Link: Google Scholar

    2019

  1. Yuan M*, Cottrell CA*, Ozorowski G*, van Gils MJ, Kumar S, Wu NC, Sarkar A, Torres JL, de Val N, Copps J, Moore JP, Sanders RW, Ward AB, Wilson IA. (2019) Conformational plasticity in the HIV-1 fusion peptide facilitates recognition by broadly neutralizing antibodies. Cell Host & Microbe. 25:873-883.e5. *Equal Contributors

  2. Wu NC, Lv H, Thompson AJ, Wu DC, Ng WWS, Kadam RU, Lin CW, Nycholat CM, McBride R, Liang W, Paulson JC, Mok CKP, Wilson IA. (2019) Preventing an antigenically disruptive mutation in egg-based H3N2 seasonal influenza vaccines by mutational incompatibility. Cell Host & Microbe. 25:836-844.e5.
  3.        - Sequencing Data: Bioproject PRJNA532726
           - Scripts: Github::incompatible_egg_muts
           - Structures: 6NS9, 6NSA, 6NSB, 6NSC, 6NSF, 6NSG

  4. LaPierre N*, Mangul S*, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E. (2019) MiCoP: Microbial Community Profiling method for detecting viral and fungal organisms in metagenomic samples. BMC Genomics. 20:423. *Equal Contributors

  5. Hong S, Shi Y, Wu NC, Grande G, Douthit L, Wang H, Zhou W, Sharpless KB, Wilson IA, Xie J, Wu P. (2019) Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Nature Communications. 10:1799.

  6. Zost SJ*, Wu NC*, Hensley SE, Wilson IA. (2019) Immunodominance and antigenic variation of influenza virus hemagglutinin: implications for design of universal vaccine immunogens. The Journal of Infectious Diseases. 219:S38-S45. *Equal Contributors

  7. Sevy AM, Wu NC, Gilchuk IM, Parrish EH, Burger S, Yousif D, Nagel MBM, Schey KL, Wilson IA, Crowe JE Jr, Meiler J. (2019) Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses. PNAS. 116:1597-1602.
  8.        - Structure: 6D0U

  9. Wu NC, Qi H. (2019) Application of deep mutational scanning in hepatitis C virus. Methods in Molecular Biology. 1911:183-190.

  10. 2018

  11. Wu NC, Ward AB. (2018) Deception through mimicry: a cellular antiviral strategy. Cell. 175:1728-1729.

  12. Credille CV, Dick B, Morrison CN, Stokes RW, Adamek R, Wu NC, Wilson IA, Cohen SM. (2018) Structure-activity relationships in metal-binding pharmacophores for influenza endonuclease. Journal of Medicinal Chemistry. 61:10206-10217.

  13. Wu NC, Yamayoshi S, Ito M, Uraki R, Kawaoka Y, Wilson IA. (2018) Recurring and adaptable binding motifs in broadly neutralizing antibodies to influenza virus are encoded on the D3-9 segment of the Ig gene. Cell Host & Microbe. 24:569-578.e4.
  14.        - Scripts: Github::S9-3-37
           - Structure: 6E3H

  15. Lee JM*, Huddleston J*, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD. (2018) Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. PNAS. 115:E8276-E8285. *Equal Contributors

  16. Guan W*, Yang Z*, Wu NC*, Lee HHY, Li Y, Jiang W, Shen L, Wu DC, Chen R, Zhong N, Wilson IA, Peiris M, Mok CKP. (2018) Clinical correlations of transcriptional profile in patients infected with avian influenza H7N9 virus. The Journal of Infectious Diseases. 218:1238-1248. *Equal Contributors
  17.        - Microarray Data: GSE114466

  18. Merkouris S, Barde YA, Binley KE, Allen ND, Stepanov AV, Wu NC, Grande G, Lin CW, Li M, Nan X, Chacon-Fernandez P, DiStefano PS, Lindsay RM, Lerner RA, Xie J. (2018) Fully human agonist antibodies to TrkB using autocrine cell-based selection from a combinatorial antibody library. PNAS. 115:E7023-E7032.

  19. Wu NC, Thompson AJ, Xie J, Lin CW, Nycholat CM, Zhu X, Lerner RA, Paulson JC, Wilson IA. (2018) A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Nature Communications. 9:1264.
  20.        - Sequencing Data: Bioproject PRJNA377321
           - Scripts: Github::H3Entrench
           - Structures: 6BKM, 6BKN, 6BKO, 6BKP, 6BKQ, 6BKR, 6BKS, 6BKT

  21. Wu NC, Wilson IA. (2018) Structural insights into the design of novel anti-influenza therapies. Nature Structural & Molecular Biology. 25:115-121.

  22. Du Y, Xin L, Shi Y, Zhang TH, Wu NC, Dai L, Gong D, Brar G, Shu S, Luo J, Reiley W, Tseng YW, Bai H, Wu TT, Wang J, Shu Y, Sun R. (2018) Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design. Science. 359:290-296.

  23. 2017

  24. Wu NC, Zost SJ, Thompson AJ, Oyen D, Nycholat CM, McBride R, Paulson JC, Hensley SE, Wilson IA. (2017) A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine. PLoS Pathogens. 13:e1006682.
  25.        - Scripts: Github::H3N2L194P
           - Structures: 6AOP, 6AOQ, 6AOR, 6AOS, 6AOT, 6AOU, 6AOV

  26. Lang S*, Xie J*, Zhu X*, Wu NC, Lerner RA, Wilson IA. (2017) Antibody 27F3 broadly targets influenza A group 1 and 2 hemagglutinins through a further variation in VH1-69 antibody orientation on the HA stem. Cell Reports. 20:2935-2943. *Equal Contributors

  27. Du Y*, Chi X*, Wang C, Jiang J, Kong F, Yan H, Wang X, Li J, Wu NC, Dai L, Zhang TH, Shu S, Zhou J, Yoshizawa JM, Li X, Bhattacharya D, Wu TT, Niu J, Sun R. (2017) Quantifying perinatal transmission of hepatitis B viral quasispecies by tag linkage deep sequencing. Scientific Reports. 7:10168. *Equal Contributors
  28.        - Sequencing Data: Bioproject PRJNA309553

  29. Wu NC, Wilson IA. (2017) A perspective on the structural and functional constraints for immune evasion: Insights from the influenza virus. Journal of Molecular Biology. 429:2694-2709.

  30. Wright ZVF, Wu NC, Kadam RU, Wilson IA, Wolan DW. (2017) Structure-based optimization and synthesis of antiviral drug Arbidol analogues with significantly improved affinity to influenza hemagglutinin. Bioorganic & Medicinal Chemistry Letters. 27:3744-3748.

  31. Wu NC*, Xie J*, Zheng T, Nycholat CM, Grande G, Paulson JC, Lerner RA, Wilson IA. (2017) Diversity of functionally permissive sequences in the receptor-binding site of influenza hemagglutinin. Cell Host & Microbe. 21:742-753.e8. *Equal Contributors
  32.        - Sequencing Data: Bioproject PRJNA353496
           - Scripts: Github::HARBS
           - Structures: 5VTQ, 5VTR, 5VTU, 5VTV, 5VTW, 5VTX, 5VTY, 5VTZ, 5VU4

  33. Wu NC, Grande G, Turner HL, Ward AB, Xie J, Lerner RA, Wilson IA. (2017) In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity. Nature Communications. 8:15371.
  34.        - Sequencing Data: Bioproject PRJNA326694
           - Scripts: Github::C05mut
           - Structure: 5UMN

  35. Lee JH*, Andrabi R*, Su CY, Yasmeen A, Julien JP, Kong L, Wu NC, McBride R, Sok D, Pauthner M, Cottrell CA, Nieusma T, Blattner C, Paulson JC, Klasse PJ, Wilson IA, Burton DR, Ward AB. (2017) A broadly neutralizing antibody targets the dynamic HIV envelope trimer apex via a long, rigidified, and anionic β-hairpin structure. Immunity. 46:690-702. *Equal Contributors

  36. Xie J, Sok D, Wu NC, Zheng T, Zhang W, Burton DR, Lerner RA. (2017) Immunochemical engineering of cell surfaces to generate virus resistance. PNAS. 114:4655-4660.

  37. Qi H, Chu V, Wu NC, Chen Z, Truong S, Brar G, Su SY, Du Y, Arumugaswami V, Olson CA, Chen SH, Lin CY, Wu TT, Sun R. (2017) Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein. PNAS. 114:2018-2023.

  38. Artyomenko A*, Wu NC*, Mangul S*, Eskin E, Sun R, Zelikovsky A. (2017) Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants. Journal of Computational Biology. 24:558-570. *Equal Contributors
  39.        - Software: Two Single Nucleotide Variants (2SNV)
           - Sequencing Data: Bioproject PRJNA284802

    2016

  40. Du Y, Wu NC, Jiang L, Zhang T, Gong D, Shu S, Wu TT, Sun R. (2016) Annotating protein functional residues by coupling high-throughput fitness profile and homologous-structure analysis. mBio. 7:e01801-16.
  41.        - Sequencing Data: Bioproject PRJNA318707

  42. Wu NC*, Dai L*, Olson CA, Lloyd-Smith JO, Sun R. (2016) Adaptation in protein fitness landscapes is facilitated by indirect paths. eLife. 5:e16965. *Equal Contributors
  43.        - Sequencing Data: Bioproject PRJNA278685
           - Scripts: Github::ProteinGFourMutants

  44. Zhang TH*, Wu NC*, Sun R. (2016) A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing. BMC Genomics. 17:108. *Equal Contributors
  45.        - Sequencing Data: Bioproject PRJNA293914
           - Scripts: Github::errorcorrection

  46. Wu NC, Olson CA, Sun R. (2016) High-throughput identification of protein mutant stability computed from a double mutant fitness landscape. Protein Science. 25:530-539.
  47.        - Scripts: Github::DoubleMutFit2DDG

  48. Wu NC*, Du Y*, Le S, Young AP, Zhang TH, Wang Y, Zhou J, Yoshizawa JM, Dong L, Li X, Wu TT, Sun R. (2016) Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. BMC Genomics. 17:46. *Equal Contributors
  49.        - Sequencing Data: Bioproject PRJNA285135

    2015

  50. York AG, Williams KJ, Argus JP, Zhou QD, Brar G, Vergnes L, Gray EE, Zhen A, Wu NC, Yamada DH, Cunningham CR, Tarling EJ, Wilks MQ, Casero D, Gray DH, Yu AK, Wang ES, Brooks DG, Sun R, Kitchen SG, Wu TT, Reue K, Stetson DB, Bensinger SJ. (2015) Limiting cholesterol biosynthetic flux spontaneously engages type I IFN signaling. Cell. 163:1716–1729.
  51.        - Sequencing Data: Bioproject PRJNA298562

  52. Qi H*, Wu NC*, Du Y, Wu TT, Sun R. (2015) High-resolution genetic profile of viral genomes: why it matters. Current Opinion in Virology. 14:62-70. *Equal Contributors

  53. Wu NC, Olson CA, Du Y, Le S, Tran K, Remenyi R, Gong D, Al-Mawsawi LQ, Qi H, Wu TT, Sun R. (2015) Functional constraint profiling of a viral protein reveals discordance of evolutionary conservation and functionality. PLoS Genetics. 11:e1005310.
  54.        - Sequencing Data: Bioproject PRJNA254185
           - Scripts: Github::PAlib240

    2014

  55. Al-Mawsawi LQ, Wu NC, Olson C, Shi V, Qi H, Zheng X, Wu TT, Sun R. (2014) High-throughput profiling of point mutations across the HIV-1 genome. Retrovirology. 11:124.
  56.        - Sequencing Data: Bioproject PRJNA259391

  57. Olson CA, Wu NC, Sun R. (2014) A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Current Biology. 24:2643-2651.
  58.        - Sequencing Data: Bioproject PRJNA285706

  59. Remenyi R*, Qi H*, Su SY, Chen Z, Wu NC, Arumugaswami V, Truong S, Chu V, Stokelman T, Lo HH, Olson CA, Wu TT, Chen SH, Lin CY, Sun R. (2014) A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. mBio. 5:e01469-14. *Equal Contributors
  60.        - Sequencing Data: Bioproject PRJNA237836

  61. Gong D, Wu NC, Xie Y, Feng J, Tong L, Brulois KF, Luan H, Du Y, Jung JU, Wang CY, Kang MK, Park NH, Sun R, Wu TT. (2014) Kaposi's sarcoma-associated herpesvirus ORF18 and ORF30 are essential for late gene expression during lytic replication. Journal of Virology. 88:11369-11382.
  62.        - Sequencing Data: Bioproject PRJNA248245

  63. Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Luan HH, Li X, Wu TT, Sun R. (2014) High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment. Journal of Virology. 88:10157-10164.
  64.        - Sequencing Data: Bioproject PRJNA230135

  65. Mangul S*, Wu NC*, Mancuso N, Zelikovsky A, Sun R, Eskin E. (2014) Accurate viral population assembly from ultra-deep sequencing data. Bioinformatics. 30:i329-i337. *Equal Contributors
  66.        - Software: Viral Genome Assembler (VGA)
           - Scripts: Github::NGSTagErrCorrect

  67. Al-Mawsawi LQ*, Wu NC*, De La Cruz J, Shi VC, Wu TT, Daar ES, Lewis MJ, Yang OO, Sun R. (2014) Short communication: HIV-1 gag genetic variation in a single acutely infected participant defined by high-resolution deep sequencing. AIDS Research and Human Retroviruses. 30:806-811. *Equal Contributors
  68.        - Sequencing Data: Bioproject PRJNA244693

  69. Wu NC, De La Cruz J, Al-Mawsawi LQ, Olson CA, Qi H, Luan HH, Nguyen N, Du Y, Le S, Wu TT, Li X, Lewis MJ, Yang OO, Sun R. (2014) HIV-1 quasispecies delineation by tag linkage deep sequencing. PLoS One. 9:e97505.
  70.        - Sequencing Data: Bioproject PRJNA227023
           - Scripts: Github::HIVTagLinkSeq

  71. Wu NC*, Young AP*, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, Luan HH, Nguyen N, Nelson SF, Li X, Wu TT, Sun R. (2014) High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Scientific Reports. 4:4942. *Equal Contributors
  72.        - Sequencing Data: Bioproject PRJNA243038

  73. Feng J, De Jesus PD, Su V, Han S, Gong D, Wu NC, Tian Y, Li X, Wu TT, Chanda SK, Sun R. (2014) RIOK3 is an adaptor protein required for IRF3-mediated antiviral type I interferon production. Journal of Virology. 88:7987-7997.

  74. Le S, Yao X, Lu S, Tan Y, Rao X, Li M, Jin X, Wang J, Zhao Y, Wu NC, Lux R, He X, Shi W, Hu F. (2014) Chromosomal DNA deletion confers phage resistance to Pseudomonas aeruginosa. Scientific Reports. 4:4738.

  75. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Remenyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin CY, Zhong W, Lloyd-Smith JO, Sun R. (2014) A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity. PLoS Pathogens. 10:e1004064.
  76.        - Sequencing Data: ;Bioproject PRJNA294006

  77. Ke R, Loverdo C, Qi H, Olson CA, Wu NC, Sun R, Lloyd-Smith JO. (2014) Modelling clinical data shows active tissue concentration of daclatasvir is 10-fold lower than its plasma concentration. Journal of Antimicrobial Chemotherapy. 69:724-727.

  78. 2013

  79. Wu NC*, Young AP*, Dandekar S, Wijersuriya H, Al-Mawsawi LQ, Wu TT, Sun R. (2013) Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. Journal of Virology. 87:1193-1199. *Equal Contributors

  80. 2011

  81. Wu N, Yang X, Li L. (2011) Identification of feed forward loops composed of microRNAs and transcription factors in arabidopsis. Journal of Biochemistry and Molecular Biology in the Post Genomic Era. 1:79-85.

  82. 2010

  83. He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L. (2010) Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics. 96:308-315.
  84.        - Microarray Data: Bioproject PRJNA124941