Department of Genetics Publications for February 26th – March 11th, 2023

Department of Genetics faculty, postdocs, students and collaborators published 12 papers during February 26^th – March 11^th, 2023.

 

IntroUNET: identifying introgressed alleles via semantic segmentation. 

Ray DD, Flagel L, Schrider DR.

bioRxiv. 2023 Feb 7:2023.02.07.527435. doi: 10.1101/2023.02.07.527435. Preprint.

PMID: 36865105 Free PMC article.

 

Landscape of Genetic Alterations Underlying Hallmark Signature Changes in Cancer Reveals TP53Aneuploidy-driven Metabolic Reprogramming. 

McClure MB, Kogure Y, Ansari-Pour N, Saito Y, Chao HH, Shepherd J, Tabata M, Olopade OI, Wedge DC, Hoadley KA, Perou CM, Kataoka K.

Cancer Res Commun. 2023 Feb 16;3(2):281-296. doi: 10.1158/2767-9764.CRC-22-0073. eCollection 2023 Feb.

PMID: 36860655 Free PMC article.

 

Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer. 

Prat A, Brasó-Maristany F, Martínez-Sáez O, Sanfeliu E, Xia Y, Bellet M, Galván P, Martínez D, Pascual T, Marín-Aguilera M, Rodríguez A, Chic N, Adamo B, Paré L, Vidal M, Margelí M, Ballana E, Gómez-Rey M, Oliveira M, Felip E, Matito J, Sánchez-Bayona R, Suñol A, Saura C, Ciruelos E, Tolosa P, Muñoz M, González-Farré B, Villagrasa P, Parker JS, Perou CM, Vivancos A.

Nat Commun. 2023 Mar 1;14(1):1157. doi: 10.1038/s41467-023-36801-9.

PMID: 36859416 Free PMC article.

 

Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS. 

Chen J, Luo T, Jiang M, Liu J, Gupta GP, Li Y.

Sci Adv. 2023 Mar;9(9):eadd9818. doi: 10.1126/sciadv.add9818. Epub 2023 Mar 1.

PMID: 36857450 Free PMC article.

 

Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing. 

Salzler HR, Vandadi V, McMichael BD, Brown JC, Boerma SA, Leatham-Jensen MP, Adams KM, Meers MP, Simon JM, Duronio RJ, McKay DJ, Matera AG.

Sci Adv. 2023 Mar;9(9):eadf2451. doi: 10.1126/sciadv.adf2451. Epub 2023 Mar 1.

PMID: 36857457 Free PMC article.

 

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data. 

Masson HO, Borland D, Reilly J, Telleria A, Shrivastava S, Watson M, Bustillos L, Li Z, Capps L, Kellman BP, King ZA, Richelle A, Lewis NE, Robasky K.

STAR Protoc. 2023 Jan 25;4(1):102069. doi: 10.1016/j.xpro.2023.102069. Online ahead of print.

PMID: 36853701 Free PMC article.

 

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundumKunth). 

Ramirez-Villacis DX, Pinos-Leon A, Vega-Polo P, Salas-González I, Jones CD, Torres ML.

Microorganisms. 2023 Feb 4;11(2):399. doi: 10.3390/microorganisms11020399.

PMID: 36838364 Free PMC article.

 

Fate of arsenicals in mice carrying the human AS3MT gene exposed to environmentally relevant levels of arsenite in drinking water. 

Douillet C, Miller M, Cable PH, Shi Q, El-Masri H, Matoušek T, Koller BH, Thomas DJ, Stýblo M.

Sci Rep. 2023 Mar 4;13(1):3660. doi: 10.1038/s41598-023-30723-8.

PMID: 36871058 Free PMC article.

 

Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC. 

Awoniyi M, Wang J, Ngo B, Meadows V, Tam J, Viswanathan A, Lai Y, Montgomery S, Farmer M, Kummen M, Thingholm L, Schramm C, Bang C, Franke A, Lu K, Zhou H, Bajaj JS, Hylemon PB, Ting J, Popov YV, Hov JR, Francis HL, Sartor RB.

Gut. 2023 Apr;72(4):671-685. doi: 10.1136/gutjnl-2021-326500. Epub 2022 Jun 15.

PMID: 35705368

 

Polishing de novo nanopore assemblies of bacteria and eukaryotes with FMLRC2. 

Mak QXC, Wick RR, Holt JM, Wang JR.

Mol Biol Evol. 2023 Mar 3:msad048. doi: 10.1093/molbev/msad048. Online ahead of print.

PMID: 36869750

 

Maternal Malignancy After Atypical Findings on Single-Nucleotide Polymorphism-Based Prenatal Cell-Free DNA Screening. 

Goldring G, Trotter C, Meltzer JT, Souter V, Pais L, DiNonno W, Xu W, Weitzel JN, Vora NL.

Obstet Gynecol. 2023 Mar 9. doi: 10.1097/AOG.0000000000005107. Online ahead of print.

PMID: 36897127

 

Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data. 

Guan PY, Lee JS, Wang L, Lin KZ, Mei W, Chen L, Jiang Y.

Front Genet. 2023 Feb 17;14:1089936. doi: 10.3389/fgene.2023.1089936. eCollection 2023.

PMID: 36873935 Free PMC article.