, Lavarino C, Chantada G, Vaur D, Odone-Filho V, Brugieres L, Else T, Stoffel EM, Maxwell KN, Achatz MI, Kowalski L, de Andrade KC, Pappo A, Letouze E, Latronico AC, Mendonca BB, Almeida MQ, Brondani VB, Bittar CM, Soares EWS, Mathias C, Ramos CRN, Machado M, Zhou W, Jones K, Vogt A, Klincha PP, Santiago KM, Komechen H, Paraizo MM, Parise IZS, Hamilton KV, Wang J, Rampersaud E, Clay MR, Murphy AJ, Lalli E, Nichols KE, Ribeiro RC, Rodriguez-Galindo C, Korbonits M, Zhang J, Thomas MG, Connelly JP, Pruett-Miller S, Diekmann Y, Neale G, Wu G, Zambetti GP. XAF1 as a modifier of p53 function and cancer susceptibility. Sci Adv. 2020 Jun; 6 (26):eaba3231 Epub 2020 June 24
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  20. Chen W, Zhang S, Williams J, Ju B, Shaner B, Easton J, Wu G, Chen X. A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing. Comput Struct Biotechnol J. 2020; 18:861-873 Epub 2020 Mar 30
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  21. Cheng C, Easton J, Rosencrance C, Li Y, Ju B, Williams J, Mulder HL, Pang Y, Chen W, Chen X. Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data. Nucleic Acids Res. 2019 Dec 16; 47 (22):e143
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  22. Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA. Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma. Cold Spring Harb Mol Case Stud. 2019 Oct; 5 (5) Epub 2019 Oct 23
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  23. Karmaus PWF, Chen X, Lim SA, Herrada AA, Nguyen TM, Xu B, Dhungana Y, Rankin S, Chen W, Rosencrance C, Yang K, Fan Y, Cheng Y, Easton J, Neale G, Vogel P, Chi H. Metabolic heterogeneity underlies reciprocal fates of T(H)17 cell stemness and plasticity. Nature. 2019 Jan; 565 (7737):101-105 Epub 2018 Dec 19
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  24. Schaid DJ, Chen W, Larson NB. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat Rev Genet. 2018 Aug; 19 (8):491-504
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  25. Brooke RJ, Im C, Wilson CL, Krasin MJ, Liu Q, Li Z, Sapkota Y, Moon W, Morton LM, Wu G, Wang Z, Chen W, Howell RM, Armstrong GT, Bhatia S, Mostoufi-Moab S, Seidel K, Chanock SJ, Zhang J, Green DM, Sklar CA, Hudson MM, Robison LL, Chemaitilly W, Yasui Y. A High-risk Haplotype for Premature Menopause in Childhood Cancer Survivors Exposed to Gonadotoxic Therapy. J Natl Cancer Inst. 2018 Aug 1; 110 (8):895-904
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  26. Wang Z, Wilson CL, Easton J, Thrasher A, Mulder H, Liu Q, Hedges DJ, Wang S, Rusch MC, Edmonson MN, Levy S, Lanctot JQ, Caron E, Shelton K, Currie K, Lear M, Patel A, Rosencrance C, Shao Y, Vadodaria B, Yergeau D, Sapkota Y, Brooke RJ, Moon W, Rampersaud E, Ma X, Chang TC, Rice SV, Pepper C, Zhou X, Chen X, Chen W, Jones A, Boone B, Ehrhardt MJ, Krasin MJ, Howell RM, Phillips NS, Lewis C, Srivastava D, Pui CH, Kesserwan CA, Wu G, Nichols KE, Downing JR, Hudson MM, Yasui Y, Robison LL, Zhang J. Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer. J Clin Oncol. 2018 Jul 10; 36 (20):2078-2087 Epub 2018 May 30
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  27. Yang K, Blanco DB, Chen X, Dash P, Neale G, Rosencrance C, Easton J, Chen W, Cheng C, Dhungana Y, Kc A, Awad W, Guo XJ, Thomas PG, Chi H. Metabolic signaling directs the reciprocal lineage decisions of alphabeta and gammadelta T cells. Sci Immunol. 2018 Jul 6; 3 (25)
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  28. Chen W, Li Y, Easton J, Finkelstein D, Wu G, Chen X. UMI-count modeling and differential expression analysis for single-cell RNA sequencing. Genome Biol. 2018 May 31; 19 (1):70
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  29. Ward J, Graham N, Strawbridge RJ, Ferguson A, Jenkins G, Chen W, Hodgson K, Frye M, Weinshilboum R, Uher R, Lewis CM, Biernacka J, Smith DJ. Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: Meta-analysis of three treatment cohorts. PLoS One. 2018; 13(9):e0203896. Epub 2018 Sep 21.
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  30. Nassan M, Li Q, Croarkin PE, Chen W, Colby CL, Veldic M, McElroy SL, Jenkins GD, Ryu E, Cunningham JM, Leboyer M, Frye MA, Biernacka JM. A genome wide association study suggests the association of muskelin with early onset bipolar disorder: Implications for a GABAergic epileptogenic neurogenesis model. J Affect Disord. 2017 Jan 15; 208:120-129. Epub 2016 Sep 30.
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  31. Chen W, McDonnell SK, Thibodeau SN, Tillmans LS, Schaid DJ. Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics. Genetics. 2016 Nov; 204 (3):933-958 Epub 2016 Sept 21
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  32. Chen J, Chen W, Zhao N, Wu MC, Schaid DJ. Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies. Genet Epidemiol. 2016 Jan; 40 (1):5-19 Epub 2015 Dec 07
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  33. Clark SL, Aberg KA, Nerella S, Kumar G, McClay JL, Chen W, Xie LY, Harada A, Shabalin AA, Gao G, Bergen SE, Hultman CM, Magnusson PK, Sullivan PF, van den Oord EJ. Combined Whole Methylome and Genomewide Association Study Implicates CNTN4 in Alcohol Use. Alcohol Clin Exp Res. 2015 Aug; 39 (8):1396-405 Epub 2015 July 04
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  34. Chen W, Larrabee BR, Ovsyannikova IG, Kennedy RB, Haralambieva IH, Poland GA, Schaid DJ. Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics. Genetics. 2015 Jul; 200 (3):719-36 Epub 2015 May 06
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  35. Chen W, Ren C, Qin H, Archer KJ, Ouyang W, Liu N, Chen X, Luo X, Zhu X, Sun S, Gao G. A Generalized Sequential Bonferroni Procedure for GWAS in Admixed Populations Incorporating Admixture Mapping Information into Association Tests. Hum Hered. 2015; 79 (2):80-92 Epub 2015 June 13
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  36. Chen W, Schaid DJ. PedBLIMP: extending linear predictors to impute genotypes in pedigrees. Genet Epidemiol. 2014 Sep; 38 (6):531-41 Epub 2014 July 12
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  37. Aberg KA, McClay JL, Nerella S, Clark S, Kumar G, Chen W, Khachane AN, Xie L, Hudson A, Gao G, Harada A, Hultman CM, Sullivan PF, Magnusson PK, van den Oord EJ. Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry. 2014 Mar; 71 (3):255-64
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  38. Zuo L, Wang KS, Zhang XY, Li CS, Zhang F, Wang X, Chen W, Gao G, Zhang H, Krystal JH, Luo X. Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent. Pharmacogenet Genomics. 2013 Aug; 23 (8):395-402
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  39. Chen W, Belle A, Cockrell C, Ward KR, Najarian K. Automated midline shift and intracranial pressure estimation based on brain CT images. J Vis Exp. 2013 Apr 13; (74)
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  40. Chen W, Gao G, Nerella S, Hultman CM, Magnusson PK, Sullivan PF, Aberg KA, van den Oord EJ. MethylPCA: a toolkit to control for confounders in methylome-wide association studies. BMC Bioinformatics. 2013 Mar 2; 14:74 Epub 2013 Mar 02
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  41. Chen W, Cockrell CH, Ward K, Najarian K. Predictability of intracranial pressure level in traumatic brain injury: features extraction, statistical analysis and machine learning-based evaluation. Int J Data Min Bioinform. 2013; 8 (4):480-94
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  42. Chen W, Chen X, Archer KJ, Liu N, Li Q, Zhao Z, Sun S, Gao G. A rapid association test procedure robust under different genetic models accounting for population stratification. Hum Hered. 2013; 75 (1):23-33 Epub 2013 Apr 03
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  43. Wang S, Chen W, Chen X, Hu F, Archer KJ, Liu HN, Sun S, Gao G. Double genomic control is not effective to correct for population stratification in meta-analysis for genome-wide association studies. Front Genet. 2012; 3:300 Epub 2012 Dec 24
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  44. Gao G, Kang G, Wang J, Chen W, Qin H, Jiang B, Li Q, Sun C, Liu N, Archer KJ, Allison DB. A generalized sequential Bonferroni procedure using smoothed weights for genome-wide association studies incorporating information on Hardy-Weinberg disequilibrium among cases. Hum Hered. 2012; 73 (1):1-13 Epub 2011 Dec 30
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  45. Chen W, Ward K, Li Q, Kecman V, Najarian K, Menke N. Agent based modeling of blood coagulation system: implementation using a GPU based high speed framework Agent based modeling of blood coagulation system: implementation using a GPU based high speed framework. 2011.
  46. Chen W, Gao X, Wang J, Sun C, Wan W, Zhi D, Liu N, Chen X, Gao G. Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data. BMC Proc. 2011; 5 Suppl 9 (Suppl 9):S86 Epub 2011 Nov 29
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  47. Chen W, Cockrell C, Ward K, Najarian K. Intracranial pressure level prediction in traumatic brain injury by extracting features from multiple sources and using machine learning methods IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2010.
  48. Chen W, Najarian K, Ward K. Actual Midline Estimation from Brain CT Scan Using Multiple Regions Shape Matching 20th International Conference on Pattern Recognition. 2010.
  49. Chen W, Smith R, Nabizadeh M, Ward K, Cockrell C, Ha J, Najarian K. Texture Analysis of Brain CT Scans for ICP Prediction International Conference on Image and Signal Processing (ICISP). 2010.
  50. Chen W, Smith R, Ji SY, Ward KR, Najarian K. Automated ventricular systems segmentation in brain CT images by combining low-level segmentation and high-level template matching. BMC Med Inform Decis Mak. 2009 Nov 3; 9 Suppl 1 (Suppl 1):S4 Epub 2009 Nov 03
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  51. Chen W, Smith R, Vasilache S, Najarian K, Ward K, Cockrell C, Ha J. Traumatic Pelvic Injury Outcome Prediction by Extracting Features from Relevant Medical Records and X-ray Images IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2009.
  52. Chen W, Najarian K. Segmentation of Ventricles in Brain CT Images Using Gaussian Mixture Model Method IEEE International Conference on Complex Medical Engineering (ICME). 2009.
  53. Ji, Chen W, Ward K, Rickards C, Ryan K, Convertino V, Najarian K. Wavelet Based Analysis of Physiological Signals for Prediction of Severity of Hemorrhagic Shock IEEE International Conference on Complex Medical Engineering (ICME). 2009.
  54. Vasilache S, Chen W, Ward K, Najarian K. Hierarchical object recognition in Pelvic CT Images. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2009:3533-6
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  55. Liu B, Zhang H, Chen W. Boundary Constrained Manifold Unfolding International Conference on Machine Learning and Applications (ICMLA). 2008.
  56. Chen W, Smith R, Ji S-J, Najarian K. Automated Segmentation of Lateral Ventricles in Brain CT images IEEE International Conference on Bioinformatics and Biomeidcine Workshops (BIBMW). 2008.
  57. Chen W, Zhang H. The Condition of Kernelizing an Algorithm and an Equivalence between Kernel Methods The 3rd Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA). 2007.
  58. Chen W, Zhang H. Weighted Projection Approach for Small Sample Size Problems The 11th Joint International Computer Conference (JICC). 2005.