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KIT D816V is dimerization-independent and activates downstream pathways frequently perturbed in mastocytosis. Rajan V, Prykhozhij SV, Pandey A, Cohen AM, Rainey JK, Berman JN. Br J Haematol. 2023 Sep;202(5):960-970. doi: 10.1111/bjh.18116. Epub 2022 Mar 4. PMID: 35245395

Modification of histidine repeat proteins by inorganic polyphosphate.Neville N, Lehotsky K, Yang Z, Klupt KA, Denoncourt A, Downey M, Jia Z.Cell Rep. 2023 Sep 1;42(9):113082. doi: 10.1016/j.celrep.2023.113082. Online ahead of print.PMID: 37660293

Mutation Knock-in Methods Using Single-Stranded DNA and Gene Editing Tools in Zebrafish.Prykhozhij SV, Berman JN.Methods Mol Biol. 2024;2707:279-303. doi: 10.1007/978-1-0716-3401-1_19.PMID: 37668920

Radiation induces long-term muscle fibrosis and promotes a fibrotic phenotype in fibro-adipogenic progenitors Nicolas CollaoDonna D'SouzaLaura MesseillerEvan PilonJessica LloydJillian LarkinMatthew NguAlexanne CuillerierAlexander E. GreenKeir J. MenziesYan BurelleMichael De LisioFirst published: 06 September 2023 https://doi.org/10.1002/jcsm.13320

MetaPep: A core peptide database for faster human gut metaproteomics database searches.Sun Z, Ning Z, Cheng K, Duan H, Wu Q, Mayne J, Figeys D.Comput Struct Biotechnol J. 2023 Aug 29;21:4228-4237. doi: 10.1016/j.csbj.2023.08.025. eCollection 2023.PMID: 37692080

The Regulation and Immune Signature of Retrotransposons in Cancer. Alkailani MI, Gibbings D.Cancers (Basel). 2023 Aug 30;15(17):4340. doi: 10.3390/cancers15174340.PMID: 37686616

Generation of the human iPSC lines AKOSi011-A carrying the mutation p.Pro65Ser/p.Asp35T and AKOSi012-A, carrying the mutation p.Tyr231His, derived from FAHN patient fibroblasts. Efendic F, Krohn S, Murua Escobar H, Venkateswaran S, Bennett SAL, Hermann A, Frech MJ. Stem Cell Res. 2023 Aug 9;71:103178. doi: 10.1016/j.scr.2023.103178. Online ahead of print. PMID: 37573804

Conventional DNA-Damaging Cancer Therapies and Emerging cGAS-STING Activation: A Review and Perspectives Regarding Immunotherapeutic Potential.Lewicky JD, Martel AL, Gupta MR, Roy R, Rodriguez GM, Vanderhyden BC, Le HT.Cancers (Basel). 2023 Aug 16;15(16):4127. doi: 10.3390/cancers15164127.PMID: 37627155

Caspase 3 exhibits a yeast metacaspase proteostasis function that protects mitochondria from toxic TDP43 aggregates.Brunette S, Sharma A, Bell R, Puente L, Megeney LA.Microb Cell. 2023 Jul 10;10(8):157-169. doi: 10.15698/mic2023.08.801. eCollection 2023 Aug 7.PMID: 37545643 

The TNFα/TNFR2 axis mediates natural killer cell proliferation by promoting aerobic glycolysis. Khan AUH, Ali AK, Marr B, Jo D, Ahmadvand S, Fong-McMaster C, Almutairi SM, Wang L, Sad S, Harper ME, Lee SH. Cell Mol Immunol. 2023 Aug 9. doi: 10.1038/s41423-023-01071-4. Online ahead of print.PMID: 37553427

Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity.Whytock KL, Pino MF, Sun Y, Yu G, De Carvalho FG, Yeo RX, Vega RB, Gaganvir P, Divoux A, Kapoor N, Yi F, Cornnell HH, Patten DA, Harper ME, Gardell SJ, Smith SR, Walsh MJ, Sparks LM.Am J Physiol Endocrinol Metab. 2023 Aug 16. doi: 10.1152/ajpendo.00143.2023. Online ahead of print.PMID: 37584609

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome. Comerlato CB, Zhang X, Walker K, Mayne J, Figeys D, Brandelli A.Probiotics Antimicrob Proteins. 2023 Aug 17. doi: 10.1007/s12602-023-10136-9. Online ahead of print.PMID: 37589783

Development of a V5-tag-directed nanobody and its implementation as an intracellular biosensor of GPCR signalling. Zeghal M, Matte K, Venes A, Patel S, Laroche G, Sarvan S, Joshi M, Rain JC, Couture JF, Giguère PM.J Biol Chem. 2023 Jul 28:105107. doi: 10.1016/j.jbc.2023.105107. Online ahead of print.PMID: 37517699  

Ketone Ester Administration Improves Glycemia in Obese Mice. Tabatabaei Dakhili SA, Yang K, Locatelli CAA, Saed CT, Greenwell AA, Chan JSF, Chahade JJ, Scharff J, Al Imarah S, Eaton F, Crawford PA, Gopal K, Mulvihill EE, Ussher JR.Am J Physiol Cell Physiol. 2023 Aug 14. doi: 10.1152/ajpcell.00300.2023. Online ahead of print.PMID: 37575059

The mitochondrial pyruvate carrier complex potentiates the efficacy of proteasome inhibitors in multiple myeloma.Findlay S, Nair R, Merrill RA, Kaiser Z, Cajelot A, Aryanpour Z, Heath J, St-Louis C, Papadopoli D, Topisirovic I, St-Pierre J, Sebag M, Kesarwala AH, Hulea L, Taylor EB, Shanmugam M, Orthwein A. Blood Adv. 2023 Jul 25;7(14):3485-3500. doi: 10.1182/bloodadvances.2022008345. PMID: 36920785

Synthesis of Sialyl LewisX Mimetics with E- and P-Selectin Binding Properties and Immunosuppressive Activity. Simard RD, Joyal M, Beaugrand T, Gauthier J, Hardine E, Desriac A, Buffet CH, Prévost M, Nemer M, Guindon Y. J Org Chem. 2023 Jul 14. doi: 10.1021/acs.joc.3c00956. Online ahead of print. PMID: 37449872

Deconstructing interindividual variability in energy metabolism: implications for metabolic health.Miles-Chan JL, Harper ME. Am J Physiol Endocrinol Metab. 2023 Aug 1;325(2):E107-E112. doi: 10.1152/ajpendo.00060.2023. Epub 2023 Jun 14. PMID: 37315156

ATF2 orchestrates macrophage differentiation and activation to promote antibacterial responses.Rajabalee N, Siushansian H, Weerapura M, Berton S, Berbatovci F, Hooks B, Geoffrion M, Yang D, Harper ME, Rayner K, Blais A, Sun J.J Leukoc Biol. 2023 Jul 4:qiad076. doi: 10.1093/jleuko/qiad076. Online ahead of print.PMID: 37403209

GDF15 promotes weight loss by enhancing energy expenditure in muscle.Wang D, Townsend LK, DesOrmeaux GJ, Frangos SM, Batchuluun B, Dumont L, Kuhre RE, Ahmadi E, Hu S, Rebalka IA, Gautam J, Jabile MJT, Pileggi CA, Rehal S, Desjardins EM, Tsakiridis EE, Lally JSV, Juracic ES, Tupling AR, Gerstein HC, Paré G, Tsakiridis T, Harper ME, Hawke TJ, Speakman JR, Blondin DP, Holloway GP, Jørgensen SB, Steinberg GR.Nature. 2023 Jun 28. doi: 10.1038/s41586-023-06249-4. Online ahead of print.PMID: 37380764

A Recent SARS-CoV-2 Infection Enhances Antibody-Dependent Cellular Cytotoxicity against Several Omicron Subvariants following a Fourth mRNA Vaccine Dose.Beaudoin-Bussières G, Tauzin A, Dionne K, Gendron-Lepage G, Medjahed H, Perreault J, Levade I, Alfadhli L, Bo Y, Bazin R, Côté M, Finzi A.Viruses. 2023 May 29;15(6):1274. doi: 10.3390/v15061274.PMID: 37376574

Tissue-Engineered Disease Modeling of Lymphangioleiomyomatosis Exposes a Therapeutic Vulnerability to HDAC Inhibition.Pietrobon A, Yockell-Lelièvre J, Melong N, Smith LJ, Delaney SP, Azzam N, Xue C, Merwin N, Lian E, Camacho-Magallanes A, Doré C, Musso G, Julian LM, Kristof AS, Tam RY, Berman JN, Shoichet MS, Stanford WL.Adv Sci (Weinh). 2023 Jul 3:e2302611. doi: 10.1002/advs.202302611. Online ahead of print.PMID: 37400371 

Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomicsLi L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos CMA, Mayne J, Stintzi A, Mack DR, Liu YY, Figeys D. Nat Commun. 2023 Jun 10;14(1):3428. doi: 10.1038/s41467-023-39149-2.PMID: 37301875

Satellite cell contribution to disease pathology in Duchenne muscular dystrophy.Kodippili K, Rudnicki MA.Front Physiol. 2023 May 30;14:1180980. doi: 10.3389/fphys.2023.1180980. eCollection 2023.PMID: 37324396 

The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.Tolbert WD, Chen Y, Sun L, Benlarbi M, Ding S, Manickam R, Pangaro E, Nguyen DN, Gottumukkala S, Côté M, Gonzalez FJ, Finzi A, Tehrani ZR, Sajadi MM, Pazgier M.Front Immunol. 2023 Jun 2;14:1178355. doi: 10.3389/fimmu.2023.1178355. eCollection 2023.PMID: 37334379

Reducing mitochondrial ribosomal gene expression does not alter metabolic health or lifespan in mice.Reid K, Daniels EG, Vasam G, Kamble R, Janssens GE, Hu IM, Green AE, Houtkooper RH, Menzies KJ.Sci Rep. 2023 May 24;13(1):8391. doi: 10.1038/s41598-023-35196-3.PMID: 37225705

Differentiation and single-cell RNA-seq analyses of human pluripotent-stem-cell-derived renal organoids.  Lian E, Pietrobon A, Stanford WL.STAR Protoc. 2023 May 22;4(2):102314. doi: 10.1016/j.xpro.2023.102314. Online ahead of print.PMID: 37220001

Pancreas-derived DPP4 is not essential for glucose homeostasis under metabolic stress.Fadzeyeva E, Locatelli CAA, Trzaskalski NA, Nguyen MA, Capozzi ME, Vulesevic B, Morrow NM, Ghorbani P, Hanson AA, Lorenzen-Schmidt I, Doyle MA, Seymour R, Varin EM, Fullerton MD, Campbell JE, Mulvihill EE.iScience. 2023 Apr 26;26(5):106748. doi: 10.1016/j.isci.2023.106748. eCollection 2023 May 19.PMID: 37216093 

TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins. Fatica T, Naas T, Liwak U, Slaa H, Souaid M, Frangione B, Kattini R, Gaudreau-Lapierre A, Trinkle-Mulcahy L, Chakraborty P, Holcik M.Genes (Basel). 2023 May 5;14(5):1043. doi: 10.3390/genes14051043.PMID: 37239403 

phox2ba: The Potential Genetic Link behind the Overlap in the Symptomatology between CHARGE and Central Congenital Hypoventilation Syndromes.MacLean JE, Wertman JN, Prykhozhij SV, Chedrawe E, Langley S, Steele SL, Ban K, Blake K, Berman JN.Genes (Basel). 2023 May 15;14(5):1086. doi: 10.3390/genes14051086.PMID: 37239446

Thermoneutral housing does not accelerate metabolic dysfunction-associated fatty liver disease in male or female C57Bl/6J mice fed a Western diet. Nunes JRC, Smith TKT, Ghorbani P, O'Dwyer C, Trzaskalski NA, Dergham H, Pember C, Kilgour MK, Mulvihill EE, Fullerton MD. Am J Physiol Endocrinol Metab. 2023 May 17. doi: 10.1152/ajpendo.00124.2023. Online ahead of print. PMID: 37196059 

Bivalent vaccines effectively protect mice against influenza A and respiratory syncytial viruses. Raman SNT, Zetner A, Hashem AM, Patel D, Wu J, Gravel C, Gao J, Zhang W, Pfeifle A, Tamming L, Parikh K, Cao J, Tam R, Safronetz D, Chen W, Johnston MJW, Wang L, Sauve S, Rosu-Myles M, Domselaar GV, Li X. Emerg Microbes Infect. 2023 Dec;12(1):2192821. doi: 10.1080/22221751.2023.2192821. PMID: 36927227

16p11.2 haploinsufficiency reduces mitochondrial biogenesis in brain endothelial cells and alters brain metabolism in adult mice.Béland-Millar A, Kirby A, Truong Y, Ouellette J, Yandiev S, Bouyakdan K, Pileggi C, Naz S, Yin M, Carrier M, Kotchetkov P, St-Pierre MK, Tremblay MÈ, Courchet J, Harper ME, Alquier T, Messier C, Shuhendler AJ, Lacoste B. Cell Rep. 2023 May 6;42(5):112485. doi: 10.1016/j.celrep.2023.112485. Online ahead of print.PMID: 37149866 

Signed distance correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis. Monti F, Stewart D, Surendra A, Alecu I, Nguyen-Tran T, Bennett SAL, Čuperlović-Culf M. Bioinformatics. 2023 May 3:btad210. doi: 10.1093/bioinformatics/btad210. Online ahead of print. PMID: 3713723

Novel Homozygous Variant in COQ7 in Siblings With Hereditary Motor Neuropathy.Smith IC, Pileggi CA, Wang Y, Kernohan K, Hartley T, McMillan HJ, Sampaio ML, Melkus G, Woulfe J, Parmar G, Bourque PR, Breiner A, Zwicker J, Pringle CE, Jarinova O, Lochmüller H, Dyment DA, Brais B, Boycott KM; Care4Rare Canada Consortium,; Hekimi S, Harper ME, Warman-Chardon J. Neurol Genet. 2023 Jan 25;9(1):e200048. doi: 10.1212/NXG.0000000000200048. eCollection 2023 Feb.

Simultaneous engineering of natural killer cells for CAR transgenesis and CRISPR-Cas9 knockout using retroviral particles.Jo DH, Kaczmarek S, Shin O, Wang L, Cowan J, McComb S, Lee SH. Mol Ther Methods Clin Dev. 2023 Mar 15;29:173-184. doi: 10.1016/j.omtm.2023.03.006. eCollection 2023 Jun 8. PMID: 37063482

Differences in Sex-Specific Frequency of Glucocerebrosidase Variant Carriers and Familial Parkinsonism.Ortega RA, Bressman SB, Raymond D, Ozelius LJ, Wang C, Bennett SAL, Saunders-Pullman R. Mov Disord. 2023 Apr;38(4):714-715. doi: 10.1002/mds.29353. PMID: 37061880

Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: A potential role for the gut microbiota.Murray E, Butcher J, May Kearns M, Lamba S, Liang J, Stintzi A, Ismail N. Brain Behav Immun. 2023 May;110:297-309. doi: 10.1016/j.bbi.2023.03.009. Epub 2023 Mar 11. PMID: 36914014

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment.Hao Z, Meng C, Li L, Feng S, Zhu Y, Yang J, Han L, Sun L, Lv W, Figeys D, Liu H.Microbiome. 2023 Apr 24;11(1):88. doi: 10.1186/s40168-023-01506-0.PMID: 37095530

Granulosa cell-derived miR-379-5p regulates macrophage polarization in polycystic ovarian syndrome.Salehi R, Asare-Werehene M, Wyse BA, Abedini A, Pan B, Gutsol A, Jahangiri S, Szaraz P, Burns KD, Vanderhyden B, Li J, Burger D, Librach CL, Tsang BK.Front Immunol. 2023 Mar 24;14:1104550. doi: 10.3389/fimmu.2023.1104550. eCollection 2023.PMID: 37033997

Molecularly Imprinted Nanobeacons Redirect Innate Immune Killing towards Triple Negative Breast Cancer.Guan P, Guo Z, Xu S, Lu H, Wang L, Gu Z, Liu Z. Angew Chem Int Ed Engl. 2023 Apr 17;62(17):e202301202. doi: 10.1002/anie.202301202. Epub 2023 Mar 10. PMID: 36814079

Characterizing the differential distribution and targets of Sumo1 and Sumo2 in the mouse brain.Suk TR, Nguyen TT, Fisk ZA, Mitkovski M, Geertsma HM, Parmasad JA, Heer MM, Callaghan SM, Benseler F, Brose N, Tirard M, Rousseaux MWC.iScience. 2023 Mar 9;26(4):106350. doi: 10.1016/j.isci.2023.106350. eCollection 2023 Apr 21.PMID: 37009224 

DNA lipid nanoparticle vaccine targeting outer surface protein C affords protection against homologous Borrelia burgdorferi needle challenge in mice.Pfeifle A, Thulasi Raman SN, Lansdell C, Zhang W, Tamming L, Cecillon J, Laryea E, Patel D, Wu J, Gravel C, Frahm G, Gao J, Chen W, Chaconas G, Sauve S, Rosu-Myles M, Wang L, Johnston MJW, Li X.Front Immunol. 2023 Mar 16;14:1020134. doi: 10.3389/fimmu.2023.1020134. eCollection 2023.PMID: 37006299 

PGC-1s shape epidermal physiology by modulating keratinocyte proliferation and terminal differentiation.Gravel SP, Ben Khalifa Y, McGuirk S, St-Louis C, Laurin KM, Lavallée É, Benas D, Desbouis S, Amaral F, D'Amours D, Breton L, Jäger S, St-Pierre J., iScience. 2023 Mar 2;26(4):106314. doi: 10.1016/j.isci.2023.106314. eCollection 2023 Apr 21.PMID: 37009228 

Fatty acid transport protein inhibition sensitizes breast and ovarian cancers to oncolytic virus therapy via lipid modulation of the tumor microenvironmentSurendran A, Jamalkhah M, Poutou J, Birtch R, Lawson C, Dave J, Crupi MJF, Mayer J, Taylor V, Petryk J, de Souza CT, Moodie N, Billingsley JL, Austin B, Cormack N, Blamey N, Rezaei R, McCloskey CW, Fekete EEF, Birdi HK, Neault S, Jamieson TR, Wylie B, Tucker S, Azad T, Vanderhyden B, Tai LH, Bell JC, Ilkow CS.Front Immunol. 2023 Mar 10;14:1099459. doi: 10.3389/fimmu.2023.1099459. eCollection 2023.PMID: 36969187 

Complexity in Hepatic Insulin Resistance - Unraveling the Role of Ubiquitin-Specific Protease 14 in Protein Homeostasis of Metabolic Transcription Factors.  Morrow NM, Mulvihill EE. J Pharmacol Exp Ther. 2023 Apr;385(1):1-4. doi: 10.1124/jpet.122.001517. PMID: 36927510

Exercise training reduces circulating cytokines in male patients with coronary artery disease and type 2 diabetes: A pilot study. Garneau L, Terada T, Mistura M, Mulvihill EE, Reed JL, Aguer C.Physiol Rep. 2023 Mar;11(5):e15634. doi: 10.14814/phy2.15634.PMID: 36905198

Evaluating mitochondrial length, volume, and cristae ultrastructure in rare mouse adult stem cell populations.  Triolo M, Wade S, Baker N, Khacho M. STAR Protoc. 2023 Feb 9;4(1):102107. doi: 10.1016/j.xpro.2023.102107. Online ahead of print. PMID: 36853728

Humoral Responses against BQ.1.1 Elicited after Breakthrough Infection and SARS-CoV-2 mRNA Vaccination.  Tauzin A, Benlarbi M, Medjahed H, Grégoire Y, Perreault J, Gendron-Lepage G, Gokool L, Morrisseau C, Arlotto P, Tremblay C, Kaufmann DE, Martel-Laferrière V, Levade I, Côté M, De Serres G, Bazin R, Finzi A. Vaccines (Basel). 2023 Jan 21;11(2):242. doi: 10.3390/vaccines11020242. PMID: 36851122

Placental Mitochondrial Function and Dysfunction in Preeclampsia.  Jahan F, Vasam G, Green AE, Bainbridge SA, Menzies KJ. Int J Mol Sci. 2023 Feb 20;24(4):4177. doi: 10.3390/ijms24044177. PMID: 36835587

Recent Developments in Islet Biology: A Review With Patient Perspectives.  Basu L, Bhagat V, Ching MEA, Di Giandomenico A, Dostie S, Greenberg D, Greenberg M, Hahm J, Hilton NZ, Lamb K, Jentz EM, Larsen M, Locatelli CAA, Maloney M, MacGibbon C, Mersali F, Mulchandani CM, Najam A, Singh I, Weisz T, Wong J, Senior PA, Estall JL, Mulvihill EE, Screaton RA; for Diabetes Action Canada and the Canadian Islet Research and Training Network.

Can J Diabetes. 2023 Mar;47(2):207-221. doi: 10.1016/j.jcjd.2022.11.003. Epub 2022 Nov 8.

PMID: 36481263

Mycobacterium tuberculosis infection triggers epigenetic changes that are enriched in a type I IFN signature.  Madden K, El Hamra R, Berton S, Felker J, Alvarez GG, Blais A, Sun J. Microlife. 2023 Feb 6;4:uqad006. doi: 10.1093/femsml/uqad006. eCollection 2023. PMID: 36820061

Early postnatal defects in neurogenesis in the 3xTg mouse model of Alzheimer's disease.  Liu Y, Bilen M, McNicoll MM, Harris RA, Fong BC, Iqbal MA, Paul S, Mayne J, Walker K, Wang J, Figeys D, Slack RS. Cell Death Dis. 2023 Feb 18;14(2):138. doi: 10.1038/s41419-023-05650-1.

PMID: 36801910

Multiomic spatial analysis reveals a distinct mucosa-associated virome.  Yan A, Butcher J, Schramm L, Mack DR, Stintzi A. Gut Microbes. 2023 Jan-Dec;15(1):2177488. doi: 10.1080/19490976.2023.2177488. PMID: 36823020

Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S.Int J Mol Sci. 2023 Feb 20;24(4):4246. doi: 10.3390/ijms24044246.PMID: 36835656 

Prenatal low-dose methylmercury exposure causes premature neuronal differentiation and autism-like behaviors in a rodent model. Loan A, Leung JW, Cook DP, Ko C, Vanderhyden BC, Wang J, Chan HM.iScience. 2023 Jan 31;26(3):106093. doi: 10.1016/j.isci.2023.106093. eCollection 2023 Mar 17.PMID: 36843845 

Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: A potential role for the gut microbiota. Murray E, Butcher J, May Kearns M, Lamba S, Liang J, Stintzi A, Ismail N.Brain Behav Immun. 2023 Mar 11:S0889-1591(23)00066-1. doi: 10.1016/j.bbi.2023.03.009. Online ahead of print.PMID: 36914014

Microbiota-directed biotherapeutics: considerations for quality and functional assessment.  Emily Ef Fekete Daniel Figeys  Xu Zhang 

Proteomics characterization of mitochondrial‐derived vesicles under oxidative stress
Goutham Vasam, Rachel Nadeau, Virgilio J. J. Cadete, Mathieu Lavallée‐Adam, Keir J. Menzies, Yan Burelle FASEB J. 2021 Apr; 35(4): e21278. Published online 2021 Mar 26. doi: 10.1096/fj.202002151R PMCID: PMC8252493

Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex to Regulate Polyphosphate Synthesis in Budding YeastAmanda Bentley-DeSousa, Michael DowneymBio. 2021 Sep-Oct; 12(5): e00994-21. Published online 2021 Sep 21. doi: 10.1128/mBio.00994-21
Correction in: mBio. 2021 Nov-Dec; 12(6): e02997-21.  PMCID: PMC8510523

Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cellsSabrina Robichaud, Garrett Fairman, Viyashini Vijithakumar, Esther Mak, David P. Cook, Alexander R. Pelletier, Sylvain Huard, Barbara C. Vanderhyden, Daniel Figeys, Mathieu Lavallée-Adam, Kristin Baetz, Mireille Ouimet
Autophagy. 2021; 17(11): 3671–3689. Published online 2021 Feb 26. doi: 10.1080/15548627.2021.1886839PMCID: PMC863232

A yeast chemogenomic screen identifies pathways that modulate adipic acid toxicity
Eugene Fletcher, Kevin Mercurio, Elizabeth A. Walden, Kristin Baetz
iScience. 2021 Apr 23; 24(4): 102327. Published online 2021 Mar 18. doi: 10.1016/j.isci.2021.102327PMCID: PMC8050732

Grx2 Regulates Skeletal Muscle Mitochondrial Structure and Autophagy
Ava Liaghati, Chantal A. Pileggi, Gaganvir Parmar, David A. Patten, Nina Hadzimustafic, Alexanne Cuillerier, Keir J. Menzies, Yan Burelle, Mary-Ellen Harper
Front Physiol. 2021; 12: 604210. Published online 2021 Mar 5. doi: 10.3389/fphys.2021.604210PMCID: PMC7982873

Naked mole-rat brown fat thermogenesis is diminished during hypoxia through a rapid decrease in UCP1
Hang Cheng, Rajaa Sebaa, Nikita Malholtra, Baptiste Lacoste, Ziyad El Hankouri, Alexia Kirby, Nigel C. Bennett, Barry van Jaarsveld, Daniel W. Hart, Glenn J. Tattersall, Mary-Ellen Harper, Matthew E. Pamenter
Nat Commun. 2021; 12: 6801. Published online 2021 Nov 23. doi: 10.1038/s41467-021-27170-2PMCID: PMC8610999

Applications of Extracellular Vesicles in Triple-Negative Breast Cancer
Frederic St-Denis-Bissonnette, Rachil Khoury, Karan Mediratta, Sara El-Sahli, Lisheng Wang, Jessie R. Lavoie  Cancers (Basel) 2022 Jan; 14(2): 451. Published online 2022 Jan 17. doi: 10.3390/cancers14020451 PMCID: PMC8773485

Ebola virus triggers receptor tyrosine kinase-dependent signaling to promote the delivery of viral particles to entry-conducive intracellular compartments
Corina M. Stewart, Alexandra Phan, Yuxia Bo, Nicholas D. LeBlond, Tyler K. T. Smith, Geneviève Laroche, Patrick M. Giguère, Morgan D. Fullerton, Martin Pelchat, Darwyn Kobasa, Marceline Côté
PLoS Pathog. 2021 Jan; 17(1): e1009275. Published online 2021 Jan 29. doi: 10.1371/journal.ppat.1009275PMCID: PMC7875390

Global analysis of Saccharomyces cerevisiae growth in mucin
Kevin Mercurio, Dylan Singh, Elizabeth Walden, KristinBaetz
G3 (Bethesda) 2021 Nov; 11(11): jkab294. Published online 2021 Aug 18. doi: 10.1093/g3journal/jkab294PMCID: PMC8527512

Relative Ratios of Human Seasonal Coronavirus Antibodies Predict the Efficiency of Cross-Neutralization of SARS-CoV-2 Spike Binding to ACE2Yannick Galipeau, Vinayakumar Siragam, Geneviève Laroche, Erika Marion, Matthew Greig, Michaeline McGuinty, Ronald A Booth, Yves Durocher, Miroslava Cuperlovic-Culf, Steffany A.L. Bennett, Angela M. Crawley, Patrick M. Giguère, Curtis Cooper, Marc-André Langlois
EBioMedicine. 2021 Dec; 74: 103700. Published online 2021 Nov 30. doi: 10.1016/j.ebiom.2021.103700PMCID: PMC8629681

Retraction Note to: Differential regulation of wild-type and mutant alpha-synuclein binding to synaptic membranes by cytosolic factorsSabine Wislet-Gendebien, Naomi P. Visanji, Shawn N. Whitehead, Diana Marsilio, Weimin Hou, Daniel Figeys, Paul E. Fraser, Steffany A. L. Bennett, Anurag Tandon
BMC Neurosci. 2021; 22: 40. Published online 2021 Jun 3. doi: 10.1186/s12868-021-00644-1Retracts: BMC Neurosci. 2008; 9: 92.PMCID: PMC8173967

Identification of pannexin 1-regulated genes, interactome, and pathways in rhabdomyosarcoma and its tumor inhibitory interaction with AHNAKXiao Xiang, Stéphanie Langlois, Marie-Eve St-Pierre, Anna Blinder, Philippe Charron, Tyson E. Graber, Stephanie L. Fowler, Stephen D. Baird, Steffany A. L. Bennett, Tommy Alain, Kyle N. Cowan Oncogene. 2021; 40(10): 1868–1883. Published online 2021 Feb 9. doi: 10.1038/s41388-020-01623-2 PMCID: PMC7946643

Serine palmitoyltransferase assembles at ER–mitochondria contact sites
Mari J Aaltonen, Irina Alecu, Tim König, Steffany AL Bennett, Eric A Shoubridge
Life Sci Alliance. 2022 Feb; 5(2): e202101278. Published online 2021 Nov 16. doi: 10.26508/lsa.202101278 PMCID: PMC8605320

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infectionMiroslava Cuperlovic-Culf, Emma L. Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green Sci Rep. 2021; 11: 10629. Published online 2021 May 20. doi: 10.1038/s41598-021-90243-1 PMCID: PMC8138024

Zebrafish Cancer Predisposition Models
Kim Kobar, Keon Collett, Sergey V. Prykhozhij, Jason N. Berman
Front Cell Dev Biol. 2021; 9: 660069. Published online 2021 Apr 27. doi: 10.3389/fcell.2021.660069 PMCID: PMC8112447

Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter
John Girgis, Dabo Yang, Imane Chakroun, Yubing Liu, Alexandre Blais
Skelet Muscle. 2021; 11: 26. Published online 2021 Nov 19. doi: 10.1186/s13395-021-00281-6 PMCID:    PMC8607597

Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag
Yuefeng Li, Kiran Nakka, Thomas Olender, Philippe Gingras-Gelinas, Matthew Man-Kin Wong, Daniel C.L. Robinson, Hina Bandukwala, Carmen G. Palii, Odile Neyret, Marjorie Brand, Alexandre Blais, F. Jeffrey Dilworth
STAR Protoc. 2021 Sep 17; 2(3): 100751. Published online 2021 Aug 19. doi: 10.1016/j.xpro.2021.100751 PMCID:  PMC8384913

Muscle Enriched Lamin Interacting Protein (Mlip) Binds Chromatin and Is Required for Myoblast DifferentiationElmira Ahmady, Alexandre Blais, Patrick G. Burgon
Cells. 2021 Mar; 10(3): 615. Published online 2021 Mar 10. doi: 10.3390/cells10030615  PMCID: PMC7998221

Epigenetic plasticity of erythroid progenitors
Marjorie Brand
Blood. 2021 Nov 4; 138(18): 1646–1648. doi: 10.1182/blood.2021013087 PMCID: PMC8569413

Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulationDaniel C.L. Robinson, Morten Ritso, Geoffrey M. Nelson, Zeinab Mokhtari, Kiran Nakka, Hina Bandukwala, Seth R. Goldman, Peter J. Park, Rémi Mounier, Bénédicte Chazaud, Marjorie Brand, Michael A. Rudnicki, Karen Adelman, F. Jeffrey Dilworth
Dev Cell. Author manuscript; available in PMC 2021 Oct 5.
Published in final edited form as: Dev Cell. 2021 Apr 5; 56(7): 1014–1029.e7. Published online 2021 Mar 17. doi: 10.1016/j.devcel.2021.02.025 PMCID: PMC8357161

Immunological and pathological outcomes of SARS-CoV-2 challenge following formalin-inactivated vaccine in ferrets and rhesus macaques
Kevin R. Bewley, Karen Gooch, Kelly M. Thomas, Stephanie Longet, Nathan Wiblin, Laura Hunter, Kin Chan, Phillip Brown, Rebecca A. Russell, Catherine Ho, Gillian Slack, Holly E. Humphries, Leonie Alden, Lauren Allen, Marilyn Aram, Natalie Baker, Emily Brunt, Rebecca Cobb, Susan Fotheringham, Debbie Harris, Chelsea Kennard, Stephanie Leung, Kathryn Ryan, Howard Tolley, Nadina Wand, Andrew White, Laura Sibley, Charlotte Sarfas, Geoff Pearson, Emma Rayner, Xiaochao Xue, Teresa Lambe, Sue Charlton, Sarah Gilbert, Quentin J. Sattentau, Fergus Gleeson, Yper Hall, Simon Funnell, Sally Sharpe, Francisco J. Salguero, Andrew Gorringe, Miles Carroll
Sci Adv. 2021 Sep; 7(37): eabg7996. Published online 2021 Sep 10. doi: 10.1126/sciadv.abg7996 PMCID: PMC8442907

Comparison of SARS-CoV-2 indirect and direct RT-qPCR detection methods
Joel D. Pearson, Daniel Trcka, Suying Lu, Sharon J. Hyduk, Mark Jen, Marie-Ming Aynaud, J. Javier Hernández, Philippos Peidis, Miriam Barrios-Rodiles, Kin Chan, Jim Woodgett, Tony Mazzulli, Liliana Attisano, Laurence Pelletier, Myron I. Cybulsky, Jeffrey L. Wrana, Rod Bremner
Virol J. 2021; 18: 99. Published online 2021 May 17. doi: 10.1186/s12985-021-01574-4 PMCID: PMC8127261

A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2
Marie-Ming Aynaud, J. Javier Hernandez, Seda Barutcu, Ulrich Braunschweig, Kin Chan, Joel D. Pearson, Daniel Trcka, Suzanna L. Prosser, Jaeyoun Kim, Miriam Barrios-Rodiles, Mark Jen, Siyuan Song, Jess Shen, Christine Bruce, Bryn Hazlett, Susan Poutanen, Liliana Attisano, Rod Bremner, Benjamin J. Blencowe, Tony Mazzulli, Hong Han, Laurence Pelletier, Jeffrey L. Wrana
Nat Commun. 2021; 12: 1405. Published online 2021 Mar 3. doi: 10.1038/s41467-021-21653-y PMCID: PMC7930244

Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between dosesAlexandra Tauzin, Shang Yu Gong, Guillaume Beaudoin-Bussières, Dani Vézina, Romain Gasser, Lauriane Nault, Lorie Marchitto, Mehdi Benlarbi, Debashree Chatterjee, Manon Nayrac, Annemarie Laumaea, Jérémie Prévost, Marianne Boutin, Gérémy Sannier, Alexandre Nicolas, Catherine Bourassa, Gabrielle Gendron-Lepage, Halima Medjahed, Guillaume Goyette, Yuxia Bo, Josée Perreault, Laurie Gokool, Chantal Morrisseau, Pascale Arlotto, Renée Bazin, Mathieu Dubé, Gaston De Serres, Nicholas Brousseau, Jonathan Richard, Roberta Rovito, Marceline Côté, Cécile Tremblay, Giulia C. Marchetti, Ralf Duerr, Valérie Martel-Laferrière, Daniel E. Kaufmann, Andrés Finzi
Cell Host Microbe. 2022 Jan 12; 30(1): 97–109.e5. Published online 2021 Dec 3. doi: 10.1016/j.chom.2021.12.004 PMCID: PMC8639412

Antiviral Potential of the Antimicrobial Drug Atovaquone against SARS-CoV-2 and Emerging Variants of ConcernMadalina Elena Carter-Timofte, Rozanne Arulanandam, Naziia Kurmasheva, Kathy Fu, Geneviève Laroche, Zaid Taha, Demi van der Horst, Lena Cassin, Renée M. van der Sluis, Enrico Palermo, Daniele Di Carlo, David Jacobs, Glib Maznyi, Taha Azad, Ragunath Singaravelu, Fanghui Ren, Anne Louise Hansen, Manja Idorn, Christian K. Holm, Martin R. Jakobsen, Julien van Grevenynghe, John Hiscott, Søren R. Paludan, John C. Bell, Jean Seguin, Luc A. Sabourin, Marceline Côté, Jean-Simon Diallo, Tommy Alain, David Olagnier
ACS Infect Dis. 2021 Oct 18 : acsinfecdis.1c00278. Published online 2021 Oct 18. doi: 10.1021/acsinfecdis.1c00278 PMCID: PMC8547501

Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity
Shang Yu Gong, Debashree Chatterjee, Jonathan Richard, Jérémie Prévost, Alexandra Tauzin, Romain Gasser, Yuxia Bo, Dani Vézina, Guillaume Goyette, Gabrielle Gendron-Lepage, Halima Medjahed, Michel Roger, Marceline Côté, Andrés Finzi
Virology. 2021 Nov; 563: 134–145. Published online 2021 Sep 11. doi: 10.1016/j.virol.2021.09.001 PMCID: PMC8433594

Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes
Debashree Chatterjee, Alexandra Tauzin, Annemarie Laumaea, Shang Yu Gong, Yuxia Bo, Aurélie Guilbault, Guillaume Goyette, Catherine Bourassa, Gabrielle Gendron-Lepage, Halima Medjahed, Jonathan Richard, Sandrine Moreira, Marceline Côté, Andrés Finzi
Viruses. 2022 Jan; 14(1): 144. Published online 2022 Jan 14. doi: 10.3390/v14010144 PMCID: PMC8780535

Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concernWenwei Li, Yaozong Chen, Jérémie Prévost, Irfan Ullah, Maolin Lu, Shang Yu Gong, Alexandra Tauzin, Romain Gasser, Dani Vézina, Sai Priya Anand, Guillaume Goyette, Debashree Chaterjee, Shilei Ding, William D. Tolbert, Michael W. Grunst, Yuxia Bo, Shijian Zhang, Jonathan Richard, Fei Zhou, Rick K. Huang, Lothar Esser, Allison Zeher, Marceline Côté, Priti Kumar, Joseph Sodroski, Di Xia, Pradeep D. Uchil, Marzena Pazgier, Andrés Finzi, Walther Mothes
Cell Rep. 2022 Jan 11; 38(2): 110210. Published online 2021 Dec 15. doi: 10.1016/j.celrep.2021.110210 PMCID: PMC8673750

Interferon-Induced HERC5 Inhibits Ebola Virus Particle Production and Is Antagonized by Ebola GlycoproteinErmela Paparisto, Nina R. Hunt, Daniel S. Labach, Macon D. Coleman, Eric J. Di Gravio, Mackenzie J. Dodge, Nicole J. Friesen, Marceline Côté, Andreas Müller, Thomas Hoenen, Stephen D. Barr
Cells. 2021 Sep; 10(9): 2399. Published online 2021 Sep 13. doi: 10.3390/cells10092399 PMCID: PMC8472148

Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern
Wenwei Li, Yaozong Chen, Jérémie Prévost, Irfan Ullah, Maolin Lu, Shang Yu Gong, Alexandra Tauzin, Romain Gasser, Dani Vézina, Sai Priya Anand, Guillaume Goyette, Debashree Chaterjee, Shilei Ding, William D. Tolbert, Michael W. Grunst, Yuxia Bo, Shijian Zhang, Jonathan Richard, Fei Zhou, Rick K. Huang, Lothar Esser, Allison Zeher, Marceline Côté, Priti Kumar, Joseph Sodroski, Di Xia, Pradeep D. Uchil, Marzena Pazgier, Andrés Finzi, Walther Mothes
Version 1. bioRxiv. Preprint. 2021 Aug 3. doi: 10.1101/2021.08.02.454546 PMCID: PMC8351775

Identification of a High-Frequency Intrahost SARS-CoV-2 Spike Variant with Enhanced Cytopathic and Fusogenic EffectsLynda Rocheleau, Geneviève Laroche, Kathy Fu, Corina M. Stewart, Abdulhamid O. Mohamud, Marceline Côté, Patrick M. Giguère, Marc-André Langlois, Martin Pelchat
mBio. 2021 May-Jun; 12(3): e00788-21. Published online 2021 Jun 29. doi: 10.1128/mBio.00788-21 PMCID:  PMC8262852

Potential Differences in Cleavage of the S Protein and Type 1 Interferon Together Control Human Coronavirus Infection, Propagation, and Neuropathology within the Central Nervous SystemAlain Le Coupanec, Marc Desforges, Benedikt Kaufer, Philippe Dubeau, Marceline Côté, Pierre J. Talbot
J Virol. 2021 May; 95(10): e00140-21. Prepublished online 2021 Feb 24. Published online 2021 Apr 26. doi: 10.1128/JVI.00140-21 PMCID: PMC8139659

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase IIMohammad S. Baig, Yimo Dou, Benjamin G. Bergey, Russell Bahar, Justin M. Burgener, Marjan Moallem, James B. McNeil, Akhi Akhter, Giovanni L. Burke, Veroni S. Sri Theivakadadcham, Patricia Richard, Damien D’Amours, Emanuel Rosonina
PLoS Genet. 2021 Sep; 17(9): e1009828. Published online 2021 Sep 29. doi: 10.1371/journal.pgen.1009828 PMCID: PMC8505008  

The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation
Tapan Sharma, Daniel C L Robinson, Hanna Witwicka, F Jeffrey Dilworth, Anthony N Imbalzano
Nucleic Acids Res. 2021 Aug 20; 49(14): 8060–8077. Published online 2021 Jul 21. doi: 10.1093/nar/gkab617 PMCID: PMC8373147

HIRA stabilizes skeletal muscle lineage identity
Joana Esteves de Lima, Reem Bou Akar, Léo Machado, Yuefeng Li, Bernadette Drayton-Libotte, F. Jeffrey Dilworth, Frédéric Relaix
Nat Commun. 2021; 12: 3450. Published online 2021 Jun 8. doi: 10.1038/s41467-021-23775-9 PMCID: PMC8187366

Targeting Polyphosphate Kinases in the Fight against Pseudomonas aeruginosa
Kanchi Baijal, Michael Downey
mBio. 2021 Jul-Aug; 12(4): e01477-21. Published online 2021 Aug 3. doi: 10.1128/mBio.01477-21 PMCID:  PMC8406150

Erratum for Bentley-DeSousa and Downey, “Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex To Regulate Polyphosphate Synthesis in Budding Yeast”Amanda Bentley-DeSousa, Michael Downey
mBio. 2021 Nov-Dec; 12(6): e02997-21. Published online 2021 Nov 2. doi: 10.1128/mBio.02997-21
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Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics ApproachJanice Mayne, Xu Zhang, James Butcher, Krystal Walker, Zhibin Ning, Ewelina Wójcik, Jarosław Dastych, Alain Stintzi, Daniel Figeys
Viruses. 2021 Sep; 13(9): 1734. Published online 2021 Aug 31. doi: 10.3390/v13091734 PMCID: PMC8473076

Propionic acid disrupts endocytosis, cell cycle, and cellular respiration in yeast
Emma W. Micalizzi, Ashkan Golshani, Myron L. Smith
BMC Res Notes. 2021; 14: 335. Published online 2021 Aug 28. doi: 10.1186/s13104-021-05752-z PMCID: PMC8403364

The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLFMatthew Jessulat, Shahreen Amin, Mohsen Hooshyar, Ramy Malty, Mohamed Taha Moutaoufik, Mara Zilocchi, Zoe Istace, Sadhna Phanse, Hiroyuki Aoki, Katayoun Omidi, Daniel Burnside, Bahram Samanfar, Khaled A Aly, Ashkan Golshani, Mohan Babu
Nucleic Acids Res. 2021 Aug 20; 49(14): 8145–8160. Published online 2021 Jul 9. doi: 10.1093/nar/gkab585 PMCID: PMC8373142

Manganese-Induced Neurotoxicity through Impairment of Cross-Talk Pathways in Human Neuroblastoma Cell Line SH-SY5Y Differentiated with Retinoic AcidRaúl Bonne Hernández, Nadja C. de Souza-Pinto, Jos Kleinjans, Marcel van Herwijnen, Jolanda Piepers, Houman Moteshareie, Daniel Burnside, Ashkan Golshani
Toxics. 2021 Dec; 9(12): 348. Published online 2021 Dec 9. doi: 10.3390/toxics9120348 PMCID: PMC8704659

Dietary Cocoa Flavanols Enhance Mitochondrial Function in Skeletal Muscle and Modify Whole-Body Metabolism in Healthy MiceFrédéric Nicolas Daussin, Alexane Cuillerier, Julianne Touron, Samir Bensaid, Bruno Melo, Ali Al Rewashdy, Goutham Vasam, Keir J. Menzies, Mary-Ellen Harper, Elsa Heyman, Yan Burelle
Nutrients. 2021 Oct; 13(10): 3466. Published online 2021 Sep 29. doi: 10.3390/nu13103466 PMCID: PMC8538722

SMN Depleted Mice Offer a Robust and Rapid Onset Model of Nonalcoholic Fatty Liver Disease
Marc-Olivier Deguise, Chantal Pileggi, Yves De Repentigny, Ariane Beauvais, Alexandra Tierney, Lucia Chehade, Jean Michaud, Maica Llavero-Hurtado, Douglas Lamont, Abdelmadjid Atrih, Thomas M. Wishart, Thomas H. Gillingwater, Bernard L. Schneider, Mary-Ellen Harper, Simon H. Parson, Rashmi Kothary
Cell Mol Gastroenterol Hepatol. 2021; 12(1): 354–377.e3. Published online 2021 Feb 2. doi: 10.1016/j.jcmgh.2021.01.019 PMCID: PMC8257458

Nuclear HKII-P-p53 (Ser15) Interaction is a Prognostic Biomarker for Chemoresponsiveness and Glycolytic Regulation in Epithelial Ovarian CancerChae Young Han, David A. Patten, Se Ik Kim, Jung Jin Lim, David W. Chan, Michelle K. Y. Siu, Youngjin Han, Euridice Carmona, Robin J. Parks, Cheol Lee, Li-Jun Di, Zhen Lu, Karen K. L. Chan, Ja-Lok Ku, Elizabeth A. Macdonald, Barbara C. Vanderhyden, Anne-Marie Mes-Masson, Hextan Y. S. Ngan, Annie N. Y. Cheung, Yong Sang Song, Robert C. Bast, Jr., Mary-Ellen Harper, Benjamin K. Tsang
Cancers (Basel) 2021 Jul; 13(14): 3399. Published online 2021 Jul 7. doi: 10.3390/cancers13143399 PMCID: PMC8306240

Exercise training and diet-induced weight loss increase markers of hepatic bile acid (BA) synthesis and reduce serum total BA concentrations in obese womenKelly E. Mercer, Adrianna Maurer, Lindsay M. Pack, Kikumi Ono-Moore, Beverly J. Spray, Caitlin Campbell, Carol J. Chandler, Dustin Burnett, Elaine Souza, Gretchen Casazza, Nancy Keim, John Newman, Gary Hunter, Jose Fernadez, W. Timothy Garvey, Mary-Ellen Harper, Charles Hoppel, Sean H. Adams, John Thyfault
Am J Physiol Endocrinol Metab. 2021 May 1; 320(5): E864–E873. Published online 2021 Mar 1. doi: 10.1152/ajpendo.00644.2020 PMCID: PMC8238126

PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomicsRachel Nadeau, Anastasiia Byvsheva, Mathieu Lavallée-Adam
BMC Bioinformatics. 2021; 22: 302. Published online 2021 Jun 4. doi: 10.1186/s12859-021-04042-6 PMCID: PMC8178832
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis
Nikta Feizi, Sisira Kadambat Nair, Petr Smirnov, Gangesh Beri, Christopher Eeles, Parinaz Nasr Esfahani, Minoru Nakano, Denis Tkachuk, Anthony Mammoliti, Evgeniya Gorobets, Arvind Singh Mer, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains
Nucleic Acids Res. 2022 Jan 7; 50(D1): D1348–D1357. Published online 2021 Nov 26. doi: 10.1093/nar/gkab1084 PMCID: PMC8728279

Orchestrating and sharing large multimodal data for transparent and reproducible research
Anthony Mammoliti, Petr Smirnov, Minoru Nakano, Zhaleh Safikhani, Christopher Eeles, Heewon Seo, Sisira Kadambat Nair, Arvind S. Mer, Ian Smith, Chantal Ho, Gangesh Beri, Rebecca Kusko, Massive Analysis Quality Control (MAQC) Society Board of Directors, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains
Nat Commun. 2021; 12: 5797. Published online 2021 Oct 4. doi: 10.1038/s41467-021-25974-w PMCID: PMC8490371

Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
Arvind Singh Mer, Emily M. Heath, Seyed Ali Madani Tonekaboni, Nergiz Dogan-Artun, Sisira Kadambat Nair, Alex Murison, Laura Garcia-Prat, Liran Shlush, Rose Hurren, Veronique Voisin, Gary D. Bader, Corey Nislow, Mattias Rantalainen, Soren Lehmann, Mark Gower, Cynthia J. Guidos, Mathieu Lupien, John E. Dick, Mark D. Minden, Aaron D. Schimmer, Benjamin Haibe-Kains
Nat Commun. 2021; 12: 1054. Published online 2021 Feb 16. doi: 10.1038/s41467-021-21233-0 PMCID: PMC7886883

Proteogenomic Characterization of Pancreatic Ductal Adenocarcinoma
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T. Mamie Lih, Sara R. Savage, Karsten Krug, David J. Clark, Michael Schnaubelt, Lijun Chen, Felipe da Veiga Leprevost, Rodrigo Vargas Eguez, Weiming Yang, Jianbo Pan, Bo Wen, Yongchao Dou, Wen Jiang, Yuxing Liao, Zhiao Shi, Nadezhda V. Terekhanova, Song Cao, Rita Jui-Hsien Lu, Yize Li, Ruiyang Liu, Houxiang Zhu, Peter Ronning, Yige Wu, Matthew A. Wyczalkowski, Hariharan Easwaran, Ludmila Danilova, Arvind Singh Mer, Seungyeul Yoo, Joshua M. Wang, Wenke Liu, Benjamin Haibe-Kains, Mathangi Thiagarajan, Scott D. Jewell, Galen Hostetter, Chelsea J. Newton, Qing Kay Li, Michael H. Roehrl, David Fenyö, Pei Wang, Alexey I. Nesvizhskii, D. R. Mani, Gilbert S. Omenn, Emily S. Boja, Mehdi Mesri, Ana I. Robles, Henry Rodriguez, Oliver F. Bathe, Daniel W Chan, Ralph H. Hruban, Li Ding, Bing Zhang, Hui Zhang, Clinical Proteomic Tumor Analysis Consortium
Cell. Author manuscript; available in PMC 2021 Dec 8.
Published in final edited form as: Cell. 2021 Sep 16; 184(19): 5031–5052.e26. doi: 10.1016/j.cell.2021.08.023 PMCID: PMC8654574

Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020
Wim L. Cuypers, Handan Melike Dönertaş, Jasleen K. Grewal, Nazeefa Fatima, Chase Donnelly, Arvind Singh Mer, Spencer Krieger, Bart Cuypers, Farzana Rahman
Version 1. F1000Res. 2021; 10: ISCB Comm J-443. Published online 2021 Jun 4. doi: 10.12688/f1000research.53408.1 PMCID: PMC8182693
Nucleotide Analogues Bearing a C2′ or C3′-Stereogenic All-Carbon Quaternary Center as SARS-CoV-2 RdRp InhibitorsAmarender Manchoju, Renaud Zelli, Gang Wang, Carla Eymard, Adrian Oo, Mona Nemer, Michel Prévost, Baek Kim, Yvan Guindon
Molecules. 2022 Jan; 27(2): 564. Published online 2022 Jan 17. doi: 10.3390/molecules27020564 PMCID: PMC8781509

WACS: improving ChIP-seq peak calling by optimally weighting controls
Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins
BMC Bioinformatics. 2021; 22: 69. Published online 2021 Feb 15. doi: 10.1186/s12859-020-03927-2 PMCID: PMC7885521

FHR-5 Serum Levels and CFHR5 Genetic Variations in Patients With Immune Complex-Mediated Membranoproliferative Glomerulonephritis and C3-Glomerulopathy
Nóra Garam, Marcell Cserhalmi, Zoltán Prohászka, Ágnes Szilágyi, Nóra Veszeli, Edina Szabó, Barbara Uzonyi, Attila Iliás, Christof Aigner, Alice Schmidt, Martina Gaggl, Gere Sunder-Plassmann, Dóra Bajcsi, Jürgen Brunner, Alexandra Dumfarth, Daniel Cejka, Stefan Flaschberger, Hana Flögelova, Ágnes Haris, Ágnes Hartmann, Andreas Heilos, Thomas Mueller, Krisztina Rusai, Klaus Arbeiter, Johannes Hofer, Dániel Jakab, Mária Sinkó, Erika Szigeti, Csaba Bereczki, Viktor Janko, Kata Kelen, György S. Reusz, Attila J. Szabó, Nóra Klenk, Krisztina Kóbor, Nika Kojc, Maarten Knechtelsdorfer, Mario Laganovic, Adrian Catalin Lungu, Anamarija Meglic, Rina Rus, Tanja Kersnik Levart, Ernesta Macioniene, Marius Miglinas, Anna Pawłowska, Tomasz Stompór, Ludmila Podracka, Michael Rudnicki, Gert Mayer, Romana Rysava, Jana Reiterova, Marijan Saraga, Tomáš Seeman, Jakub Zieg, Eva Sládková, Natasa Stajic, Tamás Szabó, Andrei Capitanescu, Simona Stancu, Miroslav Tisljar, Kresimir Galesic, András Tislér, Inga Vainumäe, Martin Windpessl, Tomas Zaoral, Galia Zlatanova, Mihály Józsi, Dorottya Csuka
Front Immunol. 2021; 12: 720183. Published online 2021 Sep 10. doi: 10.3389/fimmu.2021.720183 PMCID: PMC8461307

Antibody Response to mRNA Vaccines against SARS-CoV-2 with Chronic Kidney Disease, Hemodialysis, and after Kidney TransplantationLukas Buchwinkler, Claire Anne Solagna, Janosch Messner, Markus Pirklbauer, Michael Rudnicki, Gert Mayer, Julia Kerschbaum
J Clin Med. 2022 Jan; 11(1): 148. Published online 2021 Dec 28. doi: 10.3390/jcm11010148 PMCID: PMC8745313

Human Complement C4B Allotypes and Deficiencies in Selected Cases With Autoimmune Diseases
Danlei Zhou, Michael Rudnicki, Gilbert T. Chua, Simon K. Lawrance, Bi Zhou, Joanne L. Drew, Fatima Barbar-Smiley, Taylor K. Armstrong, Miranda E. Hilt, Daniel J. Birmingham, Werner Passler, Jeffrey J. Auletta, Sasigarn A. Bowden, Robert P. Hoffman, Yee Ling Wu, Wael N. Jarjour, Chi Chiu Mok, Stacy P. Ardoin, Yu Lung Lau, Chack Yung Yu
Front Immunol. 2021; 12: 739430. Published online 2021 Oct 26. doi: 10.3389/fimmu.2021.739430 PMCID: PMC8577214

Coregulation Analysis of Mechanistic Biomarkers in Autosomal Dominant Polycystic Kidney Disease
Johannes Leierer, Paul Perco, Benedikt Hofer, Susanne Eder, Alexander Dzien, Julia Kerschbaum, Michael Rudnicki, Gert Mayer
Int J Mol Sci. 2021 Jul; 22(13): 6885. Published online 2021 Jun 26. doi: 10.3390/ijms22136885 PMCID: PMC8269435

Acetylation of PAX7 controls muscle stem cell self-renewal and differentiation potential in mice
Marie-Claude Sincennes, Caroline E. Brun, Alexander Y. T. Lin, Tabitha Rosembert, David Datzkiw, John Saber, Hong Ming, Yoh-ichi Kawabe, Michael A. Rudnicki
Nat Commun. 2021; 12: 3253. Published online 2021 May 31. doi: 10.1038/s41467-021-23577-z PMCID: PMC8167170
STAT1 potentiates oxidative stress revealing a targetable vulnerability that increases phenformin efficacy in breast cancerStephanie P. Totten, Young Kyuen Im, Eduardo Cepeda Cañedo, Ouafa Najyb, Alice Nguyen, Steven Hébert, Ryuhjin Ahn, Kyle Lewis, Benjamin Lebeau, Rachel La Selva, Valérie Sabourin, Constanza Martínez, Paul Savage, Hellen Kuasne, Daina Avizonis, Nancy Santos Martínez, Catherine Chabot, Adriana Aguilar-Mahecha, Marie-Line Goulet, Matthew Dankner, Michael Witcher, Kevin Petrecca, Mark Basik, Michael Pollak, Ivan Topisirovic, Rongtuan Lin, Peter M. Siegel, Claudia L. Kleinman, Morag Park, Julie St-Pierre, Josie Ursini-Siegel
Nat Commun. 2021; 12: 3299. Published online 2021 Jun 3. doi: 10.1038/s41467-021-23396-2 PMCID: PMC8175605

Resistance to different anthracycline chemotherapeutics elicits distinct and actionable primary metabolic dependencies in breast cancerShawn McGuirk, Yannick Audet-Delage, Matthew G Annis, Yibo Xue, Mathieu Vernier, Kaiqiong Zhao, Catherine St-Louis, Lucía Minarrieta, David A Patten, Geneviève Morin, Celia MT Greenwood, Vincent Giguère, Sidong Huang, Peter M Siegel, Julie St-Pierre
eLife. 2021; 10: e65150. Published online 2021 Jun 28. doi: 10.7554/eLife.65150 PMCID: PMC8238502
Perturbations of cancer cell metabolism by the antidiabetic drug canagliflozin
David Papadopoli, Oro Uchenunu, Ranveer Palia, Nabila Chekkal, Laura Hulea, Ivan Topisirovic, Michael Pollak, Julie St-Pierre
Neoplasia. 2021 Apr; 23(4): 391–399. Published online 2021 Mar 27. doi: 10.1016/j.neo.2021.02.003 PMCID: PMC8027095
Glycomacropeptide for Management of Insulin Resistance and Liver Metabolic Perturbations
Mathilde Foisy Sauvé, Francis Feldman, Mireille Koudoufio, Nour-El-Houda Ould-Chikh, Lena Ahmarani, Alain Sane, Thierry N’Timbane, Ramy El-Jalbout, Nathalie Patey, Schohraya Spahis, Alain Stintzi, Edgard Delvin, Emile Levy
Biomedicines. 2021 Sep; 9(9): 1140. Published online 2021 Sep 2. doi: 10.3390/biomedicines9091140 PMCID: PMC8469639

Factors contributing to fidelity in a pilot trial of individualized resistant starches for pediatric inflammatory bowel disease: a fidelity study protocolGisell Castillo, David R. Mack, Manoj M. Lalu, Ruth Singleton, Dean A. Fergusson, Alain Stintzi, Megan Harrison, Justin Presseau Pilot Feasibility Stud. 2021; 7: 75. Published online 2021 Mar 19. doi: 10.1186/s40814-021-00815-1 PMCID: PMC7976693

Oligosaccharides and Microbiota in Human Milk Are Interrelated at 3 Months Postpartum in a Cohort of Women with a High Prevalence of Gestational Impaired Glucose ToleranceLauren LeMay-Nedjelski, Chloe Yonemitsu, Michelle R Asbury, James Butcher, Sylvia H Ley, Anthony J Hanley, Alex Kiss, Sharon Unger, Julia K Copeland, Pauline W Wang, Alain Stintzi, Lars Bode, Deborah L O'Connor
J Nutr. 2021 Nov; 151(11): 3431–3441. Published online 2021 Sep 11. doi: 10.1093/jn/nxab270 PMCID: PMC8562078

Reduced Infection Efficiency of Phage NCTC 12673 on Non-Motile Campylobacter jejuni Strains Is Related to Oxidative StressJessica C. Sacher, Muhammad Afzal Javed, Clay S. Crippen, James Butcher, Annika Flint, Alain Stintzi, Christine M. Szymanski
Viruses. 2021 Oct; 13(10): 1955. Published online 2021 Sep 29. doi: 10.3390/v13101955 PMCID: PMC8540345

Critical appraisal of the mechanisms of gastrointestinal and hepatobiliary infection by COVID-19
Emile Levy, Alain Stintzi, Albert Cohen, Yves Desjardins, André Marette, Schohraya Spahis
Am J Physiol Gastrointest Liver Physiol. 2021 Aug 1; 321(2): G99–G112. Published online 2021 May 19. doi: 10.1152/ajpgi.00106.2021 PMCID: PMC8289353

Resistant starch, microbiome, and precision modulation
Peter A. Dobranowski, Alain Stintzi
Gut Microbes. 2021; 13(1): 1926842. Published online 2021 Jul 18. doi: 10.1080/19490976.2021.1926842 PMCID: PMC8288039

Expansion microscopy-based imaging of nuclear structures in cultured cells
Antoine Gaudreau-Lapierre, Kirk Mulatz, Jean-Claude Béïque, Laura Trinkle-Mulcahy
STAR Protoc. 2021 Sep 17; 2(3): 100630. Published online 2021 Jun 26. doi: 10.1016/j.xpro.2021.100630 PMCID: PMC8243706

DNA Based Vaccine Expressing SARS-CoV-2 Spike-CD40L Fusion Protein Confers Protection Against Challenge in a Syrian Hamster ModelLevi A. Tamming, Diana Duque, Anh Tran, Wanyue Zhang, Annabelle Pfeifle, Emmanuel Laryea, Jianguo Wu, Sathya N. Thulasi Raman, Caroline Gravel, Marsha S. Russell, Anwar M. Hashem, Reem M. Alsulaiman, Rowa Y. Alhabbab, Jun Gao, David Safronetz, Jingxin Cao, Lisheng Wang, Wangxue Chen, Michael J. W. Johnston, Simon Sauve, Michael Rosu-Myles, Xuguang Li
Front Immunol. 2021; 12: 785349. Published online 2022 Jan 12. doi: 10.3389/fimmu.2021.785349 PMCID: PMC8789660

Serum Untargeted UHPLC-HRMS-Based Lipidomics to Discover the Potential Biomarker of Colorectal Advanced AdenomaYifan Zhu, Lisheng Wang, Yanying Nong, Yunxiao Liang, Zongsheng Huang, Pingchuan Zhu, Qisong Zhang
Cancer Manag Res. 2021; 13: 8865–8878. Published online 2021 Nov 26. doi: 10.2147/CMAR.S336322 PMCID: PMC8632617

Single Immunization of a Vaccine Vectored by a Novel Recombinant Vaccinia Virus Affords Effective Protection Against Respiratory Syncytial Virus Infection in Cotton RatsMarsha S. Russell, Sathya N. Thulasi Raman, Caroline Gravel, Wanyue Zhang, Annabelle Pfeifle, Wangxue Chen, Gary Van Domselaar, David Safronetz, Michael Johnston, Simon Sauve, Lisheng Wang, Michael Rosu-Myles, Jingxin Cao, Xuguang Li
Front Immunol. 2021; 12: 747866. Published online 2021 Sep 17. doi: 10.3389/fimmu.2021.747866 PMCID: PMC8484905

Carbon Material Based Electrochemical Immunosensor for Gastric Cancer Markers Detection
Zhuliang Zhang, Minsi Peng, Defeng Li, Jun Yao, Yingxue Li, Benhua Wu, Lisheng Wang, Zhenglei Xu
Front Chem. 2021; 9: 736271. Published online 2021 Aug 31. doi: 10.3389/fchem.2021.736271 PMCID: PMC8438142

Graphene-Assisted Electrochemical Sensor for Detection of Pancreatic Cancer Markers
Zhenglei Xu, Minsi Peng, Zhuliang Zhang, Haotian Zeng, Ruiyue Shi, Xiaoxin Ma, Lisheng Wang, Bihong Liao
Front Chem. 2021; 9: 733371. Published online 2021 Aug 19. doi: 10.3389/fchem.2021.733371 PMCID: PMC8416602

Hollow-fiber bioreactor production of extracellular vesicles from human bone marrow mesenchymal stromal cells yields nanovesicles that mirrors the immuno-modulatory antigenic signature of the producer cellJonathan Gobin, Gauri Muradia, Jelica Mehic, Carole Westwood, Lauren Couvrette, Andrew Stalker, Stewart Bigelow, Christian C. Luebbert, Frédéric St-Denis Bissonnette, Michael J. W. Johnston, Simon Sauvé, Roger Y. Tam, Lisheng Wang, Michael Rosu-Myles, Jessie R. Lavoie
Stem Cell Res Ther. 2021; 12: 127. Published online 2021 Feb 12. doi: 10.1186/s13287-021-02190-3 PMCID: PMC7880218
Long noncoding RNA KIF9-AS1 promotes cell apoptosis by targeting the microRNA-148a-3p/suppressor of cytokine signaling axis in inflammatory bowel diseaseJun Yao, Ruoyu Gao, Minghan Luo, Defeng Li, Liliangzi Guo, Zichao Yu, Feng Xiong, Cheng Wei, Benhua Wu, Zhenglei Xu, Dingguo Zhang, Jianyao Wang, Lisheng Wang
Eur J Gastroenterol Hepatol. 2021 Dec; 33(Suppl 1): e922–e932. Published online 2021 Nov 8. doi: 10.1097/MEG.0000000000002309 PMCID: PMC8734634

Identification of Active Ingredients of Huangqi Guizhi Wuwu Decoction for Promoting Nerve Function Recovery After Ischemic Stroke Using HT22 Live-Cell-Based Affinity Chromatography Combined with HPLC-MS/MSYingying He, Haozhen Zheng, Lanying Zhong, Nijun Zhong, Guiqing Wen, Lisheng Wang, Ying Zhang
Drug Des Devel Ther. 2021; 15: 5165–5178. Published online 2021 Dec 30. doi: 10.2147/DDDT.S333418 PMCID: PMC8722572
COVID-MTL: Multitask learning with Shift3D and random-weighted loss for COVID-19 diagnosis and severity assessmentGuoqing Bao, Huai Chen, Tongliang Liu, Guanzhong Gong, Yong Yin, Lisheng Wang, Xiuying Wang
Pattern Recognit. 2022 Apr; 124: 108499. Published online 2021 Dec 12. doi: 10.1016/j.patcog.2021.108499 PMCID: PMC8666107
Synthetic vaccine affords full protection to mice against lethal challenge of influenza B virus of both genetic lineagesCaroline Gravel, Abenaya Muralidharan, Amparo Duran, Adrian Zetner, Annabelle Pfeifle, Wanyue Zhang, Anwar Hashem, Levi Tamming, Aaron Farnsworth, Hugues Loemba, Wangxue Chen, Florian Krammer, David Safronetz, Jingxin Cao, Lisheng Wang, Simon Sauve, Michael Rosu-Myles, Gary Van Domselaar, Xuguang Li
iScience. 2021 Nov 19; 24(11): 103328. Published online 2021 Oct 21. doi: 10.1016/j.isci.2021.103328 PMCID: PMC8586812

Quantitative Prediction of Microsatellite Instability in Colorectal Cancer With Preoperative PET/CT-Based RadiomicsJiaru Li, Ziyi Yang, Bowen Xin, Yichao Hao, Lisheng Wang, Shaoli Song, Junyan Xu, Xiuying Wang
Front Oncol. 2021; 11: 702055. Published online 2021 Jul 22. doi: 10.3389/fonc.2021.702055 PMCID: PMC8339969

Correction to: Automatic identification of myopic maculopathy related imaging features in optic disc region via machine learning methodsYuchen Du, Qiuying Chen, Ying Fan, Jianfeng Zhu, Jiangnan He, Haidong Zou, Dazhen Sun, Bowen Xin, David Feng, Michael Fulham, Xiuying Wang, Lisheng Wang, Xun Xu
J Transl Med. 2021; 19: 203. Published online 2021 May 11. doi: 10.1186/s12967-021-02874-7  Corrects: J Transl Med. 2021; 19: 167. PMCID: PMC8114694

Expression of Nutrient Transporters on NK Cells During Murine Cytomegalovirus Infection Is MyD88-DependentAbrar Ul Haq Khan, Saeedah Musaed Almutairi, Alaa Kassim Ali, Rosalba Salcedo, C. Andrew Stewart, Lisheng Wang, Seung-Hwan Lee Front Immunol. 2021; 12: 654225. Published online 2021 May 3. doi: 10.3389/fimmu.2021.654225 PMCID: PMC8177011

Imaging Features by Machine Learning for Quantification of Optic Disc Changes and Impact on Choroidal Thickness in Young Myopic PatientsDandan Sun, Yuchen Du, Qiuying Chen, Luyao Ye, Huai Chen, Menghan Li, Jiangnan He, Jianfeng Zhu, Lisheng Wang, Ying Fan, Xun Xu
Front Med (Lausanne) 2021; 8: 657566. Published online 2021 Apr 29. doi: 10.3389/fmed.2021.657566 PMCID: PMC8116583

Post-Alignment Adjustment and Its Automation
Xuhua Xia
Genes (Basel) 2021 Nov; 12(11): 1809. Published online 2021 Nov 18. doi: 10.3390/genes12111809 PMCID: PMC8623120

Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines
Xuhua Xia
Vaccines (Basel) 2021 Jul; 9(7): 734. Published online 2021 Jul 3. doi: 10.3390/vaccines9070734 PMCID: PMC8310186

Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research
Alibek Kruglikov, Mohan Rakesh, Yulong Wei, Xuhua Xia
J Proteome Res. 2021 Mar 5; 20(3): 1457–1463. Published online 2021 Feb 22. doi: 10.1021/acs.jproteome.0c00734 PMCID: PMC7927282
Author Correction: Predicting mammalian species at risk of being infected by SARS-CoV-2 from an ACE2 perspectiveYulong Wei, Parisa Aris, Heba Farookhi, Xuhua Xia
Sci Rep. 2021; 11: 22016. Published online 2021 Nov 4. doi: 10.1038/s41598-021-01576-w
Corrects: Sci Rep. 2021; 11: 1702. PMCID: PMC8567729

Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 GenomesXuhua Xia
Viruses. 2021 Sep; 13(9): 1790. Published online 2021 Sep 8. doi: 10.3390/v13091790 PMCID: PMC8472983

Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up?
Ali Tehfe, Talia Roseshter, Yulong Wei, Xuhua Xia
Microorganisms. 2021 Mar; 9(3): 620. Published online 2021 Mar 17. doi: 10.3390/microorganisms9030620 PMCID: PMC8002603