2024 Computational Sciences Publications

 

1. Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI, Jr., Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2023;52(D1):D1333-D46. PMID: 37953324; PMCID: PMC10767975. https://libkey.io/libraries/3075/37953324

2. Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet. 2024;20(4):e1011228. PMID: 38598567; PMCID: PMC11034653. https://libkey.io/libraries/3075/38598567

3. Kuffler L, Skelly DA, Czechanski A, Fortin HJ, Munger SC, Baker CL, Reinholdt LG, Carter GW. Imputation of 3D genome structure by genetic-epigenetic interaction modeling in mice. Elife. 2024;12:RP88222. PMID: 38669177; PMCID: PMC11052574. https://libkey.io/libraries/3075/38669177

4. Sheehan S, Mawe SChen M, Klug J, Ladiges W, Korstanje R, Mahoney JM. A machine learning approach for quantifying age-related histological changes in the mouse kidney. Geroscience. 2024;46(2):2571-81. PMID: 38103095; PMCID: PMC10828469. https://libkey.io/libraries/3075/38103095

5. Schwartz LS, Young KA, Stearns TM, Boyer N, Mujica KD, Trowbridge JJ. Transcriptional and functional consequences of Oncostatin M signaling on young Dnmt3a-mutant hematopoietic stem cells. Exp Hematol. 2024;130:104131. PMID: 38000729. https://libkey.io/libraries/3075/38000729

6. Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res. 2024;34(1):145-59. PMID: 38290977; PMCID: PMC10903950. https://libkey.io/libraries/3075/38290977

7. Lara MK, Brabec JL, Hernan AE, Scott RC, Tyler AL, Mahoney JM. Network-based analysis predicts interacting genetic modifiers from a meta-mapping study of spike-wave discharge in mice. Genes Brain Behav. 2024;23(2):e12879. PMID: 38444174; PMCID: PMC10915378. https://libkey.io/libraries/3075/38444174

8. Ravichandran S, Erra-Diaz F, Karakaslar OE, Marches R, Kenyon-Pesce L, Rossi R, Chaussabel D, Nehar-Belaid D, LaFon DC, Pascual V, Palucka K, Paust S, Nahm MH, Kuchel GA, Banchereau J, Ucar D. Distinct baseline immune characteristics associated with responses to conjugated and unconjugated pneumococcal polysaccharide vaccines in older adults. Nat Immunol. 2024;25(2):316-29. PMID: 38182669; PMCID: PMC10834365. https://libkey.io/libraries/3075/38182669

9.  Rinchai D, Brummaier T, A AM, Habib T, Toufiq M, Kino T, Nosten F, Al Khodor S, Terranegra A, McGready R, Kabeer BSA, Chaussabel D. A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings. Database (Oxford). 2024;2024:baae021. PMID: 38564425; PMCID: PMC10986794. https://libkey.io/libraries/3075/38564425

10.  Singh P, Al Mohannadi N, Murugesan S, Almarzooqi F, Kabeer BSA, Marr AK, Kino T, Brummaier T, Terranegra A, McGready R, Nosten F, Chaussabel D, Al Khodor S. Unveiling the dynamics of the breast milk microbiome: impact of lactation stage and gestational age. J Transl Med. 2023;21(1):784. PMID: 37932773; PMCID: PMC10629158. https://libkey.io/libraries/3075/37932773

11. Kurtz SL, Baker RE, Boehm FJ, Lehman CC, Mittereder LR, Khan H, Rossi AP, Gatti DM, Beamer G, Sassetti CM, Elkins KL. Multiple genetic loci influence vaccine-induced protection against Mycobacterium tuberculosis in genetically diverse mice. PLoS Pathog. 2024;20(3):e1012069. PMID: 38452145; PMCID: PMC10950258. https://libkey.io/libraries/3075/38452145

12. Brummaier T, Rinchai D, Toufiq M, Karim MY, Habib T, Utzinger J, Paris DH, McGready R, Marr AK, Kino T, Terranegra A, Al Khodor S, Chaussabel D, Syed Ahamed Kabeer B. Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy. Front Immunol. 2024;15:1319949. PMID: 38352867; PMCID: PMC10861739. https://libkey.io/libraries/3075/38352867

13. Roy TA, Bubier JA, Dickson PE, Wilcox TD, Ndukum J, Clark JW, Sukoff Rizzo SJ, Crabbe JC, Denegre JM, Svenson KL, Braun RE, Kumar V, MurraySA, White JK, Philip VM, Chesler EJ. Discovery and validation of genes driving drug-intake and related behavioral traits in mice. Genes Brain Behav. 2024;23(1):e12875. PMID: 38164795; PMCID: PMC10780947. https://libkey.io/libraries/3075/38164795