Department of Genetics Publications for April 9th – 22nd, 2023

Department of Genetics faculty, postdocs, students and collaborators published 15 papers during April 9^th – 22^nd, 2023.

 

Integration of clinical features and deep learning on pathology for the prediction of breast cancer recurrence assays and risk of recurrence. 

Howard FM, Dolezal J, Kochanny S, Khramtsova G, Vickery J, Srisuwananukorn A, Woodard A, Chen N, Nanda R, Perou CM, Olopade OI, Huo D, Pearson AT.

NPJ Breast Cancer. 2023 Apr 14;9(1):25. doi: 10.1038/s41523-023-00530-5.

PMID: 37059742

 

Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. 

Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium (Li Y); Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy AT, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S.

Nature. 2023 Apr 12. doi: 10.1038/s41586-023-05806-1. Online ahead of print.

PMID: 37046083

 

Pre-Diagnostic Glycoprotein Acetyl Levels and Incident and Recurrent Flare Risk, Accounting for Serum Urate Levels: A Population-Based, Prospective Study and Mendelian Randomization Analysis. 

Joshi AD, McCormick N, Yokose C, Yu B, Tin A, Terkeltaub R, Merriman TR, Eliassen AH, Curhan GC, Raffield LM, Choi HK.

Arthritis Rheumatol. 2023 Apr 12. doi: 10.1002/art.42523. Online ahead of print.

PMID: 37043280

 

bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing. 

Mu W, Davis ES, Lee S, Dozmorov MG, Phanstiel DH, Love MI.

Bioinformatics. 2023 Apr 12:btad190. doi: 10.1093/bioinformatics/btad190. Online ahead of print.

PMID: 37042725

 

Cardiomyocyte ploidy is dynamic during postnatal development and varies across genetic backgrounds. 

Swift SK, Purdy AL, Kolell ME, Andresen KG, Lahue C, Buddell T, Akins KA, Rau CD, O’Meara CC, Patterson M.

Development. 2023 Apr 1;150(7):dev201318. doi: 10.1242/dev.201318. Epub 2023 Apr 13.

PMID: 36912240

 

Genome-wide contributions of the MutSα- and MutSβ-dependent DNA mismatch repair pathways to the maintenance of genetic stability in S. cerevisiae. 

Kadyrova LY, Mieczkowski PA, Kadyrov FA.

J Biol Chem. 2023 Apr 12:104705. doi: 10.1016/j.jbc.2023.104705. Online ahead of print.

PMID: 37059180

 

matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling. 

Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH.

Bioinformatics. 2023 Apr 21:btad197. doi: 10.1093/bioinformatics/btad197. Online ahead of print.

PMID: 37084270

 

Trends in Prevalence of Gout Among US Asian Adults, 2011-2018. 

Yokose C, McCormick N, Lu N, Tanikella S, Lin K, Joshi AD, Raffield LM, Warner E, Merriman T, Hsu J, Saag K, Zhang Y, Choi HK.

JAMA Netw Open. 2023 Apr 3;6(4):e239501. doi: 10.1001/jamanetworkopen.2023.9501.

PMID: 37083663

 

Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. 

Adler FR, Anderson ARA, Bhushan A, Bogdan P, Bravo-Cordero JJ, Brock A, Chen Y, Cukierman E, DelGiorno KE, Denis GV, Ferrall-Fairbanks MC, Gartner ZJ, Germain RN, Gordon DM, Hunter G, Jolly MK, Karacosta LG, Mythreye K, Katira P, Kulkarni RP, Kutys ML, Lander AD, Laughney AM, Levine H, Lou E, Lowenstein PR, Masters KS, Pe’er D, Peyton SR, Platt MO, Purvis JE, Quon G, Richer JK, Riddle NC, Rodriguez A, Snyder JC, Lee Szeto G, Tomlin CJ, Yanai I, Zervantonakis IK, Dueck H.

Cell Syst. 2023 Apr 19;14(4):252-257. doi: 10.1016/j.cels.2023.03.002.

PMID: 37080161

 

Probing different paradigms of morphine withdrawal on sleep behavior in male and female C57BL/6 J mice. 

Bedard ML, Lord JS, Perez PJ, Bravo IM, Teklezghi AT, Tarantino L, Diering G, McElligott ZA.

Behav Brain Res. 2023 Apr 17:114441. doi: 10.1016/j.bbr.2023.114441. Online ahead of print.

PMID: 37075956

 

This population does not exist: learning the distribution of evolutionary histories with generative adversarial networks. 

Booker WW, Ray DD, Schrider DR.

Genetics. 2023 Apr 17:iyad063. doi: 10.1093/genetics/iyad063. Online ahead of print.

PMID: 37067864

 

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. 

Ogata JD, Mu W, Davis ES, Xue B, Harrell JC, Sheffield NC, Phanstiel DH, Love MI, Dozmorov MG.

Bioinformatics. 2023 Apr 17:btad198. doi: 10.1093/bioinformatics/btad198. Online ahead of print.

PMID: 37067481

 

ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel. 

McCabe SD, Nobel AB, Love MI.

Biostatistics. 2023 Apr 14;24(2):388-405. doi: 10.1093/biostatistics/kxab013.

PMID: 33948626 Free PMC article.

 

Coumestrol Induces Oxidative Stress and Impairs Migration and Embryonic Growth. 

Marbrey MW, Douglas ES, Goodwin ER, Caron KM.

Reproduction. 2023 Apr 1:REP-23-0017. doi: 10.1530/REP-23-0017. Online ahead of print.

PMID: 37078791

 

Position statement from the International Society for Prenatal Diagnosis (ISPD) on the use of non-invasive prenatal testing (NIPT) for the detection of fetal chromosomal conditions in singleton pregnancies. 

Hui L, Ellis K, Mayen D, Pertile MD, Riemers R, Sun L, Vermeesch J, Vora NL, Chitty LS.

Prenat Diagn. 2023 Apr 19. doi: 10.1002/pd.6357. Online ahead of print.

PMID: 37076973