Recent Publications

picture of Dr. Shawn Li

2024

Jan 2024    Feb 2024   Mar 2024   Apr 2024   May 2024   June 2024 

Archives

June 2024

  1. Zhang Y, Hawboldt K, MacQuarrie S, Thomas R, Gebregiworgis T. Alkaline subcritical water extraction of bioactive compounds and antioxidants from beach-cast brown algae (Ascophyllum Nodosum). Chemical Engineering Journal. 2024; 494:153109.
  2. Spagnuolo CM, Hegele RA. Etiology and emerging treatments for familial chylomicronemia syndrome. Expert Rev Endocrinol Metab. 2024 Jun 12:1-8.
  3. Frederick MI, Nassef MZ, Borrelli MJ, Kuang S, Buensuceso A, More T, Cordes T, O'Donoghue P, Shepherd TG, Hiller K, Heinemann IU. Metabolic adaptation in epithelial ovarian cancer metastasis. Biochim Biophys Acta Mol Basis Dis. 2024 Jun 18;1870(7):167312. 
  4. Jin YW, Hu P, Liu Q. NNICE: a deep quantile neural network algorithm for expression deconvolution. Sci Rep. 2024 Jun 18;14(1):14040.
  5. Hanifi K, Scrosati PM, Konermann L. MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation. J Phys Chem B. 2024 Jun 12.
  6. Volgman AS, Koschinsky ML, Mehta A, Rosenson RS. Genetics and Pathophysiological Mechanisms of Lipoprotein(a)-Associated Cardiovascular Risk. J Am Heart Assoc. 2024 Jun 18;13(12):e033654. 
  7. Lu KP, Zhou XZ. Pin1-catalyzed conformational regulation after phosphorylation: A distinct checkpoint in cell signaling and drug discovery. Sci Signal. 2024 Jun 18;17(841):eadi8743. 
  8. Koszela J, Rintala-Dempsey A, Salzano G, Pimenta V, Kamarainen O, Gabrielsen M, Parui AL, Shaw GS, Walden H. A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1. bioRxiv [Preprint]. 2024 Jun 3:2024.06.03.597144. 
  9. Ahmad P, Escalante-Herrera A, Marin LM, Siqueira WL. Progression from healthy periodontium to gingivitis and periodontitis: Insights from bioinformatics-driven proteomics - A systematic review with meta-analysis. J Periodontal Res. 2024 Jun 14.

May 2024

  1. Isaacson JR, Berg MD, Yeung W, Villén J, Brandl CJ, Moehring AJ. Impact of tRNA-induced proline-to-serine mistranslation on the transcriptome of Drosophila melanogaster. bioRxiv [Preprint]. 2024 May 10:2024.05.08.593249.
  2. Siddika T, Shao R, Heinemann IU, O'Donoghue P. Delivery of AKT1 phospho-forms to human cells reveals differential substrate selectivity. IUBMB Life. 2024 May 13.
  3. Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O'Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev. 2024 May 27. 
  4. Rosenson RS, Gaudet D, Hegele RA, Ballantyne CM, Nicholls SJ, Lucas KJ, San Martin J, Zhou R, Muhsin M, Chang T, Hellawell J, Watts GF; ARCHES-2 Trial Team. Zodasiran, an RNAi Therapeutic Targeting ANGPTL3, for Mixed Hyperlipidemia. N Engl J Med. 2024 May 29. 
  5. Trinder M, Cermakova L, Ruel I, Baass A, Paquette M, Wang J, Kennedy BA, Hegele RA, Genest J, Brunham LR. Influence of Polygenic Background on the Clinical Presentation of Familial Hypercholesterolemia. Arterioscler Thromb Vasc Biol. 2024 May 23.
  6. Droppelmann CA, Campos-Melo D, Noches V, McLellan C, Szabla R, Lyons TA, Amzil H, Withers B, Kaplanis B, Sonkar KS, Simon A, Buratti E, Junop M, Kramer JM, Strong MJ. Mitigation of TDP-43 toxic phenotype by an RGNEF fragment in amyotrophic lateral sclerosis models. Brain. 2024 May 13:awae078. 
  7. Owens DDG, Maitland MER, Khalili Yazdi A, Song X, Reber V, Schwalm MP, Machado RAC, Bauer N, Wang X, Szewczyk MM, Dong C, Dong A, Loppnau P, Calabrese MF, Dowling MS, Lee J, Montgomery JI, O'Connell TN, Subramanyam C, Wang F, Adamson EC, Schapira M, Gstaiger M, Knapp S, Vedadi M, Min J, Lajoie GA, Barsyte-Lovejoy D, Owen DR, Schild-Poulter C, Arrowsmith CH. A chemical probe to modulate human GID4 Pro/N-degron interactions. Nat Chem Biol. 2024 May 21.
  8. Yaron-Barir TM, Joughin BA, Huntsman EM, Kerelsky A, Cizin DM, Cohen BM, Regev A, Song J, Vasan N, Lin TY, Orozco JM, Schoenherr C, Sagum C, Bedford MT, Wynn RM, Tso SC, Chuang DT, Li L, Li SS, Creixell P, Krismer K, Takegami M, Lee H, Zhang B, Lu J, Cossentino I, Landry SD, Uduman M, Blenis J, Elemento O, Frame MC, Hornbeck PV, Cantley LC, Turk BE, Yaffe MB, Johnson JL. The intrinsic substrate specificity of the human tyrosine kinome. Nature. 2024 May 8. 
  9. Kaneko T, Ezra S, Abdo R, Voss C, Zhong S, Liu X, Hovey O, Slessarev M, Van Nynatten LR, Ye M, Fraser DD, Li SS. Correction: Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients. Clin Proteomics. 2024 May 4;21(1):31. (Erratum for: Clin Proteomics. 2020 Jan 24;17:1)

Apr 2024

  1. Layo-Carris DE, Lubin EE, Sangree AK, Clark KJ, Durham EL, Gonzalez EM, Smith S, Angireddy R, Wang XM, Weiss E, Mendoza-Londono R, Dupuis L, Damseh N, Velasco D, Valenzuela I, Codina-Solà M, Ziats C, Have J, Clarkson K, Steel D, Kurian M, Barwick K, Carrasco D, Dagli AI, Nowaczyk MJM, Hančárová M, Bendová Š, Prchalova D, Sedláček Z, Baxová A, Nowak CB, Douglas J, Chung WK, Longo N, Platzer K, Klöckner C, Averdunk L, Wieczorek D, Krey I, Zweier C, Reis A, Balci T, Simon M, Kroes HY, Wiesener A, Vasileiou G, Marinakis NM, Veltra D, Sofocleous C, Kosma K, Traeger Synodinos J, Voudris KA, Vuillaume ML, Gueguen P, Derive N, Colin E, Battault C, Au B, Delatycki M, Wallis M, Gallacher L, Majdoub F, Smal N, Weckhuysen S, Schoonjans AS, Kooy RF, Meuwissen M, Cocanougher BT, Taylor K, Pizoli CE, McDonald MT, James P, Roeder ER, Littlejohn R, Borja NA, Thorson W, King K, Stoeva R, Suerink M, Nibbeling E, Baskin S, L E Guyader G, Kaplan J, Muss C, Carere DA, Bhoj EJK, Bryant LM. Expanded phenotypic spectrum of neurodevelopmental and neurodegenerative disorder Bryant-Li-Bhoj syndrome with 38 additional individuals. Eur J Hum Genet. 2024 Apr 27.
  2. Madarati H, DeYoung V, Singh K, Sparring T, Kwong AC, Fredenburgh JC, Teney C, Koschinsky ML, Boffa MB, Weitz JI, Kretz CA. Optimization of plasma-based BioID identifies plasminogen as a ligand of ADAMTS13. Sci Rep. 2024 Apr 20;14(1):9073.
  3. Schott C, Colaiacovo S, Baker C, Weir MA, Connaughton DM. Reclassification of Genetic Testing Results: A Case Report Demonstrating the Need for Structured Re-Evaluation of Genetic Findings. Can J Kidney Health Dis. 2024 Apr 14;11:20543581241242562.
  4. Murthy D, Attri KS, Shukla SK, Thakur R, Chaika NV, He C, Wang D, Jha K, Dasgupta A, King RJ, Mulder SE, Souchek J, Gebregiworgis T, Rai V, Patel R, Hu T, Rana S, Kollala SS, Pacheco C, Grandgenett PM, Yu F, Kumar V, Lazenby AJ, Black AR, Ulhannan S, Jain A, Edil BH, Klinkebiel DL, Powers R, Natarajan A, Hollingsworth MA, Mehla K, Ly Q, Chaudhary S, Hwang RF, Wellen KE, Singh PK.Author Correction: Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis. Nat Cell Biol. 2024 Apr 19. Erratum for: Nat Cell Biol. 2024 Apr;26(4):613-627. PMID: 38641662.
  5. Gebregiworgis T, Chan JY, Kuntz DA, Privé GG, Marshall CB, Ikura M. Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II. Eur J Cell Biol. 2024 Apr 15;103(2):151414. 
  6. Nixon MP, Gloor GB, Silverman JD. Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis. bioRxiv [Preprint]. 2024 Apr 2:2024.04.01.587602.
  7. Stroes ESG, Alexander VJ, Karwatowska-Prokopczuk E, Hegele RA, Arca M, Ballantyne CM, Soran H, Prohaska TA, Xia S, Ginsberg HN, Witztum JL, Tsimikas S; Balance Investigators. Olezarsen, Acute Pancreatitis, and Familial Chylomicronemia Syndrome. N Engl J Med. 2024 Apr 7.
  8. Ahmad M, Kennedy BA, Son S, McIntyre AD, Lazarte J, Wang J, Hegele RA. Carotid intimamedia thickness in patients with severe hypertriglyceridemia. Atheroscler Plus. 2024 Apr 21;56:7-11. 
  9. Moreau F, Atamanyuk D, Blaukopf M, Barath M, Herczeg M, Xavier NM, Monbrun J, Airiau E, Henryon V, Leroy F, Floquet S, Bonnard D, Szabla R, Brown C, Junop MS, Kosma P, Gerusz V. Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria. J Med Chem. 2024 Apr 10.
  10. Noble M, Colussi DM, Junop M, Stathopulos PB. The MCU and MCUb amino-terminal domains tightly interact: mechanisms for low conductance assembly of the mitochondrial calcium uniporter complex. iScience. 2024 Apr 10;27(5):109699. 
  11. Meaney JS, Panchal AK, Wilcox AJ, diCenzo GC, Karas B. Identifying functional multi-host shuttle plasmids to advance synthetic biology applications in Mesorhizobium and Bradyrhizobium. Can J Microbiol. 2024 Apr 2.
  12. Qiu C, Li Z, Leigh DA, Duan B, Stucky JE, Kim N, Xie G, Lu KP, Zhou XZ. The role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia. Front Cell Dev Biol. 2024 Apr 2;12:1343962.
  13. Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/CCDH1 governs mitotic protein stability and cell cycle entry. Nat Commun. 2024 Apr 15;15(1):3220. 
  14. Jeong J, Usman M, Li Y, Zhou XZ, Lu KP. Pin1-Catalyzed Conformation Changes Regulate Protein Ubiquitination and Degradation. Cells. 2024 Apr 23;13(9):731. 
  15. Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol. 2024 Apr 30;12:1343938.
  16. Gill JK, Shaw G. Using Förster resonance energy transfer (Fret) to understand the ubiquitination landscape . Chembiochem. 2024 Apr 17:e202400193.
  17. Tolg C, Hill KA, Turley EA. CD44 and RHAMM Are Microenvironmental Sensors with Dual Metastasis Promoter and Suppressor Functions. Adv Biol (Weinh). 2024 Apr 18:e2300693. 

Mar 2024

  1. Koschinsky ML, Bajaj A, Boffa MB, Dixon DL, Ferdinand KC, Gidding SS, Gill EA, Jacobson TA, Michos ED, Safarova MS, Soffer DE, Taub PR, Wilkinson MJ, Wilson DP, Ballantyne CM. A focused update to the 2019 NLA scientific statement on use of lipoprotein(a) in clinical practice. J Clin Lipidol. 2024 Mar 29:S1933-2874(24)00033-3.
  2. Murthy D, Attri KS, Shukla SK, Thakur R, Chaika NV, He C, Wang D, Jha K, Dasgupta A, King RJ, Mulder SE, Souchek J, Gebregiworgis T, Rai V, Patel R, Hu T, Rana S, Kollala SS, Pacheco C, Grandgenett PM, Yu F, Kumar V, Lazenby AJ, Black AR, Ulhannan S, Jain A, Edil BH, Klinkebiel DL, Powers R, Natarajan A, Hollingsworth MA, Mehla K, Ly Q, Chaudhary S, Hwang RF, Wellen KE, Singh PK. Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis. Nat Cell Biol. 2024 Mar 1.
  3. Berberich AJ, Hegele RA. Pancreatitis risk in genetic subtypes of multifactorial chylomicronemia syndrome. Atherosclerosis. 2024 Mar 26:117528.
  4. Sakurai R, Pieruccini-Faria F, Cornish B, Fraser J, Binns MA, Beaton D, Dilliott AA, Kwan D, Ramirez J, Tan B, Scott CJM, Sunderland KM, Tartaglia C, Finger E, Zinman L, Freedman M, McLaughlin PM, Swartz RH, Symons S, Lang AE, Bartha R, Black SE, Masellis M, Hegele RA, McIlroy W; ONDRI Investigators; Montero-Odasso M. Link among apolipoprotein E E4, gait, and cognition in neurodegenerative diseases: ONDRI study. Alzheimers Dement. 2024 Mar 12.
  5. Raal FJ, Hegele RA, Ruzza A, López JAG, Bhatia AK, Wu J, Wang H, Gaudet D, Wiegman A, Wang J, Santos RD. Evolocumab Treatment in Pediatric Patients With Homozygous Familial Hypercholesterolemia: Pooled Data From Three Open-Label Studies. Arterioscler Thromb Vasc Biol. 2024 Mar 28.
  6. Lac L, Leung CK, Hu P. Computational frameworks integrating deep learning and statistical models in mining multimodal omics data. J Biomed Inform. 2024 Mar 27:104629. 
  7. Huang ZH, Chen L, Sun Y, Liu Q, Hu P. Conditional generative adversarial network driven radiomic prediction of mutation status based on magnetic resonance imaging of breast cancer. J Transl Med. 2024 Mar 2;22(1):226. 
  8. Sun Y, Yi Li Y, Leung CK, Hu P. iNGNN-DTI: Prediction of Drug - Target Interaction with Interpretable Nested Graph Neural Network and Pretrained Molecule Models. Bioinformatics. 2024 Mar 7:btae135.
  9. Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc. 2024 Mar 13. 
  10. Hermosilla VE, Gyenis L, Rabalski AJ, Armijo ME, Sepúlveda P, Duprat F, Benítez-Riquelme D, Fuentes-Villalobos F, Quiroz A, Hepp MI, Farkas C, Mastel M, González-Chavarría I, Jackstadt R, Litchfield DW, Castro AF, Pincheira R. Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells. Cell Death Dis. 2024 Mar 16;15(3):223.
  11. Ahmad P, Siqueira WL. Mass spectrometry-based proteomics profiling of dogs with and without oral diseases: a systematic review. BMC Oral Health. 2024 Mar 22;24(1):369.
  12. iang RW, Marin LM, Jaroch K, Zhou W, Siqueira WL, Pawliszyn J. Proteomic Analysis of Human Saliva via Solid-Phase Microextraction Coupled with Liquid Chromatography-Mass Spectrometry. Anal Chem. 2024 Mar 27. 
  13. Ng THJ, Sarikahya MH, Hudson R, Szkudlarek HJ, Pérez-Valenzuela E, Uzuneser TC, Proud E, Gummerson D, Youssef M, Machado M, Zhaksylyk K, DeVuono MV, Chen C, Yeung KK, Rushlow WJ, Laviolette SR. Adolescent nicotine exposure induces long-term, sex-specific disturbances in mood and anxiety-related behavioral, neuronal and molecular phenotypes in the mesocorticolimbic system. Neuropsychopharmacology. 2024 Mar 23. 

Feb 2024

  1. Branch A, Nuaaman MM, Appleton CT, Connaughton DM, Basmaji J, Chan TLH, Budhram A. Teaching NeuroImage: Extensive Brainstem and Striatal Involvement in Neuropsychiatric Systemic Lupus Erythematosus. Neurology. 2024 Feb 27;102(4):e209153.
  2. Alexander VJ, Karwatowska-Prokopczuk E, Prohaska TA, Li L, Geary RS, Gouni-Berthold I, Oral EA, Hegele RA, Stroes ESG, Witztum JL, Tsimikas S. Volanesorsen to Prevent Acute Pancreatitis in Hypertriglyceridemia. N Engl J Med. 2024 Feb 1;390(5):476-477.
  3. Hegele RA. Inhibiting angiopoietin-like protein 3: clear skies or clouds on the horizon? Eur Heart J. 2024 Feb 16:ehae068.
  4. Kaneko T, Ezra S, Abdo R, Voss C, Zhong S, Liu X, Hovey O, Slessarev M, Van Nynatten LR, Ye M, Fraser D, Li SS. Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients. Clin Proteomics. 2024 Feb 22;21(1):13.
  5. The Critical Assessment of Genome Interpretation Consortium (includes Rogan P). CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 25, 53 (2024).
  6. Almudhry M, Prasad C, Rupar CA, Tay KY, Prasad AN. Long-term follow-up of an attenuated presentation of NAXE-related disease, a potentially actionable neurometabolic disease: a case report. Front Neurol. 2024 Feb 14;15:1204848.
  7. Al Ghanim K, Jaszkul KM, Simpson A, Turley EA. Association of Squamous Cell Carcinoma and Hyaluronan: A Scope of the Literature. Eplasty. 2024 Feb 27;24:e11.

Jan 2024

  1. Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S. Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver. J Hepatol. 2024 Jan 4:S0168-8278(24)00003-5.
  2. Davey-Young J, Hasan F, Tennakoon R, Rozik P, Moore H, Hall P, Cozma E, Genereaux J, Hoffman KS, Chan PP, Lowe TM, Brandl CJ, O'Donoghue P. Mistranslating the genetic code with leucine in yeast and mammalian cells. RNA Biol. 2024 Jan;21(1):1-23.
  3. Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. Environ Health Perspect. 2024 Jan;132(1):17008.
  4. Foo GW, Leichthammer CD, Saita IM, Lukas ND, Batko IZ, Heinrichs DE, Edgell DR. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Res. 2024 Jan 5:gkad1247.
  5. Kakadia JH, Khalid MU, Heinemann IU, Han V. AMPK-mTORC1 pathway mediates hepatic IGFBP-1 phosphorylation in glucose deprivation. J Mol Endocrinol. 2024 Jan 1:JME-23-0137.
  6. Sorci-Thomas MG, Hegele RA, Remaley AT. A Century of Milestones and Breakthroughs Related to Low- and High-Density Lipoproteins. Arterioscler Thromb Vasc Biol. 2024 Jan;44(1):7-11. 
  7. Al-Baldawi Z, Brown L, Ruel I, Baass A, Bergeron J, Cermakova L, Couture P, Gaudet D, Francis GA, Hegele RA, Iatan I, Mancini GBJ, McCrindle BW, Ransom T, Sherman MH, McPherson R, Genest J, Brunham LR. Sex differences in the presentation, treatment and outcomes of patients with homozygous familial hypercholesterolemia. J Clin Lipidol. 2024 Jan 14:S1933-2874(24)00003-5.
  8. Bily TMI, Heinemann IU, O'Donoghue P. Missense suppressor tRNA therapeutics correct disease-causing alleles by misreading the genetic code. Mol Ther. 2024 Jan 13:S1525-0016(24)00001-7.
  9. Veliz L, Cooper TT, Grenier-Pleau I, Abraham SA, Gomes J, Pasternak SH, Dauber B, Postovit LM, Lajoie GA, Lagugné-Labarthet F. Tandem SERS and MS/MS Profiling of Plasma Extracellular Vesicles for Early Ovarian Cancer Biomarker Discovery. ACS Sens. 2024 Jan 12.
  10. McLaughlin KJ, Khanna M, Allison PJ, Glogauer M, McNally ME, Quiñonez C, Rock L, Siqueira W, Madathil SA. Investigating the perceptions and experiences of Canadian dentists on dental regulatory bodies' communications and guidelines during the COVID-19 pandemic. Community Dent Oral Epidemiol. 2024 Jan 8.
  11. Dias LM, Cilli EM, Medeiros KS, Brasil MCOA, Marin LM, Siqueira WL, Pavarina AC. Antibiofilm Activity and Biocompatibility of Temporin-SHa: A Promising Antimicrobial Peptide for Control of Fluconazole-Resistant Candida albicans. Microorganisms. 2024 Jan 4;12(1):99. 
  12. Ahmad P, Marin LM, Lowe C, Katselis GS, Siqueira WL. Salivary protein homology between humans and dogs: Mass spectrometry-based proteomics analysis. J Dent. 2024 Jan 20;142:104855.