Publications of Chi Wei C. Chan    :chronological  alphabetical  combined  bibtex listing:

Papers Published

1. Wang, H-Y; Taher, H; Kreklywich, CN; Schmidt, KA; Scheef, EA; Barfield, R; Otero, CE; Valencia, SM; Zhang, K; Callahan, C; Monticolo, F; Qiao, Y; Gilbride, RM; Crooks, CM; Mirza, A; Knight, K; Moström, MJ; Manuel, TD; Sprehe, L; Kendall, S; Burgt, NV; Kowalik, TF; Barry, PA; Hansen, SG; Shu, J; Tarantal, AF; Chan, C; Streblow, DN; Picker, LJ; Kaur, A; Früh, K; Permar, SR; Malouli, D, The pentameric complex is not required for congenital CMV transmission in seronegative rhesus macaques., Sci Transl Med, vol. 17 no. 789 (March, 2025), pp. eadm8961 [doi]  [abs]
2. Otero, CE; Petkova, S; Ebermann, M; Taher, H; John, N; Hoffmann, K; Davalos, A; Moström, MJ; Gilbride, RM; Papen, CR; Barber-Axthelm, A; Scheef, EA; Barfield, R; Sprehe, LM; Kendall, S; Manuel, TD; Beechwood, T; Nguyen, LK; Vande Burgt, NH; Chan, C; Denton, M; Streblow, ZJ; Streblow, DN; Tarantal, AF; Hansen, SG; Kaur, A; Permar, S; Früh, K; Hengel, H; Malouli, D; Kolb, P, Rhesus Cytomegalovirus-encoded Fcγ-binding glycoproteins facilitate viral evasion from IgG-mediated humoral immunity., Nat Commun, vol. 16 no. 1 (January, 2025), pp. 1200 [doi]  [abs]
3. Nettere, D; White, S; Williams, G; Jha, S; Moody, MA; Chan, C; Ferrari, G; Naggie, S, Coinfection with HIV-1 skews iNKT cells toward TCR anergy and limited expansion potential in people with hepatitis C., Front Immunol, vol. 16 (2025), pp. 1469473 [doi]  [abs]
4. Myers, N; Droz, D; Rogers, BW; Tran, H; Flores, KB; Chan, C; Knechtle, SJ; Jackson, AM; Luo, X; Chambers, ET; McCarthy, JM, Modeling BK Virus Infection in Renal Transplant Recipients., Viruses, vol. 17 no. 1 (December, 2024) [doi]  [abs]
5. Zhang, HL; Nemeth, H; Woodhouse, EW; Davenport, CA; Chan, C; Okeke, NL; Naggie, S, Prevalence of and Risk Factors for Liver Enzyme Elevation After Hepatitis C Virologic Cure., J Viral Hepat, vol. 31 no. 12 (December, 2024), pp. 866-872 [doi]  [abs]
6. Shao, Y; Gao, Q; Wang, L; Li, D; Nixon, AB; Chan, C; Li, Q-J; Xie, J, B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity., Brief Bioinform, vol. 26 no. 1 (November, 2024) [doi]  [abs]
7. Woolley, G; Kroll, K; Hoffman, K; Ward, A; Corneli, A; Mudrak, SV; Qureshi, MU; Okeke, NL; Chan, C; Jones, A-AD; Tomaras, GD; Reeves, RK, The Climate Change Burden on Immune Health: Are Persons Living with HIV More at Risk?, AIDS Res Hum Retroviruses, vol. 40 no. 10 (October, 2024), pp. 549-554 [doi]  [abs]
8. Stout, JA; Allamong, M; Hung, F; Link, K; Chan, C; Muiruri, C; Sauceda, J; McKellar, MS, Engagement in Care, Awareness, and Interest in Long-Acting Injectable Anti-Retroviral Therapy., AIDS Behav, vol. 28 no. 10 (October, 2024), pp. 3315-3325 [doi]  [abs]
9. Mainou, E; Berendam, SJ; Obregon-Perko, V; Uffman, EA; Phan, CT; Shaw, GM; Bar, KJ; Kumar, MR; Fray, EJ; Siliciano, JM; Siliciano, RF; Silvestri, G; Permar, SR; Fouda, GG; McCarthy, J; Chahroudi, A; Conway, JM; Chan, C, Assessing the impact of autologous virus neutralizing antibodies on viral rebound time in postnatally SHIV-infected ART-treated infant rhesus macaques., Epidemics, vol. 48 (September, 2024), pp. 100780 [doi]  [abs]
10. Gao, Q; Ji, Z; Wang, L; Owzar, K; Li, Q-J; Chan, C; Xie, J, SifiNet: a robust and accurate method to identify feature gene sets and annotate cells., Nucleic Acids Res, vol. 52 no. 9 (May, 2024), pp. e46 [doi]  [abs]
11. Wilson, SM; Woolley, G; Hawn, C; Hoffman, K; Jones, A-AD; Chan, C; Mudrak, SV; Qureshi, MU; Ward, A; Knippler, ET; Okeke, NL; Corneli, A; Tomaras, GD; Reeves, RK, Intersectional climate justice, health equity, and HIV., Lancet HIV, vol. 11 no. 5 (May, 2024), pp. e280-e281 [doi]
12. Wang, H-Y; Li, L; Nelson, CS; Barfield, R; Valencia, S; Chan, C; Muramatsu, H; Lin, PJC; Pardi, N; An, Z; Weissman, D; Permar, SR, Multivalent cytomegalovirus glycoprotein B nucleoside modified mRNA vaccines did not demonstrate a greater antibody breadth., NPJ Vaccines, vol. 9 no. 1 (February, 2024), pp. 38 [doi]  [abs]
13. Gorsky, S; Chan, C; Ma, L, Coarsened Mixtures of Hierarchical Skew Normal Kernels for Flow and Mass Cytometry Analyses, Bayesian Analysis, vol. 19 no. 2 (January, 2024), pp. 439-463 [doi]  [abs]
14. Yin, L; Venturi, GM; Barfield, R; Fischer, BM; Kim-Chang, JJ; Chan, C; De Paris, K; Goodenow, MM; Sleasman, JW, Maternal immunity shapes biomarkers of germinal center development in HIV-exposed uninfected infants., Front Immunol, vol. 15 (2024), pp. 1443886 [doi]  [abs]
15. Dankwa, S; Kosman, C; Dennis, M; Giorgi, EE; Vuong, K; Pahountis, I; Garza, A; Binuya, C; McCarthy, J; Mayer, BT; Ngo, JT; Enemuo, CA; Carnathan, DG; Stanfield-Oakley, S; Berendam, SJ; Weinbaum, C; Engelman, K; Magnani, DM; Chan, C; Ferrari, G; Silvestri, G; Amara, RR; Chahroudi, A; Permar, SR; Fouda, GG; Goswami, R, A novel HIV triple broadly neutralizing antibody (bNAb) combination-based passive immunization of infant rhesus macaques achieves durable protective plasma neutralization levels and mediates anti-viral effector functions., PLoS One, vol. 19 no. 11 (2024), pp. e0312411 [doi]  [abs]
16. Zhang, AR; Bell, RP; An, C; Tang, R; Hall, SA; Chan, C; Al-Khalil, K; Meade, CS, Cocaine Use Prediction With Tensor-Based Machine Learning on Multimodal MRI Connectome Data., Neural Comput, vol. 36 no. 1 (December, 2023), pp. 107-127 [doi]  [abs]
17. Moris, D; Barfield, R; Chan, C; Chasse, S; Stempora, L; Xie, J; Plichta, JK; Thacker, J; Harpole, DH; Purves, T; Lagoo-Deenadayalan, S; Hwang, E-SS; Kirk, AD, Immune Phenotype and Postoperative Complications After Elective Surgery., Ann Surg, vol. 278 no. 6 (December, 2023), pp. 873-882 [doi]  [abs]
18. Otero, CE; Barfield, R; Scheef, E; Nelson, CS; Rodgers, N; Wang, H-Y; Moström, MJ; Manuel, TD; Sass, J; Schmidt, K; Taher, H; Papen, C; Sprehe, L; Kendall, S; Davalos, A; Barry, PA; Früh, K; Pollara, J; Malouli, D; Chan, C; Kaur, A; Permar, SR, Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model., PLoS Pathog, vol. 19 no. 10 (October, 2023), pp. e1011378 [doi]  [abs]
19. Gong, Y; Moström, M; Otero, C; Valencia, S; Tarantal, AF; Kaur, A; Permar, SR; Chan, C, Mathematical Modeling of Rhesus Cytomegalovirus Transplacental Transmission in Seronegative Rhesus Macaques., Viruses, vol. 15 no. 10 (October, 2023) [doi]  [abs]
20. Okeke, NL; Ware, KB; Campbell, R; Taylor, J; Hung, F; Questell, C; Brickler, MP; Smith, UD; Nawas, GT; Hanlen-Rosado, E; Chan, C; Bosworth, HB; Aifah, A; Corneli, A, Evidence2Practice (E2P): Leveraging Implementation Science to Promote Careers in HIV Research Among Students From Historically Black Colleges and Universities., J Acquir Immune Defic Syndr, vol. 94 no. Suppl 2 (October, 2023), pp. S65-S72 [doi]  [abs]
21. SoRelle, ED; Reinoso-Vizcaino, NM; Dai, J; Barry, AP; Chan, C; Luftig, MA, Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci., Cell Rep, vol. 42 no. 8 (August, 2023), pp. 112958 [doi]  [abs]
22. Crooks, CM; Chan, C; Permar, SR, Leveraging preclinical study designs to close gaps in vaccine development for perinatal pathogens., J Exp Med, vol. 220 no. 7 (July, 2023) [doi]  [abs]
23. Hansen, SG; Womack, JL; Perez, W; Schmidt, KA; Marshall, E; Iyer, RF; Cleveland Rubeor, H; Otero, CE; Taher, H; Vande Burgt, NH; Barfield, R; Randall, KT; Morrow, D; Hughes, CM; Selseth, AN; Gilbride, RM; Ford, JC; Caposio, P; Tarantal, AF; Chan, C; Malouli, D; Barry, PA; Permar, SR; Picker, LJ; Früh, K, Late gene expression-deficient cytomegalovirus vectors elicit conventional T cells that do not protect against SIV., JCI Insight, vol. 8 no. 6 (March, 2023) [doi]  [abs]
24. Pura, JA; Li, X; Chan, C; Xie, J, TEAM: A MULTIPLE TESTING ALGORITHM ON THE AGGREGATION TREE FOR FLOW CYTOMETRY ANALYSIS., Ann Appl Stat, vol. 17 no. 1 (March, 2023), pp. 621-640 [doi]  [abs]
25. Murdoch, DM; Barfield, R; Chan, C; Towe, SL; Bell, RP; Volkheimer, A; Choe, J; Hall, SA; Berger, M; Xie, J; Meade, CS, Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV., J Neurovirol, vol. 29 no. 1 (February, 2023), pp. 78-93 [doi]  [abs]
26. Sass, J; Awasthi, A; Obregon-Perko, V; McCarthy, J; Lloyd, AL; Chahroudi, A; Permar, S; Chan, C, A simple model for viral decay dynamics and the distribution of infected cell life spans in SHIV-infected infant rhesus macaques., Math Biosci, vol. 356 (February, 2023), pp. 108958 [doi]  [abs]
27. Tuyishime, M; Spreng, RL; Hueber, B; Nohara, J; Goodman, D; Chan, C; Barfield, R; Beck, WE; Jha, S; Asdell, S; Wiehe, K; He, MM; Easterhoff, D; Conley, HE; Hoxie, T; Gurley, T; Jones, C; Adhikary, ND; Villinger, F; Thomas, R; Denny, TN; Moody, MA; Tomaras, GD; Pollara, J; Reeves, RK; Ferrari, G, Multivariate analysis of FcR-mediated NK cell functions identifies unique clustering among humans and rhesus macaques, Frontiers in Immunology, vol. 14 (January, 2023) [doi]  [abs]
28. Baloh, CH; Venturi, GM; Fischer, BM; Sadder, LS; Kim-Chang, JJ; Chan, C; De Paris, K; Yin, L; Aldrovandi, GM; Goodenow, MM; Sleasman, JW, Biomarkers detected in cord blood predict vaccine responses in young infants., Front Immunol, vol. 14 (2023), pp. 1152538 [doi]  [abs]
29. Fang, J; Chan, C; Owzar, K; Wang, L; Qin, D; Li, Q-J; Xie, J, Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering., Genome Biol, vol. 23 no. 1 (December, 2022), pp. 269 [doi]  [abs]
30. SenNet Consortium, NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health., Nat Aging, vol. 2 no. 12 (December, 2022), pp. 1090-1100 [doi]  [abs]
31. Pomann, G-M; Boulware, LE; Chan, C; Grambow, SC; Hanlon, AL; Neely, ML; Peskoe, SB; Samsa, G; Troy, JD; Yang, LZ; Thomas, SM, Experiential Learning Methods for Biostatistics Students: A Model for Embedding Student Interns in Academic Health Centers., Stat, vol. 11 no. 1 (December, 2022) [doi]  [abs]
32. Harnois, MJ; Dennis, M; Stöhr, D; Valencia, SM; Rodgers, N; Semmes, EC; Webster, HS; Jenks, JA; Barfield, R; Pollara, J; Chan, C; Sinzger, C; Permar, SR, Characterization of Plasma Immunoglobulin G Responses in Elite Neutralizers of Human Cytomegalovirus., J Infect Dis, vol. 226 no. 9 (November, 2022), pp. 1667-1677 [doi]  [abs]
33. Chen, J-L; Fries, CN; Berendam, SJ; Rodgers, NS; Roe, EF; Wu, Y; Li, SH; Jain, R; Watts, B; Eudailey, J; Barfield, R; Chan, C; Moody, MA; Saunders, KO; Pollara, J; Permar, SR; Collier, JH; Fouda, GG, Self-assembling peptide nanofiber HIV vaccine elicits robust vaccine-induced antibody functions and modulates Fc glycosylation., Sci Adv, vol. 8 no. 38 (September, 2022), pp. eabq0273 [doi]  [abs]
34. SoRelle, ED; Dai, J; Reinoso-Vizcaino, NM; Barry, AP; Chan, C; Luftig, MA, Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection., Cell Rep, vol. 40 no. 9 (August, 2022), pp. 111286 [doi]  [abs]
35. Eckhoff, AM; Connor, AA; Thacker, JKM; Blazer, DG; Moore, HG; Scheri, RP; Lagoo-Deenadayalan, SA; Harpole, DH; Seymour, KA; Purves, JT; Ravindra, KV; Southerland, KW; Rocke, DJ; Gilner, JB; Parker, DC; Bain, JR; Muehlbauer, MJ; Ilkayeva, OR; Corcoran, DL; Modliszewski, JL; Devos, N; Foster, MW; Moseley, MA; Dressman, HK; Chan, C; Huebner, JL; Chasse, S; Stempora, L; Aschenbrenner, ME; Joshi, M-B; Hollister, B; Henao, R; Barfield, RT; Ellison, MA; Bailey, S; Woody, S; Huang, ES; Kirk, A; Hwang, ES, A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery., Ann Surg, vol. 275 no. 6 (June, 2022), pp. 1094-1102 [doi]  [abs]
36. SoRelle, ED; Dai, J; Bonglack, EN; Heckenberg, EM; Zhou, JY; Giamberardino, SN; Bailey, JA; Gregory, SG; Chan, C; Luftig, MA, Correction: Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines., Elife, vol. 10 (November, 2021), pp. e75422 [doi]
37. Telzrow, CL; Zwack, PJ; Esher Righi, S; Dietrich, FS; Chan, C; Owzar, K; Alspaugh, JA; Granek, JA, Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries., G3 (Bethesda), vol. 11 no. 11 (October, 2021) [doi]  [abs]
38. Shaw, BI; Ochoa, A; Chan, C; Nobuhara, C; Gbadegesin, R; Jackson, AM; Chambers, ET, HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation., Transplant Direct, vol. 7 no. 10 (October, 2021), pp. e748 [doi]  [abs]
39. Webster, H; Valencia, S; Kumar, A; Chan, C; Dennis, M; Roark, H; Woods, A; John, S; Carfi, A; Permar, SR, Pre-existing immunity to cytomegalovirus in macaques influences human CMV vaccine responses in preclinical models., Vaccine, vol. 39 no. 38 (September, 2021), pp. 5358-5367 [doi]  [abs]
40. Fries, CN; Chen, J-L; Dennis, ML; Votaw, NL; Eudailey, J; Watts, BE; Hainline, KM; Cain, DW; Barfield, R; Chan, C; Moody, MA; Haynes, BF; Saunders, KO; Permar, SR; Fouda, GG; Collier, JH, HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth., Sci Rep, vol. 11 no. 1 (July, 2021), pp. 14494 [doi]  [abs]
41. Klus, J; Ly, VT; Chan, C; Le, T, Prognosis and treatment effects of HIV-associated talaromycosis in a real-world patient cohort., Med Mycol, vol. 59 no. 4 (April, 2021), pp. 392-399 [doi]  [abs]
42. Guptill, JT; Barfield, R; Chan, C; Russo, MA; Emmett, D; Raja, S; Massey, JM; Juel, VC; Hobson-Webb, LD; Gable, KL; Gonzalez, N; Hammett, A; Howard, JF; Chopra, M; Kaminski, HJ; Siddiqi, ZA; Migdal, M; Yi, JS, Reduced plasmablast frequency is associated with seronegative myasthenia gravis., Muscle Nerve, vol. 63 no. 4 (April, 2021), pp. 577-585 [doi]  [abs]
43. Masci, AM; White, S; Neely, B; Ardini-Polaske, M; Hill, CB; Misra, RS; Aronow, B; Gaddis, N; Yang, L; Wert, SE; Palmer, SM; Chan, C; LungMAP Consortium, Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images., BMC Bioinformatics, vol. 22 no. 1 (February, 2021), pp. 82 [doi]  [abs]
44. Terrando, N; Park, JJ; Devinney, M; Chan, C; Cooter, M; Avasarala, P; Mathew, JP; Quinones, QJ; Maddipati, KR; Berger, M; MADCO-PC Study Team, Immunomodulatory lipid mediator profiling of cerebrospinal fluid following surgery in older adults., Sci Rep, vol. 11 no. 1 (February, 2021), pp. 3047 [doi]  [abs]
45. Shaw, BI; Lee, H-J; Chan, C; Ettenger, R; Grimm, P; Pearl, M; Reed, EF; Robien, MA; Sarwal, M; Stempora, L; Warshaw, B; Zhao, C; Martinez, OM; Kirk, AD; Chambers, ET, Relationship between antithymocyte globulin, T cell phenotypes, and clinical outcomes in pediatric kidney transplantation., Am J Transplant, vol. 21 no. 2 (February, 2021), pp. 766-775 [doi]  [abs]
46. Xu, Y; Lin, Y; Bell, RP; Towe, SL; Pearson, JM; Nadeem, T; Chan, C; Meade, CS, Machine learning prediction of neurocognitive impairment among people with HIV using clinical and multimodal magnetic resonance imaging data., J Neurovirol, vol. 27 no. 1 (February, 2021), pp. 1-11 [doi]  [abs]
47. SoRelle, ED; Dai, J; Bonglack, EN; Heckenberg, EM; Zhou, JY; Giamberardino, SN; Bailey, JA; Gregory, SG; Chan, C; Luftig, MA, Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines., Elife, vol. 10 (January, 2021), pp. e62586 [doi]  [abs]
48. Johnson-Weaver, BT; Choi, HW; Yang, H; Granek, JA; Chan, C; Abraham, SN; Staats, HF, Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens., Front Immunol, vol. 12 (2021), pp. 730346 [doi]  [abs]
49. White, S; Quinn, J; Enzor, J; Staats, J; Mosier, SM; Almarode, J; Denny, TN; Weinhold, KJ; Ferrari, G; Chan, C, FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows., Front Immunol, vol. 12 (2021), pp. 768541 [doi]  [abs]
50. Obregon-Perko, V; Bricker, KM; Mensah, G; Uddin, F; Kumar, MR; Fray, EJ; Siliciano, RF; Schoof, N; Horner, A; Mavigner, M; Liang, S; Vanderford, T; Sass, J; Chan, C; Berendam, SJ; Bar, KJ; Shaw, GM; Silvestri, G; Fouda, GG; Permar, SR; Chahroudi, A, Simian-Human Immunodeficiency Virus SHIV.C.CH505 Persistence in ART-Suppressed Infant Macaques Is Characterized by Elevated SHIV RNA in the Gut and a High Abundance of Intact SHIV DNA in Naive CD4+ T Cells., J Virol, vol. 95 no. 2 (December, 2020) [doi]  [abs]
51. Jenks, JA; Nelson, CS; Roark, HK; Goodwin, ML; Pass, RF; Bernstein, DI; Walter, EB; Edwards, KM; Wang, D; Fu, T-M; An, Z; Chan, C; Permar, SR, Antibody binding to native cytomegalovirus glycoprotein B predicts efficacy of the gB/MF59 vaccine in humans., Sci Transl Med, vol. 12 no. 568 (November, 2020) [doi]  [abs]
52. Zhang, T; Harrison, MR; O'Donnell, PH; Alva, AS; Hahn, NM; Appleman, LJ; Cetnar, J; Burke, JM; Fleming, MT; Milowsky, MI; Mortazavi, A; Shore, N; Sonpavde, GP; Schmidt, EV; Bitman, B; Munugalavadla, V; Izumi, R; Patel, P; Staats, J; Chan, C; Weinhold, KJ; George, DJ, A randomized phase 2 trial of pembrolizumab versus pembrolizumab and acalabrutinib in patients with platinum-resistant metastatic urothelial cancer., Cancer, vol. 126 no. 20 (October, 2020), pp. 4485-4497 [doi]  [abs]
53. Sung, AD; Jauhari, S; Siamakpour-Reihani, S; Rao, AV; Staats, J; Chan, C; Meyer, E; Gadi, VK; Nixon, AB; Lyu, J; Xie, J; Bohannon, L; Li, Z; Hourigan, CS; Dillon, LW; Wong, HY; Shelby, R; Diehl, L; de Castro, C; LeBlanc, T; Brander, D; Erba, H; Galal, A; Stefanovic, A; Chao, N; Rizzieri, DA, Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects., Am J Hematol, vol. 95 no. 6 (June, 2020), pp. 662-671 [doi]  [abs]
54. Berger, M; Murdoch, DM; Staats, JS; Chan, C; Thomas, JP; Garrigues, GE; Browndyke, JN; Cooter, M; Quinones, QJ; Mathew, JP; Weinhold, KJ; MADCO-PC Study Team, Flow Cytometry Characterization of Cerebrospinal Fluid Monocytes in Patients With Postoperative Cognitive Dysfunction: A Pilot Study., Anesth Analg, vol. 129 no. 5 (November, 2019), pp. e150-e154 [doi]  [abs]
55. Goswami, R; Nelson, AN; Tu, JJ; Dennis, M; Feng, L; Kumar, A; Mangold, J; Mangan, RJ; Mattingly, C; Curtis, AD; Obregon-Perko, V; Mavigner, M; Pollara, J; Shaw, GM; Bar, KJ; Chahroudi, A; De Paris, K; Chan, C; Van Rompay, KKA; Permar, SR, Analytical Treatment Interruption after Short-Term Antiretroviral Therapy in a Postnatally Simian-Human Immunodeficiency Virus-Infected Infant Rhesus Macaque Model., mBio, vol. 10 no. 5 (September, 2019) [doi]  [abs]
56. Kim-Chang, JJ; Wilson, L; Chan, C; Fischer, B; Venturi, G; Goodenow, MM; Aldrovandi, G; Weber, TJ; Sleasman, JW; Adolescent Medicine Trials Network for HIV/AIDS Interventions, Tenofovir Has Minimal Effect on Biomarkers of Bone Health in Youth with HIV Receiving Initial Antiretroviral Therapy., AIDS Res Hum Retroviruses, vol. 35 no. 8 (August, 2019), pp. 746-754 [doi]  [abs]
57. Choi, HW; Chan, C; Shterev, ID; Lynch, HE; Robinette, TJ; Johnson-Weaver, BT; Shi, J; Sempowski, GD; Kim, SY; Dickson, JK; Gooden, DM; Abraham, SN; Staats, HF, Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening., SLAS Discov, vol. 24 no. 6 (July, 2019), pp. 628-640 [doi]  [abs]
58. Lin, J; Sibley, A; Shterev, I; Nixon, A; Innocenti, F; Chan, C; Owzar, K, fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies., BMC Bioinformatics, vol. 20 no. 1 (June, 2019), pp. 333 [doi]  [abs]
59. Berger, M; Oyeyemi, D; Olurinde, MO; Whitson, HE; Weinhold, KJ; Woldorff, MG; Lipsitz, LA; Moretti, E; Giattino, CM; Roberts, KC; Zhou, J; Bunning, T; Ferrandino, M; Scheri, RP; Cooter, M; Chan, C; Cabeza, R; Browndyke, JN; Murdoch, DM; Devinney, MJ; Shaw, LM; Cohen, HJ; Mathew, JP; INTUIT Investigators, The INTUIT Study: Investigating Neuroinflammation Underlying Postoperative Cognitive Dysfunction., J Am Geriatr Soc, vol. 67 no. 4 (April, 2019), pp. 794-798 [doi]  [abs]
60. Yi, JS; Rosa-Bray, M; Staats, J; Zakroysky, P; Chan, C; Russo, MA; Dumbauld, C; White, S; Gierman, T; Weinhold, KJ; Guptill, JT, Establishment of normative ranges of the healthy human immune system with comprehensive polychromatic flow cytometry profiling., PLoS One, vol. 14 no. 12 (2019), pp. e0225512 [doi]  [abs]
61. Lin, J; Gresham, J; Wang, T; Kim, SY; Alvarez, J; Damrauer, JS; Floyd, S; Granek, J; Allen, A; Chan, C; Xie, J; Owzar, K, bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens., Bioinformatics, vol. 34 no. 20 (October, 2018), pp. 3581-3583 [doi]  [abs]
62. Shterev, ID; Dunson, DB; Chan, C; Sempowski, GD, Bayesian Multi-Plate High-Throughput Screening of Compounds., Sci Rep, vol. 8 no. 1 (June, 2018), pp. 9551 [doi]  [abs]
63. Johnson-Weaver, BT; McRitchie, S; Mercier, KA; Pathmasiri, W; Sumner, SJ; Chan, C; Germolec, D; Kulis, M; Burks, AW; Staats, HF, Effect of endotoxin and alum adjuvant vaccine on peanut allergy., J Allergy Clin Immunol, vol. 141 no. 2 (February, 2018), pp. 791-794.e8 [doi]
64. Sibley, A; Li, Z; Jiang, Y; Li, Y-J; Chan, C; Allen, A; Owzar, K, Facilitating the Calculation of the Efficient Score Using Symbolic Computing., Am Stat, vol. 72 no. 2 (2018), pp. 199-205 [doi]  [abs]
65. Ardini-Poleske, ME; Clark, RF; Ansong, C; Carson, JP; Corley, RA; Deutsch, GH; Hagood, JS; Kaminski, N; Mariani, TJ; Potter, SS; Pryhuber, GS; Warburton, D; Whitsett, JA; Palmer, SM; Ambalavanan, N; LungMAP Consortium, LungMAP: The Molecular Atlas of Lung Development Program., Am J Physiol Lung Cell Mol Physiol, vol. 313 no. 5 (November, 2017), pp. L733-L740 [doi]  [abs]
66. Norton, JN; Reynolds, RP; Chan, C; Valdivia, RH; Staats, HF, Assessing the satisfaction and burden within an academic animal care and use program., FASEB J, vol. 31 no. 9 (September, 2017), pp. 3913-3921 [doi]  [abs]
67. Pedersen, NW; Chandran, PA; Qian, Y; Rebhahn, J; Petersen, NV; Hoff, MD; White, S; Lee, AJ; Stanton, R; Halgreen, C; Jakobsen, K; Mosmann, T; Gouttefangeas, C; Chan, C; Scheuermann, RH; Hadrup, SR, Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells., Front Immunol, vol. 8 (2017), pp. 858 [doi]  [abs]
68. Himes, JE; Ho, C; Nguyen, QN; Amos, JD; Xu, H; Chan, C; Chow, S-C; Ochsenbauer, C; Kaidarova, Z; Keating, SM; Fouda, GG; Permar, SR, Characterization of Simian Immunodeficiency Virus Variants Anatomically Compartmentalized in Plasma and Milk in Chronically Infected African Green Monkeys., J Virol, vol. 90 no. 19 (October, 2016), pp. 8795-8808 [doi]  [abs]
69. Zidar, DA; Mudd, JC; Juchnowski, S; Lopes, JP; Sparks, S; Park, SS; Ishikawa, M; Osborne, R; Washam, JB; Chan, C; Funderburg, NT; Owoyele, A; Alaiti, MA; Mayuga, M; Orringer, C; Costa, MA; Simon, DI; Tatsuoka, C; Califf, RM; Newby, LK; Lederman, MM; Weinhold, KJ, Altered Maturation Status and Possible Immune Exhaustion of CD8 T Lymphocytes in the Peripheral Blood of Patients Presenting With Acute Coronary Syndromes., Arterioscler Thromb Vasc Biol, vol. 36 no. 2 (February, 2016), pp. 389-397 [doi]  [abs]
70. Snyder, LD; Chan, C; Kwon, D; Yi, JS; Martissa, JA; Copeland, CAF; Osborne, RJ; Sparks, SD; Palmer, SM; Weinhold, KJ, Polyfunctional T-Cell Signatures to Predict Protection from Cytomegalovirus after Lung Transplantation., Am J Respir Crit Care Med, vol. 193 no. 1 (January, 2016), pp. 78-85 [doi]  [abs]
71. Lin, L; Chan, C; West, M, Discriminative variable subsets in Bayesian classification with mixture models, with application in flow cytometry studies., Biostatistics, vol. 17 no. 1 (January, 2016), pp. 40-53 [doi]  [abs]
72. Lai, W; Huang, L; Zhu, L; Ferrari, G; Chan, C; Li, W; Lee, K-H; Chen, C-H, Gnidimacrin, a Potent Anti-HIV Diterpene, Can Eliminate Latent HIV-1 Ex Vivo by Activation of Protein Kinase C β., J Med Chem, vol. 58 no. 21 (November, 2015), pp. 8638-8646 [doi]  [abs]
73. Gouttefangeas, C; Chan, C; Attig, S; Køllgaard, TT; Rammensee, H-G; Stevanović, S; Wernet, D; thor Straten, P; Welters, MJP; Ottensmeier, C; van der Burg, SH; Britten, CM, Data analysis as a source of variability of the HLA-peptide multimer assay: from manual gating to automated recognition of cell clusters., Cancer Immunol Immunother, vol. 64 no. 5 (May, 2015), pp. 585-598, Springer Nature, ISSN 0340-7004 [doi]  [abs]
74. Kvistborg, P; Gouttefangeas, C; Aghaeepour, N; Cazaly, A; Chattopadhyay, PK; Chan, C; Eckl, J; Finak, G; Hadrup, SR; Maecker, HT; Maurer, D; Mosmann, T; Qiu, P; Scheuermann, RH; Welters, MJP; Ferrari, G; Brinkman, RR; Britten, CM, Thinking outside the gate: single-cell assessments in multiple dimensions., Immunity, vol. 42 no. 4 (April, 2015), pp. 591-592, ISSN 1074-7613 [doi]
75. Gouttefangeas, C; Walter, S; Welters, MJP; Ottensmeier, C; Van Der Burg, SH; Britten, CM; Chan, C, Flow cytometry in cancer immunotherapy: Applications, quality assurance, and future (January, 2015), pp. 471-490 [doi]  [abs]
76. Staats, JS; Enzor, JH; Sanchez, AM; Rountree, W; Chan, C; Jaimes, M; Chan, RC-F; Gaur, A; Denny, TN; Weinhold, KJ, Toward development of a comprehensive external quality assurance program for polyfunctional intracellular cytokine staining assays., J Immunol Methods, vol. 409 (July, 2014), pp. 44-53, ISSN 0022-1759 [doi]  [abs]
77. Richards, AJ; Staats, J; Enzor, J; McKinnon, K; Frelinger, J; Denny, TN; Weinhold, KJ; Chan, C, Setting objective thresholds for rare event detection in flow cytometry., J Immunol Methods, vol. 409 (July, 2014), pp. 54-61, ISSN 0022-1759 [doi]  [abs]
78. Nair, SK; Tomaras, GD; Sales, AP; Boczkowski, D; Chan, C; Plonk, K; Cai, Y; Dannull, J; Kepler, TB; Pruitt, SK; Weinhold, KJ, High-throughput identification and dendritic cell-based functional validation of MHC class I-restricted Mycobacterium tuberculosis epitopes., Sci Rep, vol. 4 (April, 2014), pp. 4632 [doi]  [abs]
79. White, S; Laske, K; Welters, MJ; Bidmon, N; van der Burg, SH; Britten, CM; Enzor, J; Staats, J; Weinhold, KJ; Gouttefangeas, C; Chan, C, Managing Multi-center Flow Cytometry Data for Immune Monitoring., Cancer Inform, vol. 13 no. Suppl 7 (2014), pp. 111-122 [doi]  [abs]
80. Lin, L; Chan, C; Hadrup, SR; Froesig, TM; Wang, Q; West, M, Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies., Stat Appl Genet Mol Biol, vol. 12 no. 3 (June, 2013), pp. 309-331, ISSN 2194-6302 [Gateway.cgi], [doi]  [abs]
81. Shetty, G; Beasley, GM; Sparks, S; Barfield, M; Masoud, M; Mosca, PJ; Pruitt, SK; Salama, AKS; Chan, C; Tyler, DS; Weinhold, KJ, Plasma cytokine analysis in patients with advanced extremity melanoma undergoing isolated limb infusion., Ann Surg Oncol, vol. 20 no. 4 (April, 2013), pp. 1128-1135 [23456379], [doi]  [abs]
82. Aghaeepour, N; Finak, G; FlowCAP Consortium; DREAM Consortium; Hoos, H; Mosmann, TR; Brinkman, R; Gottardo, R; Scheuermann, RH, Critical assessment of automated flow cytometry data analysis techniques., Nat Methods, vol. 10 no. 3 (March, 2013), pp. 228-238, ISSN 1548-7091 [doi]  [abs]
83. Chan, C; Billard, M; Ramirez, SA; Schmidl, H; Monson, E; Kepler, TB, A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields., Bull Math Biol, vol. 75 no. 1 (January, 2013), pp. 185-205 [23296998], [doi]  [abs]
84. Cron, A; Gouttefangeas, C; Frelinger, J; Lin, L; Singh, SK; Britten, CM; Welters, MJP; van der Burg, SH; West, M; Chan, C, Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples., PLoS Comput Biol, vol. 9 no. 7 (2013), pp. e1003130 [23874174], [doi]  [abs]
85. Chan, C; Billard, M; Ramirez, SA; Schmidl, H; Monson, E; Kepler, TB, A Model for Migratory B Cell Oscillations from Receptor Down-Regulation Induced by External Chemokine Fields, Bulletin of Mathematical Biology, vol. 75 no. 1 (2013), pp. 185-205, ISSN 0092-8240 [doi]  [abs]
86. Snyder, LD; Medinas, R; Chan, C; Sparks, S; Davis, WA; Palmer, SM; Weinhold, KJ, Polyfunctional cytomegalovirus-specific immunity in lung transplant recipients receiving valganciclovir prophylaxis., Am J Transplant, vol. 11 no. 3 (March, 2011), pp. 553-560 [21219584], [doi]  [abs]
87. Manolopoulou, I; Chan, C; West, M, Rejoinder, Bayesian Analysis, vol. 5 no. 3 (December, 2010), pp. 461-464, Institute of Mathematical Statistics, ISSN 1936-0975 [doi]  [abs]
88. Chan, C; Lin, L; Frelinger, J; Hérbert, V; Gagnon, D; Landry, C; Sékaly, R-P; Enzor, J; Staats, J; Weinhold, KJ; Jaimes, M; West, M, Optimization of a highly standardized carboxyfluorescein succinimidyl ester flow cytometry panel and gating strategy design using discriminative information measure evaluation., Cytometry A, vol. 77 no. 12 (December, 2010), pp. 1126-1136 [21053294], [doi]  [abs]
89. Frelinger, J; Ottinger, J; Gouttefangeas, C; Chan, C, Modeling flow cytometry data for cancer vaccine immune monitoring., Cancer Immunol Immunother, vol. 59 no. 9 (September, 2010), pp. 1435-1441, Springer Nature, ISSN 0340-7004 [doi]  [abs]
90. Suchard, MA; Wang, Q; Chan, C; Frelinger, J; Cron, A; West, M, Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures., J Comput Graph Stat, vol. 19 no. 2 (June, 2010), pp. 419-438, ISSN 1061-8600 [repository], [doi]  [abs]
91. Manolopoulou, I; Chan, C; West, M, Selection sampling from large data sets for targeted inference in mixture modeling, Bayesian Analysis, vol. 5 no. 3 (2010), pp. 429-450, ISSN 1936-0975 [doi]  [abs]
92. Chan, C; Feng, F; Ottinger, J; Foster, D; West, M; Kepler, TB, Statistical mixture modeling for cell subtype identification in flow cytometry., Cytometry A, vol. 73 no. 8 (August, 2008), pp. 693-701, ISSN 1552-4930 [18496851], [doi]  [abs]
93. Frelinger, J; Kepler, TB; Chan, C, Flow: Statistics, visualization and informatics for flow cytometry., Source Code Biol Med, vol. 3 (June, 2008), pp. 10, ISSN 1751-0473 [18559108], [doi]  [abs]
94. Mitha, F; Lucas, TA; Feng, F; Kepler, TB; Chan, C, The Multiscale Systems Immunology project: software for cell-based immunological simulation., Source Code Biol Med, vol. 3 (April, 2008), pp. 6, ISSN 1751-0473 [18442405], [doi]  [abs]
95. Yates, A; Chan, C; Strid, J; Moon, S; Callard, R; George, AJT; Stark, J, Reconstruction of cell population dynamics using CFSE., BMC Bioinformatics, vol. 8 (June, 2007), pp. 196, ISSN 1471-2105 [17565685], [doi]  [abs]
96. Kepler, TB; Chan, C, Spatiotemporal programming of a simple inflammatory process., Immunol Rev, vol. 216 (April, 2007), pp. 153-163, ISSN 0105-2896 [17367341], [doi]  [abs]
97. Stark, J; Chan, C; George, AJT, Oscillations in the immune system., Immunol Rev, vol. 216 (April, 2007), pp. 213-231, ISSN 0105-2896 [17367345], [doi]  [abs]
98. Chan, C; Kepler, TB, Computational immunology--from bench to virtual reality., Ann Acad Med Singap, vol. 36 no. 2 (February, 2007), pp. 123-127, ISSN 0304-4602 [17364079]  [abs]
99. Chan, C; George, AJT; Stark, J, Cytotoxic killing and immune evasion by repair, Journal of Statistical Physics, vol. 128 no. 1-2 (January, 2007), pp. 393-411, Springer Nature, ISSN 0022-4715 [doi]  [abs]
100. Alam, AKMS; Florey, O; Weber, M; Pillai, RG; Chan, C; Tan, PH; Lechler, RI; McClure, MO; Haskard, DO; George, AJT, Knockdown of mouse VCAM-1 by vector-based siRNA., Transpl Immunol, vol. 16 no. 3-4 (November, 2006), pp. 185-193, ISSN 0966-3274 [17138052], [doi]  [abs]
101. Yates, AJ; Chan, CCT; Callard, RE, 16 Modelling T cell activation, proliferation, and homeostasis, Studies in Multidisciplinarity, vol. 3 no. C (December, 2005), pp. 281-308, Elsevier, ISSN 1571-0831 [doi]
102. Chan, C; Stark, J; George, AJT, The impact of multiple T cell - APC encounters and the role of anergy, Journal of Computational and Applied Mathematics, vol. 184 no. 1 (December, 2005), pp. 101-120, Elsevier BV [doi]  [abs]
103. George, AJT; Stark, J; Chan, C, Understanding specificity and sensitivity of T-cell recognition., Trends Immunol, vol. 26 no. 12 (December, 2005), pp. 653-659, ISSN 1471-4906 [16236548], [doi]  [abs]
104. Tan, PH; Chan, CLH; Chan, C; George, AJT, The evolving role of gene-based treatment in surgery., Br J Surg, vol. 92 no. 12 (December, 2005), pp. 1466-1480, ISSN 0007-1323 [16273530], [doi]  [abs]
105. Tan, PH; Yates, JB; Xue, S-A; Chan, C; Jordan, WJ; Harper, JE; Watson, MP; Dong, R; Ritter, MA; Lechler, RI; Lombardi, G; George, AJT, Creation of tolerogenic human dendritic cells via intracellular CTLA4: a novel strategy with potential in clinical immunosuppression., Blood, vol. 106 no. 9 (November, 2005), pp. 2936-2943, ISSN 0006-4971 [15994283], [doi]  [abs]
106. Tan, PH; Sagoo, P; Chan, C; Yates, JB; Campbell, J; Beutelspacher, SC; Foxwell, BMJ; Lombardi, G; George, AJT, Inhibition of NF-kappa B and oxidative pathways in human dendritic cells by antioxidative vitamins generates regulatory T cells., J Immunol, vol. 174 no. 12 (June, 2005), pp. 7633-7644, ISSN 0022-1767 [15944264], [doi]  [abs]
107. Chan C, Stark J and George AJT. The impact of multiple T cell–APC encounters and the role of anergy. Journal of Computational and Applied Mathematics, (2005) 184:101-120
108. Chan, C; Stark, J; George, AJT, Feedback control of T-cell receptor activation., Proc Biol Sci, vol. 271 no. 1542 (May, 2004), pp. 931-939, ISSN 0962-8452 [15255048], [doi]  [abs]
109. Tan, PH; Chan, C; Xue, SA; Dong, R; Ananthesayanan, B; Manunta, M; Kerouedan, C; Cheshire, NJW; Wolfe, JH; Haskard, DO; Taylor, KM; George, AJT, Phenotypic and functional differences between human saphenous vein (HSVEC) and umbilical vein (HUVEC) endothelial cells., Atherosclerosis, vol. 173 no. 2 (April, 2004), pp. 171-183, ISSN 0021-9150 [15064090], [doi]  [abs]
110. Chan, C; Lechler, RI; George, AJT, Tolerance mechanisms and recent progress., Transplant Proc, vol. 36 no. 2 Suppl (March, 2004), pp. 561S-569S, ISSN 0041-1345 [15041406], [doi]  [abs]
111. Chan, C; George, AJT; Stark, J, T cell sensitivity and specificity - Kinetic proofreading revisited, Discrete and Continuous Dynamical Systems Series B, vol. 3 no. 3 (January, 2003), pp. 343-360 [doi]  [abs]
112. Chan C, George AJT and Stark J, T cell sensitivity and specificity – kinetic proofreading revisited. Discrete and Continuous Dynamical Systems – Series B, 3, (2003), 343-360.
113. Yates, A; Chan, CC; Callard, RE; George, AJ; Stark, J, An approach to modelling in immunology., Brief Bioinform, vol. 2 no. 3 (September, 2001), pp. 245-257, ISSN 1467-5463 [11589585], [doi]  [abs]
114. Chan, C; George, AJ; Stark, J, Cooperative enhancement of specificity in a lattice of T cell receptors., Proc Natl Acad Sci U S A, vol. 98 no. 10 (May, 2001), pp. 5758-5763, ISSN 0027-8424 [11344310], [doi]  [abs]
115. Yates A, Chan C, Callard RE, George AJT and Stark J. An approach to modelling in immunology. Briefings in Bioinformatics, 2001, 2, 1-13.
116. Chan, CC; Stark, J; George, AJ, Analysis of cytokine dynamics in corneal allograft rejection., Proc Biol Sci, vol. 266 no. 1434 (November, 1999), pp. 2217-2223, ISSN 0962-8452 [10649636], [doi]  [abs]

Chapters

1. Gouttefangeas, C; Walter, S; Welters, MJP; Ottensmeier, C; Van der Burg, SH; Chan, C, Flow cytometry in cancer immunotherapy: Applications, quality assurance, and future, in Cancer Immunology A Translational Medicine Context Second Edition (January, 2020), pp. 761-783, ISBN 9783030308445 [doi]  [abs]
2. Chan, C; Hudgens, MG; Chow, SC, Preface (January, 2017), pp. xi-xv, ISBN 9781498734233 [doi]
3. Lin, L; Chan, C, Quantitative methods and bayesian models for flow cytometry analysis in HIV/AIDS research, in Quantitative Methods for HIV AIDS Research (January, 2017), pp. 135-156, ISBN 9781498734233 [doi]  [abs]