2024 Computational Sciences Publications

2024 Publications: 

1.  El Kassaby B, Castellanos F, Gerring M, Kunde-Ramamoorthy G, Bult CJ. MVAR: A Mouse Variation Registry. J Mol Biol. 2024;436(17):168518. PMID: 38458603. https://libkey.io/libraries/3075/38458603

2.  Poirion OB, Zuo W, Spruce C, Baker CN, Daigle SL, Olson A, Skelly DA, Chesler EJ, Baker CL, White BS. Enhlink infers distal and context-specific enhancer-promoter linkages. Genome Biol. 2024;25(1):235. PMID: 39223609; PMCID: PMC11368035. https://libkey.io/libraries/3075/39223609

3.  White BS, Woo XY, Koc S, Sheridan T, Neuhauser SB, Wang S, Evrard YA, Chen L, Foroughi pour A, Landua JD, Mashl RJ, Davies SR, Fang B, Rosa MG, Evans KW, Bailey MH, Chen Y, Xiao M, Rubinstein JC, Sanderson BJ, Lloyd MW, Domanskyi S, Dobrolecki LE, Fujita M, Fujimoto J, Xiao G, Fields RC, Mudd JL, Xu X, Hollingshead MG, Jiwani S, Acevedo S, PDXNet Consortium, Davis-Dusenbery BN, Robinson PN, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan C-x, Carvajal-Carmona LG, Welm AL, Welm BE, Govindan R, Li S, Davies MA, Roth JA, Meric-Bernstam F, Xie Y, Herlyn M, Ding L, Lewis MT, Bult CJ, Dean DA, II, Chuang JH. A Pan-Cancer Patient-Derived Xenograft Histology Image Repository with Genomic and Pathologic Annotations Enables Deep Learning Analysis. Cancer Research. 2024;84(13):2060-72. PMID: 10.1158/0008-5472.Can-23-1349. https://libkey.io/libraries/3075/10.1158/0008-5472.Can-23-1349

4.  Gatti DM, Tyler AL, Mahoney JM, Churchill GA, Yener B, Koyuncu D, Gurcan MN, Niazi MK, Tavolara T, Gower A, Dayao D, McGlone E, Ginese ML, Specht A, Alsharaydeh A, Tessier PA, Kurtz SL, Elkins KL, Kramnik I, Beamer G. Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice. PLoS Pathog. 2024;20(6):e1011915. PMID: 38861581; PMCID: PMC11195971. https://libkey.io/libraries/3075/388615811. 

3.  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

4.  Meric-Bernstam F, Lloyd MW, Koc S, Evrard YA, McShane LM, Lewis MT, Evans KW, Li D, Rubinstein LV, Welm AL, Dean DA, Srivastava A, Grover JW, Ha MJ, Chen H, Huang X, Varadarajan K, Wang J, Roth JA, Welm BE, Govindan R, Ding L, Kaochar S, Mitsiades N, Carvajal-Carmona LG, Herlyn M, Davies MA, Shapiro GI, Fields RC, Trevino JG, Harrell JC, NCI PDXNet Consortium, Doroshow JH, Chuang JH, Moscow JA. Assessment of Patient-Derived Xenograft Growth and Antitumor Activity: The NCI PDXNet Consensus Recommendations. Mol Cancer Ther. 2024;23(7):924-38. PMID: 38641411; PMCID: PMC11217730. https://libkey.io/libraries/3075/38641411

5. 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

6. 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

7. Sheehan S, Mawe S, Chen 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

8. 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

9.  Suh YS, Lee J, George J, Seol D, Jeong K, Oh SY, Bang C, Jun Y, Kong SH, Lee HJ, Kim JI, Kim WH, Yang HK, Lee C. RNA expression of 6 genes from metastatic mucosal gastric cancer serves as the global prognostic marker for gastric cancer with functional validation. Br J Cancer. 2024;130(9):1571-84. PMID: 38467827; PMCID: PMC11059174. https://libkey.io/libraries/3075/38467827

10.  Koyuncu D, Tavolara T, Gatti DM, Gower AC, Ginese ML, Kramnik I, Yener B, Sajjad U, Niazi MKK, Gurcan M, Alsharaydeh A, Beamer G. B cells in perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell signatures identify asymptomatic Mycobacterium tuberculosis lung infection in Diversity Outbred mice. Infect Immun. 2024;92(7):e0026323. PMID: 38899881; PMCID: PMC11238564. https://libkey.io/libraries/3075/38899881

11.  Bettacchioli E, Chiche L, Chaussabel D, Cornec D, Jourde-Chiche N, Rinchai D. An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity. Database (Oxford). 2024;2024. PMID: 38805754; PMCID: PMC11131423. https://libkey.io/libraries/3075/38805754

12.  Subba B, Toufiq M, Omi F, Yurieva M, Khan T, Rinchai D, Palucka K, Chaussabel D. Human-augmented large language model-driven selection of glutathione peroxidase 4 as a candidate blood transcriptional biomarker for circulating erythroid cells. Sci Rep. 2024;14(1):23225. PMID: 39369090; PMCID: PMC11455862. https://libkey.io/libraries/3075/39369090

13.  Royer S-J, Wolter H, Delorme AE, Lebreton L, Poirion OB. Computer vision segmentation model—deep learning for categorizing microplastic debris. Frontiers in Environmental Science. 2024;12. PMID: 10.3389/fenvs.2024.1386292. https://libkey.io/libraries/3075/10.3389/fenvs.2024.1386292

14. Lott PC, Chiu K, Quino JE, Vang AP, Lloyd MW, Srivastava A, Chuang JH, PDXNet Consortium, Carvajal-Carmona LG. Development and Application of Genetic Ancestry Reconstruction Methods to Study Diversity of Patient-Derived Models in the NCI PDXNet Consortium. Cancer Res Commun. 2024;4(8):2147-52. PMID: 39056190; PMCID: PMC11328913. https://libkey.io/libraries/3075/39056190

15.  Karginov TA, Ménoret A, Leclair NK, Harrison AG, Chandiran K, Suarez-Ramirez JE, Yurieva M, Karlinsey K, Wang P, O'Neill RJ, Murphy PA, Adler AJ, Cauley LS, Anczuków O, Zhou B, Vella AT. Autoregulated splicing of TRA2β programs T cell fate in response to antigen-receptor stimulation. Science. 2024;385(6714):eadj1979. PMID: 39265028. https://libkey.io/libraries/3075/39265028

16.  Mills M, Emori C, Kumar P, Boucher Z, George J, Bolcun-Filas E. Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes. Dev Biol. 2024;517:55-72. PMID: 39306223. https://libkey.io/libraries/3075/39306223

17. 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

18. Jian Wei,Colleen L. Mayberry,Xiaoting Lv,Fangyan Hu,Taushif Khan,Natalie A. Logan,John J. Wilson,John D. Sears,Damien Chaussabel,Chih-Hao Chang; IL3-Driven T Cell–Basophil Crosstalk Enhances Antitumor Immunity.Cancer Immunol Res2024;https://doi.org/10.1158/2326-6066.CIR-23-0851

19.  O'Connor C, Keele GR, Martin W, Stodola T, Gatti D, Hoffman BR, Korstanje R, Churchill GA, Reinholdt LG. Unraveling the genetics of arsenic toxicity with cellular morphology QTL. PLoS Genet. 2024;20(4):e1011248. PMID: 38662777; PMCID: PMC11075906. https://libkey.io/libraries/3075/38662777

20.  Zhang B, Chen S, Yin X, McBride CD, Gertie JA, Yurieva M, Bielecka AA, Hoffmann B, Hinson JT, Grassmann J, Xu L, Siniscalco ER, Soldatenko A, Hoyt L, Joseph J, Norton EB, Uthaman G, Palm NW, Liu E, Eisenbarth SC, Williams A. Metabolic fitness of IgA(+) plasma cells in the gut requires DOCK8. Mucosal Immunol. 2024;17(3):431-49. PMID: 38159726. https://libkey.io/libraries/3075/38159726

22.  Oliveira TY, Merkenschlager J, Eisenreich T, Bortolatto J, Yao KH, Gatti DM, Churchill GA, Nussenzweig MC, Breton G. Quantitative trait loci mapping provides insights into the genetic regulation of dendritic cell numbers in mouse tissues. Cell Rep. 2024;43(6):114296. PMID: 38823019. https://libkey.io/libraries/3075/38823019

23. 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

24.  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

25.  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

26. 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

27. 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

28. 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

29.  Wei J, Mayberry CL, Lv X, Hu F, Khan T, Logan NA, Wilson JJ, Sears JD, Chaussabel D, Chang CH. IL3-Driven T Cell-Basophil Crosstalk Enhances Antitumor Immunity. Cancer Immunol Res. 2024;12(7):822-39. PMID: 38739030; PMCID: PMC11219266. https://libkey.io/libraries/3075/38739030