Department of Genetics Publications for January 7th – 20th 2024

Department of Genetics faculty, postdocs, students and collaborators published 12 papers during January 7th – 20th 2024.

Diet Quality and Epigenetic Aging in the Women’s Health Initiative. 

Reynolds LM, Houston DK, Skiba MB, Whitsel EA, Stewart JD, Li Y, Zannas AS, Assimes TL, Horvath S, Bhatti P, Baccarelli AA, Tooze JA, Vitolins MZ.

J Acad Nutr Diet. 2024 Jan 10:S2212-2672(24)00002-9. doi: 10.1016/j.jand.2024.01.002. Online ahead of print.

PMID: 38215906

 

HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets. 

Rosen J, Lee L, Abnousi A, Chen J, Wen J, Hu M, Li Y.

Comput Struct Biotechnol J. 2023 Jan 9;21:931-939. doi: 10.1016/j.csbj.2023.01.003. eCollection 2023.

PMID: 38213897 Free PMC article.

 

Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. 

Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N.

Cell Genom. 2023 Dec 20:100468. doi: 10.1016/j.xgen.2023.100468. Online ahead of print.

PMID: 38190104

 

Metabolic status differentiates Trp53inp2 function in pressure-overload induced heart failure. 

Liu J, Liu T, Ren SV, Zhu C, Bouso E, Mamlouk S, Rau CD, Wang Y, Gao C.

Front Cardiovasc Med. 2023 Dec 18;10:1226586. doi: 10.3389/fcvm.2023.1226586. eCollection 2023.

PMID: 38188257 Free PMC article.

 

Genetic diversity drives extreme responses to traumatic brain injury and post-traumatic epilepsy. 

Shannon T, Cotter C, Fitzgerald J, Houle S, Levine N, Shen Y, Rajjoub N, Dobres S, Iyer S, Xenakis J, Lynch R, de Villena FP, Kokiko-Cochran O, Gu B.

Exp Neurol. 2024 Jan 5:114677. doi: 10.1016/j.expneurol.2024.114677. Online ahead of print.

PMID: 38185315

 

Robust Low-rank Tensor Decomposition with the L2 Criterion. 

Heng Q, Chi EC, Liu Y.

Technometrics. 2023;65(4):537-552. doi: 10.1080/00401706.2023.2200541. Epub 2023 May 22.

PMID: 38213317 Free PMC article.

 

G protein-coupled estrogen receptor (GPER)/GPR30 forms a complex with the β₁-adrenergic receptor, a membrane-associated guanylate kinase (MAGUK) scaffold protein, and protein kinase a anchoring protein (AKAP) 5 in MCF7 breast cancer cells. 

Tutzauer J, Serafin DS, Schmidt T, Olde B, Caron KM, Leeb-Lundberg LMF.

Arch Biochem Biophys. 2024 Jan 9:109882. doi: 10.1016/j.abb.2024.109882. Online ahead of print.

PMID: 38211639

 

Identification and validation of supervariants reveal novel loci associated with human white matter microstructure. 

Wang S, Li T, Zhao B, Dai W, Yao Y, Li C, Li T, Zhu H, Zhang H.

Genome Res. 2023 Dec 12:gr.277905.123. doi: 10.1101/gr.277905.123. Online ahead of print.

PMID: 38190638

 

X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements. 

Scholz M, Horn K, Pott J, Wuttke M, Kühnapfel A, Nasr MK, Kirsten H, Li Y, Hoppmann A, Gorski M, Ghasemi S, Li M, Tin A, Chai JF, Cocca M, Wang J, Nutile T, Akiyama M, Åsvold BO, Bansal N, Biggs ML, Boutin T, Brenner H, Brumpton B, Burkhardt R, Cai J, Campbell A, Campbell H, Chalmers J, Chasman DI, Chee ML, Chee ML, Chen X, Cheng CY, Cifkova R, Daviglus M, Delgado G, Dittrich K, Edwards TL, Endlich K, Michael Gaziano J, Giri A, Giulianini F, Gordon SD, Gudbjartsson DF, Hallan S, Hamet P, Hartman CA, Hayward C, Heid IM, Hellwege JN, Holleczek B, Holm H, Hutri-Kähönen N, Hveem K, Isermann B, Jonas JB, Joshi PK, Kamatani Y, Kanai M, Kastarinen M, Khor CC, Kiess W, Kleber ME, Körner A, Kovacs P, Krajcoviechova A, Kramer H, Krämer BK, Kuokkanen M, Kähönen M, Lange LA, Lash JP, Lehtimäki T, Li H, Lin BM, Liu J, Loeffler M, Lyytikäinen LP, Magnusson PKE, Martin NG, Matsuda K, Milaneschi Y, Mishra PP, Mononen N, Montgomery GW, Mook-Kanamori DO, Mychaleckyj JC, März W, Nauck M, Nikus K, Nolte IM, Noordam R, Okada Y, Olafsson I, Oldehinkel AJ, Penninx BWJH, Perola M, Pirastu N, Polasek O, Porteous DJ, Poulain T, Psaty BM, Rabelink TJ, Raffield LM, Raitakari OT, Rasheed H, Reilly DF, Rice KM, Richmond A, Ridker PM, Rotter JI, Rudan I, Sabanayagam C, Salomaa V, Schneiderman N, Schöttker B, Sims M, Snieder H, Stark KJ, Stefansson K, Stocker H, Stumvoll M, Sulem P, Sveinbjornsson G, Svensson PO, Tai ES, Taylor KD, Tayo BO, Teren A, Tham YC, Thiery J, Thio CHL, Thomas LF, Tremblay J, Tönjes A, van der Most PJ, Vitart V, Völker U, Wang YX, Wang C, Wei WB, Whitfield JB, Wild SH, Wilson JF, Winkler TW, Wong TY, Woodward M, Sim X, Chu AY, Feitosa MF, Thorsteinsdottir U, Hung AM, Teumer A, Franceschini N, Parsa A, Köttgen A, Schlosser P, Pattaro C.

Nat Commun. 2024 Jan 18;15(1):586. doi: 10.1038/s41467-024-44709-1.

PMID: 38233393 Free PMC article.

 

Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes. 

Bradfield JP, Kember RL, Ulrich A, Balkiyarova Z, Alyass A, Aris IM, Bell JA, Broadaway KA, Chen Z, Chai JF, Davies NM, Fernandez-Orth D, Bustamante M, Fore R, Ganguli A, Heiskala A, Hottenga JJ, Íñiguez C, Kobes S, Leinonen J, Lowry E, Lyytikainen LP, Mahajan A, Pitkänen N, Schnurr TM, Have CT, Strachan DP, Thiering E, Vogelezang S, Wade KH, Wang CA, Wong A, Holm LA, Chesi A, Choong C, Cruz M, Elliott P, Franks S, Frithioff-Bøjsøe C, Gauderman WJ, Glessner JT, Gilsanz V, Griesman K, Hanson RL, Kaakinen M, Kalkwarf H, Kelly A, Kindler J, Kähönen M, Lanca C, Lappe J, Lee NR, McCormack S, Mentch FD, Mitchell JA, Mononen N, Niinikoski H, Oken E, Pahkala K, Sim X, Teo YY, Baier LJ, van Beijsterveldt T, Adair LS, Boomsma DI, de Geus E, Guxens M, Eriksson JG, Felix JF, Gilliland FD, Biobank PM, Hansen T, Hardy R, Hivert MF, Holm JC, Jaddoe VWV, Järvelin MR, Lehtimäki T, Mackey DA, Meyre D, Mohlke KL, Mykkänen J, Oberfield S, Pennell CE, Perry JRB, Raitakari O, Rivadeneira F, Saw SM, Sebert S, Shepherd JA, Standl M, Sørensen TIA, Timpson NJ, Torrent M, Willemsen G, Hypponen E, Power C; Early Growth Genetics Consortium; McCarthy MI, Freathy RM, Widén E, Hakonarson H, Prokopenko I, Voight BF, Zemel BS, Grant SFA, Cousminer DL.

Genome Biol. 2024 Jan 16;25(1):22. doi: 10.1186/s13059-023-03136-z.

PMID: 38229171 Free PMC article.

 

Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. 

Shahir JA, Stanley N, Purvis JE.

BMC Bioinformatics. 2024 Jan 15;25(1):25. doi: 10.1186/s12859-024-05641-9.

PMID: 38221640 Free PMC article.

 

FGFR inhibition augments anti-PD-1 efficacy in murine FGFR3-mutant bladder cancer by abrogating immunosuppression. 

Okato A, Utsumi T, Ranieri M, Zheng X, Zhou M, Pereira LD, Chen T, Kita Y, Wu D, Hyun H, Lee H, Gdowski AS, Raupp JD, Clark-Garvey S, Manocha U, Chafitz A, Sherman F, Stephens J, Rose TL, Milowsky MI, Wobker SE, Serody JS, Damrauer JS, Wong KK, Kim WY.

J Clin Invest. 2024 Jan 16;134(2):e169241. doi: 10.1172/JCI169241.

PMID: 38226620 Free PMC article.