Publications

GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. Mitchell Conery, James A. Pippin, Yadav Wagley, Khanh Trang1, Matthew C. Pahl, David A. Villani, Lacey J. Favazzo, Cheryl L. Ackert‑Bicknell, Michael J. Zuscik, Eugene Katsevich, Andrew D. Wells, Babette S. Zemel, Benjamin F. Voight, Kurt D. Hankenson, Alessandra Chesi, and Struan F. A. Grant. Genome Biol 26, 331 (2025). https://doi.org/10.1186/s13059-025-03802-4.

Complex genetic variation in nearly complete human genomes. Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Scholz S, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T.  Nature 2025 Jul 23. doi: 10.1038/s41586-025-09140-6. 

Exclusion-based exome sequencing in critically ill adults 18–40 years old has a 24% diagnostic rate and finds racial disparities in access to genetic testing. Jessica I. Gold, Colleen M. Kripke, Regeneron Genetics Center, Penn Medicine BioBank, Theodore G. Drivas. Am J Hum Genet. 2025 Jun 30:S0002-9297(25)00238-1.

Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae. Large CRL, Khanal R, Hillier L, Huynh C, Kubo C, Kim J, Waterston RH, Murray JI. Science. 2025 Jun 19;388(6753):eadu8249.

Characterization of non-coding variants associated with transcription-factor binding through ATAC-seq-defined footprint QTLs in liver. Dudek MF, Wenz BM, Brown CD, Voight BF, Almasy L, Grant SFA. Am J Hum Genet. 2025 Apr 10:S0002-9297(25)00140-5.

A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice. Trigg NA, Zhou SK, Harris JC, Lamonica MN, Nelson MA, Silverman MA, Kambayashi T, Conine CC. Reproduction. 2025 Mar 4;169(4):e240204. 

Nuclear speckles regulate functional programs in cancer. Alexander KA, Yu R, Skuli N, Coffey NJ, Nguyen S, Faunce CL, Huang H, Dardani IP, Good AL, Lim J, Li CY, Biddle N, Joyce EF, Raj A, Lee D, Keith B, Simon MC, Berger SL. Nat Cell Biol. 2025 Feb;27(2):322-335.

 Independent genetic strategies define the scope and limits of CDKL5 deficiency disorder reversal. Song X, Xia Z, Martinez D, Xu B, Spritzer Z, Zhang Y, Nugent E, Ho Y, Terzic B, Zhou Z. Cell Rep Med. 2025 Feb 18;6(2):101926.

Insufficient evidence for natural selection associated with the Black Death. Barton AR, Santander CG, Skoglund P, Moltke I, Reich D, Mathieson I. Nature. 2025 Feb;638(8051):E19-E22.

 Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer's disease. Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins JE. Nat Commun. 2025 Jan 28;16(1):1126.

Risk factors affecting polygenic score performance across diverse cohorts. Hui D, Dudek S, Kiryluk K, Walunas TL, Kullo IJ, Wei WQ, Tiwari H, Peterson JF, Chung WK, Davis BH, Khan A, Kottyan LC, Limdi NA, Feng Q, Puckelwartz MJ, Weng C, Smith JL, Karlson EW; Regeneron Genetics Center; Penn Medicine BioBank; Jarvik GP, Ritchie MD. Elife. 2025 Jan 24;12:RP88149.

G6PC2 controls glucagon secretion by defining the set point for glucose in pancreatic α cells. Bahl V, Rifkind R, Waite E, Hamdan Z, May CL, Manduchi E, Voight BF, Lee MYY, Tigue M, Manuto N, Glaser B, Avrahami D, Kaestner KH. Sci Transl Med. 2025 Jan;17(779):eadi6148.

 The Pax transcription factor EGL-38 links EGFR signaling to assembly of a cell type-specific apical extracellular matrix in the Caenorhabditis elegans vulva. Schmidt HF, Darwin CB, Sundaram MV. Dev Biol. 2025 Jan;517:265-277.

Bidirectional Risk Modulator and Modifier Variant of Dilated and Hypertrophic Cardiomyopathy in BAG3. Park J, Levin MG, Zhang D, Reza N, Mead JO, Carruth ED, Kelly MA, Winters A, Kripke CM, Judy RL, Damrauer SM, Owens AT, Bastarache L, Verma A, Kinnamon DD, Hershberger RE, Ritchie MD, Rader DJ. JAMA Cardiol. 2024 Dec 1;9(12):1124-1133.

FMRP regulates MFF translation to locally direct mitochondrial fission in neurons. Fenton AR, Peng R, Bond C, Hugelier S, Lakadamyali M, Chang YW, Holzbaur ELF, Jongens TA. Nat Cell Biol. 2024 Dec;26(12):2061-2074.

Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain. Harke J, Lee JR, Nguyen SC, Arab A, Rakowiecki SM, Hugelier S, Paliou C, Rauseo A, Yunker R, Xu K, Yao Y, Lakadamyali M, Andrey G, Epstein DJ, Joyce EF. Mol Cell. 2024 Dec 19;84(24):4698-4710.e6.

 Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data. Aubin RG, Montelongo J, Hu R, Gunther E, Nicodemus P, Camara PG. Cell Rep Methods. 2024 Nov 18;4(11):100905.

Conserved autism-associated genes tune social feeding behavior in C. elegans. Cowen MH, Haskell D, Zoga K, Reddy KC, Chalasani SH, Hart MP. Nat Commun. 2024 Oct 28;15(1):9301.

 Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads. Han SW, Jewell S, Thomas-Tikhonenko A, Barash Y. Genome Res. 2024 Oct 29;34(10):1624-1635.

Pooled endogenous protein tagging and recruitment for systematic profiling of protein function. Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O. Cell Genom. 2024 Oct 9;4(10):100651.

 Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Mol Cell. 2024 Aug 8;84(15):2822-2837.e11.

 Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Nat Biotechnol. 2024 Jun;42(6):960-974.

Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Patil AR, Schug J, Liu C, Lahori D, Descamps HC; Human Pancreas Analysis Consortium; Naji A, Kaestner KH, Faryabi RB, Vahedi G. Cell Rep Med. 2024 May 21;5(5):101535.

Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Nat Genet. 2024 Feb;56(2):258-272.

Unveiling recent and ongoing adaptive selection in human populations. Gao Z. PLoS Biol. 2024 Jan 18;22(1):e3002469.

Sweat gland development requires an eccrine dermal niche and couples two epidermal programs. Dingwall HL, Tomizawa RR, Aharoni A, Hu P, Qiu Q, Kokalari B, Martinez SM, Donahue JC, Aldea D, Mendoza M, Glass IA; Birth Defects Research Laboratory (BDRL); Wu H, Kamberov YG. Dev Cell. 2024 Jan 8;59(1):20-32.e6.