SHI LAB’s PUBLICATIONS

PUBLICATIONS

Selected Publications (Scopus Citations: 1551; H-index: 21)

2022

  1. Dong H, Zhang Y, Wang J, Xiang H, Lv T, Wei L, Yang S, Liu X, Ren B, Zhang X, Liu L, Cao J, Wang M, Shi J#, Yang N#., “Cas9-Based Local Enrichment and Genomics Sequence Revision of Megabase-Sized Shark IgNAR Loci.”, J Immunol. 2022 Jan 1;208(1):181-189. doi: 10.4049/jimmunol.2100844., (#: co-corresponding author).

2021

  1. Wei L, Wang M, Xiang H, Jiang Y, Gong J, Su D, Al Azad MAR, Dong H, Feng L, Wu J, Chan LL, Yang N#, Shi J#, “Bamboo Shark as a Small Animal Model for Single Domain Antibody Production.”, Front Bioeng Biotechnol. 2021 Dec 8;9:792111. doi: 10.3389/fbioe.2021.792111. (#: co-corresponding author).

  2. Li Q, Madden JA, Lin J, Shi J, Rosen SM, Schmitz-Abe K, Agrawal PB., “Reanalysis of Exome Data Identifies Novel SLC25A46 Variants Associated with Leigh Syndrome.”, J Pers Med. 2021 Dec 2;11(12):1277. doi: 10.3390/jpm11121277.

  3. Wang N, Deng Z, Zhu Q, Zhao J, Xie K, Shi P, Wang Z, Chen X, Wang F, Shi J, Zhu G., “An erythrocyte-delivered photoactivatable oxaliplatin nanoprodrug for enhanced antitumor efficacy and immune response”, Chem Sci. 2021 Oct 6;12(43):14353-14362. doi: 10.1039/d1sc02941j.

  4. Shuo Qi, Yachao Zhang, Gongyuan Liu, Jiangbo Chen, Xiaozhen Li, Qi Zhu, Yuqi Yang, Feng Wang, Jiahai Shi, Chun-Sing Lee, Guangyu Zhu, Puxiang Lai, Lidai Wang, Chihua Fang, “Plasmonic-doped melanin-mimic for CXCR4-targeted NIR-II photoacoustic computed tomography-guided photothermal ablation of orthotopic hepatocellular carcinoma”, Acta Biomater. 2021 Jul 15;129:245-257. doi: 10.1016/j.actbio.2021.05.034.

  5. Linyun He, Yachao Zhang, Jiangbo Chen, Gongyuan Liu, Jingyi Zhu, Xiaozhen Li, Dengfeng Li, Yuqi Yang, Chun-Sing Lee, Jiahai Shi, Chao Yin, Puxiang Lai, Lidai Wang, Chihua Fang, “A multifunctional targeted nanoprobe with high NIR-II PAI/MRI performance for precise theranostics of orthotopic early-stage hepatocellular carcinoma”, J Mater Chem B. 2021 Nov 3;9(42):8779-8792. doi: 10.1039/d1tb01729b.

  6. #, Yajing Shen#, “Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes.” Proc Natl Acad Sci U S A. 2021, accepted, (#: co-corresponding author).

  7. Pham TC, Jayasinghe MK, Pham TT, Yang Y, Wei L, Usman WM, Chen H, Pirisinu M, Gong J, Kim S, Peng B, Wang W, Chan C, Ma V, Nguyen NTH, Kappei D, Nguyen XH, Cho WC, Shi J#, Le MTN#, “Covalent conjugation of extracellular vesicles with peptides and nanobodies for targeted therapeutic delivery.” J Extracell Vesicles. 2021 Feb;10(4):e12057. doi: 10.1002/jev2.12057. Epub 2021 Feb 16. (#: co-corresponding author).

2020

  1. Duncan AR, Vitobello A, Collins SC, Vancollie VE, Lelliott CJ, Rodan L, Shi J, Seman AR, Agolini E, Novelli A, Prontera P, Guillen Sacoto MJ, Santiago-Sim T, Trimouille A, Goizet C, Nizon M, Bruel AL, Philippe C, Grant PE, Wojcik MH, Stoler J, Genetti CA, van Dooren MF, Maas SM, Alders M, Faivre L, Sorlin A, Yoon G, Yalcin B, Agrawal PB, “Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.” Am J Hum Genet. 2020 Dec 3;107(6):1170-1177. doi: 10.1016/j.ajhg.2020.11.001. Epub 2020 Nov 23.

  2. Zhang Y, Gao H, Li H, Guo J, Ouyang B, Wang M, Xu Q, Wang J, Lv M, Guo X, Liu Q, Wei L, Ren H, Xi Y, Guo Y, Ren B, Pan S, Liu C, Ding X, Xiang H, Yu Y, Song Y, Meng L, Liu S, Wang J, Jiang Y, Shi J, Liu S, Sabir JSM, Sabir MJ, Khan M, Hajrah NH, Ming-Yuen Lee S, Xu X, Yang H, Wang J, Fan G, Yang N, Liu X, “The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish.” iScience. 2020 Nov 2;23(11):101754. doi: 10.1016/j.isci.2020.101754. eCollection 2020 Nov 20.

  3. Liang S, Su YQ, Liang YL, Wu F, Zhang H, Shi JH, Hong WX, Xu YP, “ DNA sequence analysis and Jk blood group genotype-phenotype assessment.” Ann Transl Med. 2020 Oct;8(19):1242. doi: 10.21037/atm-20-6504.

  4. Sterling N, Duncan AR, Park R, Koolen DA, Shi J, Cho SH, Benke PJ, Grant PE, Genetti CA, VanNoy GE, Juusola J, McWalter K, Parboosingh JS, Lamont RE, Bernier FP, Smith C, Harris DJ, Stegmann APA, Innes AM, Kim S, Agrawal PB, “De novo variants in MPP5 cause global developmental delay and behavioral changes.” Hum Mol Genet. 2020 Dec 18;29(20):3388-3401. doi: 10.1093/hmg/ddaa224.

  5. D’Gama AM, England E, Madden JA, Shi J, Chao KR, Wojcik MH, Torres AR, Tan WH, Berry GT, Prabhu SP, Agrawal PB, “Exome sequencing identifies novel missense and deletion variants in RTN4IP1 associated with optic atrophy, global developmental delay, epilepsy, ataxia, and choreoathetosis.” Am J Med Genet A. 2021 Jan;185(1):203-207. doi: 10.1002/ajmg.a.61910. Epub 2020 Oct 9.

  6. D’Gama AM, Brucker WJ, Zhang T, Gubbels CS, Ferdinandusse S, Shi J, Grant PE, VanNoy G, Genetti CA, Juusola J, Yu TW, Kritzer A, Agrawal PB, “A phenotypically severe, biochemically “silent” case of HIBCH deficiency in a newborn diagnosed by rapid whole exome sequencing and enzymatic testing.” Am J Med Genet A. 2020 Apr;182(4):780-784. doi: 10.1002/ajmg.a.61498.

2019

  1. Ru Zhen, Chingyee Moo, Zhenzhen Zhao, Mengying Chen, He Feng, Xiaojun Zheng, Liang Zhang, Jiahai Shi#, Caiyong Chen#, “Wdr26 regulates nuclear condensation in developing erythroblasts” Blood, 2020 Jan 16;135(3):208-219. doi: 10.1182/blood.2019002165 (#: co-corresponding author) (cover story).

  2. Yuanyan Tan, Athena H. Y. Chu, Siyu Bao, Duc Anh Hoang, Firaol Tamiru Kebede, Wenjun Xiong, Mingfang Ji, Jiahai Shi#, Zongli Zheng#, “Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity”, Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):20969-20976. doi: 10.1073/pnas.1906843116. Epub 2019 Sep 30 (#: co-corresponding author)

2018

  1. Chrystal F Mavros, Catherine A. Brownstein, Roshni Thyagrajan, Casie A. Genetti, Sahil Tembulkar, Kelsey Graber, Quinn Murphy, Kristin Cabral, Grace E. VanNoy, Matthew Bainbridge, Jiahai Shi, Pankaj B. Agrawal, Alan H. Beggs, Eugene D’Angelo, Joseph Gonzalez-Heydrich, “De Novo Variant of TRRAP in a patient with Very Early Onset Psychosis in the Context of Non-Verbal Learning Disability and Obsessive-Compulsive Disorder: A Case Report”, BMC Med Genet. 2018 Nov 13;19(1):197.

  2. Yien YY, Shi J*, Chen C*, Cheung JT, Grillo AS, Shrestha R, Li L, Zhang X, Kafina MD, Kingsley PD, King MJ, Ablain J, Li H, Zon L, Palis J, Burke MD, Bauer DE, Orkin SH, Koehler CM, Phillips JD, Kaplan J, Ward DM, Lodish HF, Paw BH, “FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity”, J Biol Chem. 2018 Oct 26. pii: jbc.RA118.002742. *: Equal contribution.

  3. Zheng L, Shi J, Mu Y., “Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations”, Phys Chem Chem Phys. 2018 Oct 25.

  4. Lim L, Gupta G, Roy A, Kang J, Srivastava S, Shi J#, Song J#, “Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses”, Prog Biophys Mol Biol. 2018 Sep 11. (#: co-corresponding author).

  5. Usman WM, Pham TC, Kwok YY, Vu LT, Ma V, Peng B, Chan YS, Wei L, Chin SM, Azad A, He AB, Leung AYH, Yang M, Shyh-Chang N, Cho WC, Shi J, Le MTN, “Efficient RNA drug delivery using red blood cell extracellular vesicles”, Nat Commun. 2018 Jun 15;9(1):2359.

  6. Wojcik MH, Okada K, Prabhu SP, Nowakowski DW, Ramsey K, Balak C, Rangasamy S, Brownstein CA, Schmitz-Abe K, Cohen JS, Fatemi A, Shi J, Grant EP, Narayanan V, Ho HH, Agrawal PB., “De novo variant in KIF26B is associated with pontocerebellar hypoplasia with infantile spinal muscular atrophy”, Am J Med Genet A. 2018 Aug 27.

  7. Katwa U, D’Gama AM, Qualls AE, Donovan LM, Heffernan J, Shi J, Agrawal PB., “Atypical presentations associated with non-polyalanine repeat PHOX2B mutations”, Am J Med Genet A. 2018 Jul;176(7):1627-1631.

2017

  1. Agrawal PB, Wang R, Li HL, Schmitz-Abe K, Simone-Roach C, Chen J, Shi J, Louie T, Sheng S, Towne MC, Brainson CF, Matthay MA, Kim CF, Bamshad M, Emond MJ, Gerard NP, Kleyman TR, Gerard C, “Epithelial Sodium Channel ENaC is a modifier of the long term non-progressive phenotype associated with F508del CFTR mutations”, Am J Respir Cell Mol Biol. 2017 Jul 14. doi: 10.1165/rcmb.2017-0166OC.

  2. Cao S, Smith LL, Padilla-Lopez SR, Guida BS, Blume E, Shi J, Morton SU, Brownstein CA, Beggs AH, Kruer MC, Agrawal PB, “Homozygous EEF1A2 mutation causes dilated cardiomyopathy, failure to thrive, global developmental delay, epilepsy and early death.”, Hum Mol Genet. 2017 Sep 15;26(18):3545-3552. doi: 10.1093/hmg/ddx239.

  3. Mehta P, Küspert M, Bale T, Brownstein CA, Towne MC, De Girolami U, Shi J, Beggs AH, Darras BT, Wegner M, Piao X, Agrawal PB, “Novel mutation in CNTNAP1 results in congenital hypomyelinating neuropathy”, Muscle Nerve. 2017 May;55(5):761-765. doi: 10.1002/mus.25416.

2016

  1. Palmer S, Towne MC, Pearl PL, Pelletier RC, Genetti CA, Shi J, Beggs AH, Agrawal PB, Brownstein CA, “SLC6A1 Mutation and Ketogenic Diet in epilepsy with myoclonic-atonic seizures”, Pediatr Neurol. 2016 Nov;64:77-79. doi: 10.1016/j.pediatrneurol.2016.07.012.

  2. Shi J, Yuan B, Hu W, Lodish H, “JAK2 V617F stimulates proliferation of erythropoietin- dependent erythroid progenitors and delays their differentiation by activating Stat1 and other non-erythroid signaling pathways”, Exp Hematol. 2016 Nov;44(11):1044-1058.e5. doi: 10.1016/j.exphem.2016.07.010.

  3. Brownstein CA, Beggs AH, Rodan L, Shi J, Towne MC, Pelletier R, Cao S, Rosenberg PA, Urion DK, Picker J, Tan WH, Agrawal PB, “Clinical heterogeneity associated with KCNA1 mutations include cataplexy and non-ataxic presentations”, Neurogenetics. 2016 Jan;17(1):11-6. doi: 10.1007/s10048-015-0460-2.

  4. Li H*, Shi J*, Huang NJ, Pishesha N, Natarajan A, Eng JC, Lodish HF, “Efficient CRISPR-Cas9 mediated gene disruption in primary erythroid progenitor cells”, Haematologica. 2016 Jun;101(6):e216-9. doi: 10.3324/haematol.2015.135723. *: Equal contribution.

2015

  1. Patterson HC, Gerbeth C, Thiru P, Vögtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP, Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF, “A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates H2O2 signaling” Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):E5679-88. doi: 10.1073/pnas.1517932112.

  2. Vijay G. Sankaran, Jacob C. Ulirsch, Vassili Tchaikovskii, Leif S. Ludwig, Aoi Wakabayashi, Senkottuvelan Kadirvel, R. Coleman Lindsley, Rafael Bejar, Jiahai Shi, Scott B. Lovitch, David F. Bishop, David P. Steensma, “X-linked macrocytic dyserythropoietic anemia in females with an ALAS2 mutation”, Journal of Clinical Investigation, 2015 Apr;125(4):1665-9.

2014-2004

  1. Jiahai Shi*, Lenka Kundrat*, Novalia Pishesha, Angelina Bilate, Chris Theile, Takeshi Maruyama, Stephanie K. Dougan, Hidde Ploegh, and Harvey Lodish, “Engineered red cells as carriers for systemic delivery of a wide array of functional probes”, Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10131-6. *: Equal contribution
    Featured in “In This Issue” by the editorial board of PNAS
    Highlighted in Science News, New Scientist, PBS NOVA and 11 other news reports

  2. Jiahai Shi*, Piu Wong­­*, Katherine K. Luo, Paula Trepman, Eric T. Wang, Christopher B. Burge, and Harvey F. Lodish, “Mbnl1 regulates alternative RNA splicing in terminal erythropoiesis”, 2014 Jul 24;124(4):598-610., *: Equal contribution
    Commented in Don M. Wojchowski, “Erythroid mRNA processing: a “splice of life”, Blood. 2014 Jul 24;124(4):474-5.

  3. Shilpa M. Hattangadi, Sandra Martinez-Morilla, Heide Christine Christine Patterson, Jiahai Shi, Karly A Burke, Amalia Avila Figueroa, Srividhya Venkatesan, Junxia Wang, Katherina Paulsen, Cher Huang, Dirk Gorlich, Maki Murata-Hori, and Harvey F Lodish, “Histones to the cytosol: Exportin 7 plays an important role in terminal erythroid nuclear maturation,” Blood. 2014 Aug 4. pii: blood-2013-11-537761.

  4. Pishesha N., Thiru P., Shi J., Eng J.C., Sankaran V.G., Lodish H.F., “Transcriptional divergence and conservation of human and mouse erythropoiesis”, Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4103-8.

  5. Alvarez-Dominguez J.R., Hu W., Yuan B., Shi J., Park S.S., Gromatzky A.A., van Oudenaarden A., Lodish H.F., “Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation”, Blood. 2014 Jan 23;123(4):570-81.

  6. Lim L.*, Shi J.*, Mu Y., Song J., “Dynamically-Driven Enhancement of the Catalytic Machinery of the SARS 3C-Like Protease by the S284-T285-I286/A Mutations on the Extra Domain.” PLoS One. 2014 Jul 18;9(7) *: Equal contribution.

  7. Huan X.*, Shi J.*, Lim L.*, Mitra S., Zhu W., Qin H., Pasquale E.B., Song J., “Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.” PLoS One. 2013 Sep 24;8(9) *: Equal contribution.

  8. Lua S., Qin H., Lim L., Shi J., Gupta G., Song J., ‘Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.’ PLoS One. (2011) 6(11).

  9. Shi J.*, Han N.*, Lim L., Lua S., Sivaraman J., Wang L., Mu Y., Song J., ‘Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain,’ PLoS Comput Biol (2011) 7(2) *: Equal contribution.

  10. Shi J., Sivaraman J., Song J., ‘Mechanism for Controlling Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the SARS-CoV 3C-like protease,’ Journal of Virology, (2008) 82(9): 4620-9.

  11. Shi J.*, Lua S.*, Tong J., Song J., ‘Elimination of the Native Structure and Solubility of the hVAPB MSP Domain by the Pro56Ser Mutation which Causes Amyotrophic Lateral Sclerosis’ Biochemistry. (2010) 49(18):3887-97 *: Equal contribution.

  12. Shaveta G., Shi J., Chow VT, Song J., ‘Structural characterization reveals that viperin is a radical S-adenosyl-L-methionine (SAM) enzyme,’ Biochem Biophys Res Commun. (2010) 391(3):1390-5.

  13. Qin H., Noberini R., Huan X., Shi J., Pasquale EB, Song J., ‘Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity,’ J Biol Chem. (2010) 285(1):644-54.

  14. Shi J.*, Lua S.*, Du N., Liu X., Song J., ‘Identification, recombinant production and structural characterization of four silk proteins from the Asiatic honeybee Apis cerana,’ Biomaterials, (2008) 29(18): 2820-8 *: Equal contribution.

  15. Qin H.*, Shi J.*, Noberini R., Pasquale B.E., Song J., ‘Crystal Structure and NMR Binding Reveal that Two Small Molecule Antagonists Target the High-Affinity Ephrin-Binding Channel of the EphA4 Receptor,’ J Biol Chem. (2008) 283: 29473-84 *: Equal contribution.

  16. Ran X., Qin H., Liu J., Fan J., Shi J., Song J., ‘NMR structure and dynamics of human ephrin-B2 ectodomain: The functionally critical C-D and G-H loops are highly dynamic in solution,’ Proteins: Structure, Function, and Bioinformatics (2008) 72: 1019-29.

  17. Shi J and Song J, ‘The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain’, FEBS Journal (2006) 273: 1035–45.

  18. Li M, Liu J, Ran X, Fang M, Shi J, Qin H, Goh J, Song J, ‘Resurrecting Abandoned Proteins with Pure Water: CD and NMR Studies of Protein Fragments Solubilized in Salt-Free Water’ Biophysics J. (2006) 91(11):4201-9.

  19. Shi J, Wei Z, Song J, ‘Dissection study on the SARS 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: Defining the extra domain as a new target for design of highly-specific protease inhibitors’, J Biol Chem. (2004) 279: 24765-73.

  20. Li M, Shi J, Wei Z, Teng FY, Tang BL, Song J, ‘Structural characterization of the human Nogo-A functional domains’, Eur J Biochem. (2004) 271: 3512-22.

  1. Dong H, Zhang Y, Wang J, Xiang H, Lv T, Wei L, Yang S, Liu X, Ren B, Zhang X, Liu L, Cao J, Wang M, Shi J#, Yang N#., “Cas9-Based Local Enrichment and Genomics Sequence Revision of Megabase-Sized Shark IgNAR Loci.”, J Immunol. 2022 Jan 1;208(1):181-189. doi: 10.4049/jimmunol.2100844., (#: co-corresponding author)
  1. Wei L, Wang M, Xiang H, Jiang Y, Gong J, Su D, Al Azad MAR, Dong H, Feng L, Wu J, Chan LL, Yang N#, Shi J#, “Bamboo Shark as a Small Animal Model for Single Domain Antibody Production.”, Front Bioeng Biotechnol. 2021 Dec 8;9:792111. doi: 10.3389/fbioe.2021.792111. (#: co-corresponding author).

  2. Li Q, Madden JA, Lin J, Shi J, Rosen SM, Schmitz-Abe K, Agrawal PB., “Reanalysis of Exome Data Identifies Novel SLC25A46 Variants Associated with Leigh Syndrome.”, J Pers Med. 2021 Dec 2;11(12):1277. doi: 10.3390/jpm11121277.

  3. Wang N, Deng Z, Zhu Q, Zhao J, Xie K, Shi P, Wang Z, Chen X, Wang F, Shi J, Zhu G., “An erythrocyte-delivered photoactivatable oxaliplatin nanoprodrug for enhanced antitumor efficacy and immune response”, Chem Sci. 2021 Oct 6;12(43):14353-14362. doi: 10.1039/d1sc02941j.

  4. Shuo Qi, Yachao Zhang, Gongyuan Liu, Jiangbo Chen, Xiaozhen Li, Qi Zhu, Yuqi Yang, Feng Wang, Jiahai Shi, Chun-Sing Lee, Guangyu Zhu, Puxiang Lai, Lidai Wang, Chihua Fang, “Plasmonic-doped melanin-mimic for CXCR4-targeted NIR-II photoacoustic computed tomography-guided photothermal ablation of orthotopic hepatocellular carcinoma”, Acta Biomater. 2021 Jul 15;129:245-257. doi: 10.1016/j.actbio.2021.05.034.

  5. Linyun He, Yachao Zhang, Jiangbo Chen, Gongyuan Liu, Jingyi Zhu, Xiaozhen Li, Dengfeng Li, Yuqi Yang, Chun-Sing Lee, Jiahai Shi, Chao Yin, Puxiang Lai, Lidai Wang, Chihua Fang, “A multifunctional targeted nanoprobe with high NIR-II PAI/MRI performance for precise theranostics of orthotopic early-stage hepatocellular carcinoma”, J Mater Chem B. 2021 Nov 3;9(42):8779-8792. doi: 10.1039/d1tb01729b.

  6. #, Yajing Shen#, “Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes.” Proc Natl Acad Sci U S A. 2021, accepted, (#: co-corresponding author).

  7. Pham TC, Jayasinghe MK, Pham TT, Yang Y, Wei L, Usman WM, Chen H, Pirisinu M, Gong J, Kim S, Peng B, Wang W, Chan C, Ma V, Nguyen NTH, Kappei D, Nguyen XH, Cho WC, Shi J#, Le MTN#, “Covalent conjugation of extracellular vesicles with peptides and nanobodies for targeted therapeutic delivery.” J Extracell Vesicles. 2021 Feb;10(4):e12057. doi: 10.1002/jev2.12057. Epub 2021 Feb 16. (#: co-corresponding author).

  1. Duncan AR, Vitobello A, Collins SC, Vancollie VE, Lelliott CJ, Rodan L, Shi J, Seman AR, Agolini E, Novelli A, Prontera P, Guillen Sacoto MJ, Santiago-Sim T, Trimouille A, Goizet C, Nizon M, Bruel AL, Philippe C, Grant PE, Wojcik MH, Stoler J, Genetti CA, van Dooren MF, Maas SM, Alders M, Faivre L, Sorlin A, Yoon G, Yalcin B, Agrawal PB, “Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.” Am J Hum Genet. 2020 Dec 3;107(6):1170-1177. doi: 10.1016/j.ajhg.2020.11.001. Epub 2020 Nov 23.

  2. Zhang Y, Gao H, Li H, Guo J, Ouyang B, Wang M, Xu Q, Wang J, Lv M, Guo X, Liu Q, Wei L, Ren H, Xi Y, Guo Y, Ren B, Pan S, Liu C, Ding X, Xiang H, Yu Y, Song Y, Meng L, Liu S, Wang J, Jiang Y, Shi J, Liu S, Sabir JSM, Sabir MJ, Khan M, Hajrah NH, Ming-Yuen Lee S, Xu X, Yang H, Wang J, Fan G, Yang N, Liu X, “The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish.” iScience. 2020 Nov 2;23(11):101754. doi: 10.1016/j.isci.2020.101754. eCollection 2020 Nov 20.

  3. Liang S, Su YQ, Liang YL, Wu F, Zhang H, Shi JH, Hong WX, Xu YP, “ DNA sequence analysis and Jk blood group genotype-phenotype assessment.” Ann Transl Med. 2020 Oct;8(19):1242. doi: 10.21037/atm-20-6504.

  4. Sterling N, Duncan AR, Park R, Koolen DA, Shi J, Cho SH, Benke PJ, Grant PE, Genetti CA, VanNoy GE, Juusola J, McWalter K, Parboosingh JS, Lamont RE, Bernier FP, Smith C, Harris DJ, Stegmann APA, Innes AM, Kim S, Agrawal PB, “De novo variants in MPP5 cause global developmental delay and behavioral changes.” Hum Mol Genet. 2020 Dec 18;29(20):3388-3401. doi: 10.1093/hmg/ddaa224.

  5. D’Gama AM, England E, Madden JA, Shi J, Chao KR, Wojcik MH, Torres AR, Tan WH, Berry GT, Prabhu SP, Agrawal PB, “Exome sequencing identifies novel missense and deletion variants in RTN4IP1 associated with optic atrophy, global developmental delay, epilepsy, ataxia, and choreoathetosis.” Am J Med Genet A. 2021 Jan;185(1):203-207. doi: 10.1002/ajmg.a.61910. Epub 2020 Oct 9.

  6. D’Gama AM, Brucker WJ, Zhang T, Gubbels CS, Ferdinandusse S, Shi J, Grant PE, VanNoy G, Genetti CA, Juusola J, Yu TW, Kritzer A, Agrawal PB, “A phenotypically severe, biochemically “silent” case of HIBCH deficiency in a newborn diagnosed by rapid whole exome sequencing and enzymatic testing.” Am J Med Genet A. 2020 Apr;182(4):780-784. doi: 10.1002/ajmg.a.61498.

  1. Ru Zhen, Chingyee Moo, Zhenzhen Zhao, Mengying Chen, He Feng, Xiaojun Zheng, Liang Zhang, Jiahai Shi#, Caiyong Chen#, “Wdr26 regulates nuclear condensation in developing erythroblasts” Blood, 2020 Jan 16;135(3):208-219. doi: 10.1182/blood.2019002165 (#: co-corresponding author) (cover story).

  2. Yuanyan Tan, Athena H. Y. Chu, Siyu Bao, Duc Anh Hoang, Firaol Tamiru Kebede, Wenjun Xiong, Mingfang Ji, Jiahai Shi#, Zongli Zheng#, “Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity”, Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):20969-20976. doi: 10.1073/pnas.1906843116. Epub 2019 Sep 30 (#: co-corresponding author)

  1. Chrystal F Mavros, Catherine A. Brownstein, Roshni Thyagrajan, Casie A. Genetti, Sahil Tembulkar, Kelsey Graber, Quinn Murphy, Kristin Cabral, Grace E. VanNoy, Matthew Bainbridge, Jiahai Shi, Pankaj B. Agrawal, Alan H. Beggs, Eugene D’Angelo, Joseph Gonzalez-Heydrich, “De Novo Variant of TRRAP in a patient with Very Early Onset Psychosis in the Context of Non-Verbal Learning Disability and Obsessive-Compulsive Disorder: A Case Report”, BMC Med Genet. 2018 Nov 13;19(1):197.

  2. Yien YY, Shi J*, Chen C*, Cheung JT, Grillo AS, Shrestha R, Li L, Zhang X, Kafina MD, Kingsley PD, King MJ, Ablain J, Li H, Zon L, Palis J, Burke MD, Bauer DE, Orkin SH, Koehler CM, Phillips JD, Kaplan J, Ward DM, Lodish HF, Paw BH, “FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity”, J Biol Chem. 2018 Oct 26. pii: jbc.RA118.002742. *: Equal contribution.

  3. Zheng L, Shi J, Mu Y., “Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations”, Phys Chem Chem Phys. 2018 Oct 25.

  4. Lim L, Gupta G, Roy A, Kang J, Srivastava S, Shi J#, Song J#, “Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses”, Prog Biophys Mol Biol. 2018 Sep 11. (#: co-corresponding author).

  5. Usman WM, Pham TC, Kwok YY, Vu LT, Ma V, Peng B, Chan YS, Wei L, Chin SM, Azad A, He AB, Leung AYH, Yang M, Shyh-Chang N, Cho WC, Shi J, Le MTN, “Efficient RNA drug delivery using red blood cell extracellular vesicles”, Nat Commun. 2018 Jun 15;9(1):2359.

  6. Wojcik MH, Okada K, Prabhu SP, Nowakowski DW, Ramsey K, Balak C, Rangasamy S, Brownstein CA, Schmitz-Abe K, Cohen JS, Fatemi A, Shi J, Grant EP, Narayanan V, Ho HH, Agrawal PB., “De novo variant in KIF26B is associated with pontocerebellar hypoplasia with infantile spinal muscular atrophy”, Am J Med Genet A. 2018 Aug 27.

  7. Katwa U, D’Gama AM, Qualls AE, Donovan LM, Heffernan J, Shi J, Agrawal PB., “Atypical presentations associated with non-polyalanine repeat PHOX2B mutations”, Am J Med Genet A. 2018 Jul;176(7):1627-1631.

  1. Agrawal PB, Wang R, Li HL, Schmitz-Abe K, Simone-Roach C, Chen J, Shi J, Louie T, Sheng S, Towne MC, Brainson CF, Matthay MA, Kim CF, Bamshad M, Emond MJ, Gerard NP, Kleyman TR, Gerard C, “Epithelial Sodium Channel ENaC is a modifier of the long term non-progressive phenotype associated with F508del CFTR mutations”, Am J Respir Cell Mol Biol. 2017 Jul 14. doi: 10.1165/rcmb.2017-0166OC.

  2. Cao S, Smith LL, Padilla-Lopez SR, Guida BS, Blume E, Shi J, Morton SU, Brownstein CA, Beggs AH, Kruer MC, Agrawal PB, “Homozygous EEF1A2 mutation causes dilated cardiomyopathy, failure to thrive, global developmental delay, epilepsy and early death.”, Hum Mol Genet. 2017 Sep 15;26(18):3545-3552. doi: 10.1093/hmg/ddx239.

  3. Mehta P, Küspert M, Bale T, Brownstein CA, Towne MC, De Girolami U, Shi J, Beggs AH, Darras BT, Wegner M, Piao X, Agrawal PB, “Novel mutation in CNTNAP1 results in congenital hypomyelinating neuropathy”, Muscle Nerve. 2017 May;55(5):761-765. doi: 10.1002/mus.25416.

  1. Palmer S, Towne MC, Pearl PL, Pelletier RC, Genetti CA, Shi J, Beggs AH, Agrawal PB, Brownstein CA, “SLC6A1 Mutation and Ketogenic Diet in epilepsy with myoclonic-atonic seizures”, Pediatr Neurol. 2016 Nov;64:77-79. doi: 10.1016/j.pediatrneurol.2016.07.012.

  2. Shi J, Yuan B, Hu W, Lodish H, “JAK2 V617F stimulates proliferation of erythropoietin- dependent erythroid progenitors and delays their differentiation by activating Stat1 and other non-erythroid signaling pathways”, Exp Hematol. 2016 Nov;44(11):1044-1058.e5. doi: 10.1016/j.exphem.2016.07.010.

  3. Brownstein CA, Beggs AH, Rodan L, Shi J, Towne MC, Pelletier R, Cao S, Rosenberg PA, Urion DK, Picker J, Tan WH, Agrawal PB, “Clinical heterogeneity associated with KCNA1 mutations include cataplexy and non-ataxic presentations”, Neurogenetics. 2016 Jan;17(1):11-6. doi: 10.1007/s10048-015-0460-2.

  4. Li H*, Shi J*, Huang NJ, Pishesha N, Natarajan A, Eng JC, Lodish HF, “Efficient CRISPR-Cas9 mediated gene disruption in primary erythroid progenitor cells”, Haematologica. 2016 Jun;101(6):e216-9. doi: 10.3324/haematol.2015.135723. *: Equal contribution.

  1. Patterson HC, Gerbeth C, Thiru P, Vögtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP, Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF, “A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates H2O2 signaling” Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):E5679-88. doi: 10.1073/pnas.1517932112.

  2. Vijay G. Sankaran, Jacob C. Ulirsch, Vassili Tchaikovskii, Leif S. Ludwig, Aoi Wakabayashi, Senkottuvelan Kadirvel, R. Coleman Lindsley, Rafael Bejar, Jiahai Shi, Scott B. Lovitch, David F. Bishop, David P. Steensma, “X-linked macrocytic dyserythropoietic anemia in females with an ALAS2 mutation”, Journal of Clinical Investigation, 2015 Apr;125(4):1665-9.

  1. Jiahai Shi*, Lenka Kundrat*, Novalia Pishesha, Angelina Bilate, Chris Theile, Takeshi Maruyama, Stephanie K. Dougan, Hidde Ploegh, and Harvey Lodish, “Engineered red cells as carriers for systemic delivery of a wide array of functional probes”, Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10131-6. *: Equal contribution
    Featured in “In This Issue” by the editorial board of PNAS
    Highlighted in Science News, New Scientist, PBS NOVA and 11 other news reports

  2. Jiahai Shi*, Piu Wong­­*, Katherine K. Luo, Paula Trepman, Eric T. Wang, Christopher B. Burge, and Harvey F. Lodish, “Mbnl1 regulates alternative RNA splicing in terminal erythropoiesis”, 2014 Jul 24;124(4):598-610., *: Equal contribution
    Commented in Don M. Wojchowski, “Erythroid mRNA processing: a “splice of life”, Blood. 2014 Jul 24;124(4):474-5.

  3. Shilpa M. Hattangadi, Sandra Martinez-Morilla, Heide Christine Christine Patterson, Jiahai Shi, Karly A Burke, Amalia Avila Figueroa, Srividhya Venkatesan, Junxia Wang, Katherina Paulsen, Cher Huang, Dirk Gorlich, Maki Murata-Hori, and Harvey F Lodish, “Histones to the cytosol: Exportin 7 plays an important role in terminal erythroid nuclear maturation,” Blood. 2014 Aug 4. pii: blood-2013-11-537761.

  4. Pishesha N., Thiru P., Shi J., Eng J.C., Sankaran V.G., Lodish H.F., “Transcriptional divergence and conservation of human and mouse erythropoiesis”, Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4103-8.

  5. Alvarez-Dominguez J.R., Hu W., Yuan B., Shi J., Park S.S., Gromatzky A.A., van Oudenaarden A., Lodish H.F., “Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation”, Blood. 2014 Jan 23;123(4):570-81.

  6. Lim L.*, Shi J.*, Mu Y., Song J., “Dynamically-Driven Enhancement of the Catalytic Machinery of the SARS 3C-Like Protease by the S284-T285-I286/A Mutations on the Extra Domain.” PLoS One. 2014 Jul 18;9(7) *: Equal contribution.

  7. Huan X.*, Shi J.*, Lim L.*, Mitra S., Zhu W., Qin H., Pasquale E.B., Song J., “Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.” PLoS One. 2013 Sep 24;8(9) *: Equal contribution.

  8. Lua S., Qin H., Lim L., Shi J., Gupta G., Song J., ‘Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.’ PLoS One. (2011) 6(11).

  9. Shi J.*, Han N.*, Lim L., Lua S., Sivaraman J., Wang L., Mu Y., Song J., ‘Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain,’ PLoS Comput Biol (2011) 7(2) *: Equal contribution.

  10. Shi J., Sivaraman J., Song J., ‘Mechanism for Controlling Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the SARS-CoV 3C-like protease,’ Journal of Virology, (2008) 82(9): 4620-9.

  11. Shi J.*, Lua S.*, Tong J., Song J., ‘Elimination of the Native Structure and Solubility of the hVAPB MSP Domain by the Pro56Ser Mutation which Causes Amyotrophic Lateral Sclerosis’ Biochemistry. (2010) 49(18):3887-97 *: Equal contribution.

  12. Shaveta G., Shi J., Chow VT, Song J., ‘Structural characterization reveals that viperin is a radical S-adenosyl-L-methionine (SAM) enzyme,’ Biochem Biophys Res Commun. (2010) 391(3):1390-5.

  13. Qin H., Noberini R., Huan X., Shi J., Pasquale EB, Song J., ‘Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity,’ J Biol Chem. (2010) 285(1):644-54.

  14. Shi J.*, Lua S.*, Du N., Liu X., Song J., ‘Identification, recombinant production and structural characterization of four silk proteins from the Asiatic honeybee Apis cerana,’ Biomaterials, (2008) 29(18): 2820-8 *: Equal contribution.

  15. Qin H.*, Shi J.*, Noberini R., Pasquale B.E., Song J., ‘Crystal Structure and NMR Binding Reveal that Two Small Molecule Antagonists Target the High-Affinity Ephrin-Binding Channel of the EphA4 Receptor,’ J Biol Chem. (2008) 283: 29473-84 *: Equal contribution.

  16. Ran X., Qin H., Liu J., Fan J., Shi J., Song J., ‘NMR structure and dynamics of human ephrin-B2 ectodomain: The functionally critical C-D and G-H loops are highly dynamic in solution,’ Proteins: Structure, Function, and Bioinformatics (2008) 72: 1019-29.

  17. Shi J and Song J, ‘The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain’, FEBS Journal (2006) 273: 1035–45.

  18. Li M, Liu J, Ran X, Fang M, Shi J, Qin H, Goh J, Song J, ‘Resurrecting Abandoned Proteins with Pure Water: CD and NMR Studies of Protein Fragments Solubilized in Salt-Free Water’ Biophysics J. (2006) 91(11):4201-9.

  19. Shi J, Wei Z, Song J, ‘Dissection study on the SARS 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: Defining the extra domain as a new target for design of highly-specific protease inhibitors’, J Biol Chem. (2004) 279: 24765-73.

  20. Li M, Shi J, Wei Z, Teng FY, Tang BL, Song J, ‘Structural characterization of the human Nogo-A functional domains’, Eur J Biochem. (2004) 271: 3512-22.

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