Department of Genetics Publications for May 21st – June 3rd, 2023

Department of Genetics faculty, postdocs, students and collaborators published 15 papers during May 21^st – June 3^rd, 2023.

 

A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data. 

Little P, Liu S, Zhabotynsky V, Li Y, Lin DY, Sun W.

Nat Commun. 2023 May 25;14(1):3030. doi: 10.1038/s41467-023-38795-w.

PMID: 37231002

 

Canonical correlation analysis for multi-omics: Application to cross-cohort analysis. 

Jiang MZ, Aguet F, Ardlie K, Chen J, Cornell E, Cruz D, Durda P, Gabriel SB, Gerszten RE, Guo X, Johnson CW, Kasela S, Lange LA, Lappalainen T, Liu Y, Reiner AP, Smith J, Sofer T, Taylor KD, Tracy RP, VanDenBerg DJ, Wilson JG, Rich SS, Rotter JI, Love MI, Raffield LM, Li Y; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Analysis Working Group.

PLoS Genet. 2023 May 22;19(5):e1010517. doi: 10.1371/journal.pgen.1010517. Online ahead of print.

PMID: 37216410

 

Information-Seeking Preferences in Diverse Patients Receiving a Genetic Testing Result in the Clinical Sequencing Evidence-Generating Research (CSER) Study. 

Slavotinek A, Prasad H, Outram S, Scollon S, Rego S, Yip T, Hoban H, Foreman KM, Kelley W, Finnila C, Berg J, Murali P, Bonini KE, Martin LJ, Hott A.

Genet Med. 2023 May 19:100899. doi: 10.1016/j.gim.2023.100899. Online ahead of print.

PMID: 37212252

 

Empirical evidence that complexity limits horizontal gene transfer. 

Burch CL, Romanchuk A, Kelly M, Wu Y, Jones CD.

Genome Biol Evol. 2023 May 26:evad089. doi: 10.1093/gbe/evad089. Online ahead of print.

PMID: 37232518

 

Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. 

Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE.

Nat Struct Mol Biol. 2023 May 25. doi: 10.1038/s41594-023-00991-z. Online ahead of print.

PMID: 37231153

 

A tissue dissociation method for ATAC-seq and CUT&RUN in Drosophila pupal tissues. 

Buchert EM, Fogarty EA, Uyehara CM, McKay DJ, Buttitta LA.

Fly (Austin). 2023 Dec;17(1):2209481. doi: 10.1080/19336934.2023.2209481.

PMID: 37211836 Free PMC article.

 

Heart-brain connections: Phenotypic and genetic insights from magnetic resonance images. 

Zhao B, Li T, Fan Z, Yang Y, Shu J, Yang X, Wang X, Luo T, Tang J, Xiong D, Wu Z, Li B, Chen J, Shan Y, Tomlinson C, Zhu Z, Li Y, Stein JL, Zhu H.

Science. 2023 Jun 2;380(6648):abn6598. doi: 10.1126/science.abn6598. Epub 2023 Jun 2.

PMID: 37262162

 

Inferring cell-type-specific causal gene regulatory networks during human neurogenesis. 

Aygün N, Liang D, Crouse WL, Keele GR, Love MI, Stein JL.

Genome Biol. 2023 May 30;24(1):130. doi: 10.1186/s13059-023-02959-0.

PMID: 37254169 Free PMC article.

 

Effect of Viral Strain and Host Age on Clinical Disease and Viral Replication in Immunocompetent Mouse Models of Chikungunya Encephalomyelitis. 

Anderson EJ, Knight AC, Heise MT, Baxter VK.

Viruses. 2023 Apr 26;15(5):1057. doi: 10.3390/v15051057.

PMID: 37243143 Free PMC article.

 

A 360° view of the inflammasome: Mechanisms of activation, cell death, and diseases. 

Barnett KC, Li S, Liang K, Ting JP.

Cell. 2023 May 25;186(11):2288-2312. doi: 10.1016/j.cell.2023.04.025.

PMID: 37236155 Review.

 

Evaluating the strength of evidence for genes implicated in peroxisomal disorders using the ClinGen clinical validity framework and providing updates to the peroxisomal disease nomenclature. 

Mohan S, Mayers M, Weaver M, Baudet H, De Biase I, Goldstein J, Mao R, McGlaughon J, Moser A, Pujol A, Suchy S, Yuzyuk T, Braverman NE.

Mol Genet Metab. 2023 May 11;139(3):107604. doi: 10.1016/j.ymgme.2023.107604. Online ahead of print.

PMID: 37236006

 

Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1. 

Shi W, Scialdone AP, Emerson JI, Mei L, Wasson LK, Davies HA, Seidman CE, Seidman JG, Cook JG, Conlon FL.

Circ Res. 2023 May 31. doi: 10.1161/CIRCRESAHA.122.322223. Online ahead of print.

PMID: 37254794

 

MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients. 

Gonzalez RD, Small GW, Green AJ, Akhtari FS, Motsinger-Reif AA, Quintanilha JCF, Havener TM, Reif DM, McLeod HL, Wiltshire T.

Pharmaceuticals (Basel). 2023 May 17;16(5):757. doi: 10.3390/ph16050757.

PMID: 37242540 Free PMC article.

 

RYK Gene Expression Associated with Drug Response Variation of Temozolomide and Clinical Outcomes in Glioma Patients. 

Gonzalez RD, Small GW, Green AJ, Akhtari FS, Havener TM, Quintanilha JCF, Cipriani AB, Reif DM, McLeod HL, Motsinger-Reif AA, Wiltshire T.

Pharmaceuticals (Basel). 2023 May 10;16(5):726. doi: 10.3390/ph16050726.

PMID: 37242509 Free PMC article.

 

Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. ‘Natal Brier’. 

Ramirez-Villacis DX, Erazo-Garcia P, Quijia-Pillajo J, Llerena-Llerena S, Barriga-Medina N, Jones CD, Leon-Reyes A.

Biology (Basel). 2023 Apr 27;12(5):663. doi: 10.3390/biology12050663.

PMID: 37237477 Free PMC article.