Department of Genetics

2023

Transcription factor fluctuations underlie cell-to-cell variability in a signaling pathway response

Ramu, A. & Cohen, B. A., Jul 2023, In: Genetics. 224, 3, iyad094.

Research output: Contribution to journal › Article › peer-review

Open Access

Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome

Russell, S. K., Harrison, J. K., Olson, B. S., Lee, H. J., O’Brien, V. P., Xing, X., Livny, J., Yu, L., Roberson, E. D. O., Bomjan, R., Fan, C., Sha, M., Estfanous, S., Amer, A. O., Colonna, M., Stappenbeck, T. S., Wang, T., Hannan, T. J. & Hultgren, S. J., May 2023, In: Nature microbiology. 8, 5, p. 875-888 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Maeng, J. H., Jang, H. J., Du, A. Y., Tzeng, S. C. & Wang, T., Dec 2023, In: Genome research. 33, 12, p. 2143-2155 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants

Young, K. L., Fisher, V., Deng, X., Brody, J. A., Graff, M., Lim, E., Lin, B. M., Xu, H., Amin, N., An, P., Aslibekyan, S., Fohner, A. E., Hidalgo, B., Lenzini, P., Kraaij, R., Medina-Gomez, C., Prokić, I., Rivadeneira, F., Sitlani, C. & Tao, R. & 42 others, van Rooij, J., Zhang, D., Broome, J. G., Buth, E. J., Heavner, B. D., Jain, D., Smith, A. V., Barnes, K., Boorgula, M. P., Chavan, S., Darbar, D., De Andrade, M., Guo, X., Haessler, J., Irvin, M. R., Kalyani, R. R., Kardia, S. L. R., Kooperberg, C., Kim, W., Mathias, R. A., McDonald, M. L., Mitchell, B. D., Peyser, P. A., Regan, E. A., Redline, S., Reiner, A. P., Rich, S. S., Rotter, J. I., Smith, J. A., Weiss, S., Wiggins, K. L., Yanek, L. R., Arnett, D., Heard-Costa, N. L., Leal, S., Lin, D., McKnight, B., Province, M., van Duijn, C. M., North, K. E., Cupples, L. A. & Liu, C. T., Jan 12 2023, In: Human Genetics and Genomics Advances. 4, 1, 100163.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Choudhary, M. N. K., Quaid, K., Xing, X., Schmidt, H. & Wang, T., Dec 2023, In: Nature communications. 14, 1, 634.

Research output: Contribution to journal › Article › peer-review

Open Access

25 Scopus citations

Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode

Recio, P. S., Mitra, N. J., Shively, C. A., Song, D., Jaramillo, G., Lewis, K. S., Chen, X. & Mitra, R. D., Jun 9 2023, In: Nucleic acids research. 51, 10, p. 5006-5021 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2024

Adipocyte-specific inactivation of NAMPT, a key NAD⁺ biosynthetic enzyme, causes a metabolically unhealthy lean phenotype in female mice during aging

Qi, N., Franczyk, M. P., Yamaguchi, S., Kojima, D., Hayashi, K., Satoh, A., Ogiso, N., Kanda, T., Sasaki, Y., Finck, B. N., DeBosch, B. J. & Yoshino, J., Jul 2024, In: American Journal of Physiology - Endocrinology and Metabolism. 327, 1, p. E81-E88

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels

Trans-Omics for Precision Medicine (TOPMed) program, The INVENT Consortium, de Vries, P. S., Reventun, P., Brown, M. R., Heath, A. S., Huffman, J. E., Le, N. Q., Bebo, A., Brody, J. A., Temprano-Sagrera, G., Raffield, L. M., Ozel, A. B., Thibord, F., Jain, D., Lewis, J. P., Rodriguez, B. A. T., Pankratz, N., Taylor, K. D. & Polasek, O. & 182 others, Chen, M. H., Yanek, L. R., Carrasquilla, G. D., Marioni, R. E., Kleber, M. E., Trégouët, D. A., Yao, J., Li-Gao, R., Joshi, P. K., Trompet, S., Martinez-Perez, A., Ghanbari, M., Howard, T. E., Reiner, A. P., Arvanitis, M., Ryan, K. A., Bartz, T. M., Rudan, I., Faraday, N., Linneberg, A., Ekunwe, L., Davies, G., Delgado, G. E., Suchon, P., Guo, X., Rosendaal, F. R., Klaric, L., Noordam, R., van Rooij, F., Curran, J. E., Wheeler, M. M., Osburn, W. O., O'Connell, J. R., Boerwinkle, E., Beswick, A., Psaty, B. M., Kolcic, I., Souto, J. C., Becker, L. C., Hansen, T., Doyle, M. F., Harris, S. E., Moissl, A. P., Deleuze, J. F., Rich, S. S., van Hylckama Vlieg, A., Campbell, H., Stott, D. J., Soria, J. M., de Maat, M. P. M., Almasy, L., Brody, L. C., Auer, P. L., Abe, N., Abecasis, G., Aguet, F., Albert, C., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Blue, N., Bowden, D. W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carson, A. P., Carty, C., Casaburi, R., Casas Romero, J. P., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Ida Chen, Y. D., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Correa, A., Crandall, C., Crapo, J., Cupples, L. A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., de las Fuentes, L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Durda, J. P., Dutcher, S. K., Eaton, C., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Gu, C. C., Rao, D. C. & Sung, Y. J., May 2 2024, In: Blood. 143, 18, p. 1845-1855 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

A genetic screen in Drosophila uncovers a role for senseless-2 in surface glia in the peripheral nervous system to regulate CNS morphology

Lacin, H., Zhu, Y., DiPaola, J. T., Wilson, B. A., Zhu, Y. & Skeath, J. B., Sep 2024, In: G3: Genes, Genomes, Genetics. 14, 9, jkae152.

Research output: Contribution to journal › Article › peer-review

Open Access

A methodology for gene level omics-WAS integration identifies genes influencing traits associated with cardiovascular risks: the Long Life Family Study

Acharya, S., Liao, S., Jung, W. J., Kang, Y. S., Moghaddam, V. A., Feitosa, M. F., Wojczynski, M., Lin, S., Anema, J. A., Schwander, K., Connell, J. O., Province, M. & Brent, M. R., Oct 2024, In: Human genetics. 143, 9-10, p. 1241-1252 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

A microbiome-directed therapeutic food for children recovering from severe acute malnutrition

Hartman, S. J., Hibberd, M. C., Mostafa, I., Naila, N. N., Islam, M. M., Zaman, M. U., Huq, S., Mahfuz, M., Islam, M. T., Mukherji, K., Moghaddam, V. A., Chen, R. Y., Province, M. A., Webber, D. M., Henrissat, S., Henrissat, B., Terrapon, N., Rodionov, D. A., Osterman, A. L. & Barratt, M. J. & 2 others, Ahmed, T. & Gordon, J. I., Oct 2 2024, In: Science translational medicine. 16, 767, eadn2366.

Research output: Contribution to journal › Article › peer-review

Open Access

A molecular mechanism for bright color variation in parrots

Arbore, R., Barbosa, S., Brejcha, J., Ogawa, Y., Liu, Y., Nicolaï, M. P. J., Pereira, P., Sabatino, S. J., Cloutier, A., Poon, E. S. K., Marques, C. I., Andrade, P., Debruyn, G., Afonso, S., Afonso, R., Roy, S. G., Abdu, U., Lopes, R. J., Mojzeš, P. & Maršík, P. & 5 others, Sin, S. Y. W., White, M. A., Araújo, P. M., Corbo, J. C. & Carneiro, M., Nov 1 2024, In: Journal of Bio-X Research. 386, 6721, eadp7710.

Research output: Contribution to journal › Article › peer-review

An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination

Barclay, K. M., Abduljawad, N., Cheng, Z., Kim, M. W., Zhou, L., Yang, J., Rustenhoven, J., Mazzitelli, J. A., Smyth, L. C. D., Kapadia, D., Brioschi, S., Beatty, W., Hou, J. C., Saligrama, N., Colonna, M., Yu, G., Kipnis, J. & Li, Q., Jun 11 2024, In: Immunity. 57, 6, p. 1394-1412.e8

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus

Singh, A. K., Allington, G., Viviano, S., McGee, S., Kiziltug, E., Ma, S., Zhao, S., Mekbib, K. Y., Shohfi, J. P., Duy, P. Q., DeSpenza, T., Furey, C. G., Reeves, B. C., Smith, H., Sousa, A. M. M., Cherskov, A., Allocco, A., Nelson-Williams, C., Haider, S. & Rizvi, S. R. A. & 10 others, Alper, S. L., Sestan, N., Shimelis, H., Walsh, L. K., Lifton, R. P., Moreno-De-Luca, A., Jin, S. C., Kruszka, P., Deniz, E. & Kahle, K. T., Apr 1 2024, In: Brain. 147, 4, p. 1553-1570 18 p.

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Assembly of FAP93 at the proximal axoneme in Chlamydomonas cilia

Hwang, J., Yanagisawa, H., Davis, K. C., Hunter, E. L., Fox, L. A., Jimenez, A. R., Goodwin, R. E., Gordon, S. A., Stuart, C. D. E., Bower, R., Porter, M. E., Dutcher, S. K., Sale, W. S., Lechtreck, K. F. & Alford, L. M., Nov 2024, In: Cytoskeleton. 81, 11, p. 539-555 17 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3

Undiagnosed Diseases Network, Paul, M. S., Michener, S. L., Pan, H., Chan, H., Pfliger, J. M., Rosenfeld, J. A., Lerma, V. C., Tran, A., Longley, M. A., Lewis, R. A., Weisz-Hubshman, M., Bekheirnia, M. R., Bekheirnia, N., Massingham, L., Zech, M., Wagner, M., Engels, H., Cremer, K. & Mangold, E. & 181 others, Peters, S., Trautmann, J., Mester, J. L., Guillen Sacoto, M. J., Person, R., McDonnell, P. P., Cohen, S. R., Lusk, L., Cohen, A. S. A., Le Pichon, J. B., Pastinen, T., Zhou, D., Engleman, K., Racine, C., Faivre, L., Moutton, S., Denommé-Pichon, A. S., Koh, H. Y., Poduri, A., Bolton, J., Knopp, C., Julia Suh, D. S., Maier, A., Toosi, M. B., Karimiani, E. G., Maroofian, R., Schaefer, G. B., Ramakumaran, V., Vasudevan, P., Prasad, C., Osmond, M., Schuhmann, S., Vasileiou, G., Russ-Hall, S., Scheffer, I. E., Carvill, G. L., Mefford, H., Acosta, M. T., Adam, M., Adams, D. R., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C. P., Chanprasert, S., Chao, H. T., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A. S., Mahoney, R., Pak, S., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Jan 4 2024, In: American journal of human genetics. 111, 1, p. 96-118 23 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Baf155 controls hematopoietic differentiation and regeneration through chromatin priming

Wu, J., Fan, C., Kabir, A. U., Krchma, K., Kim, M., Kwon, Y., Xing, X., Wang, T. & Choi, K., Aug 27 2024, In: Cell Reports. 43, 8, 114558.

Research output: Contribution to journal › Article › peer-review

Open Access

BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data

Tian, W., Ding, W., Shen, J., Li, D., Wang, T. & Ecker, J. R., Jul 1 2024, In: Bioinformatics. 40, 7, btae404.

Research output: Contribution to journal › Article › peer-review

Open Access

Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections

Deciphering Developmental Disorders, Genomics England Research Consortium, Undiagnosed Disease Network, Jeffries, L., Mis, E. K., McWalter, K., Donkervoort, S., Brodsky, N. N., Carpier, J. M., Ji, W., Ionita, C., Roy, B., Morrow, J. S., Darbinyan, A., Iyer, K., Aul, R. B., Banka, S., Chao, K. R., Cobbold, L. & Cohen, S. & 183 others, Custodio, H. M., Drummond-Borg, M., Elmslie, F., Finanger, E., Hainline, B. E., Helbig, I., Hewson, S., Hu, Y., Jackson, A., Josifova, D., Konstantino, M., Leach, M. E., Mak, B., McCormick, D., McGee, E., Nelson, S., Nguyen, J., Nugent, K., Ortega, L., Goodkin, H. P., Roeder, E., Roy, S., Sapp, K., Saade, D., Sisodiya, S. M., Stals, K., Towner, S., Wilson, W., Borras, S., Clark, C., Dean, J., Miedzybrodzka, Z., Ross, A., Tennant, S., Dabir, T., Donnelly, D., Humphreys, M., Magee, A., McConnell, V., McKee, S., McNerlan, S., Morrison, P. J., Rea, G., Stewart, F., Cole, T., Cooper, N., Cooper-Charles, L., Cox, H., Islam, L., Jarvis, J., Keelagher, R., Lim, D., McMullan, D., Morton, J., Naik, S., O'Driscoll, M., Ong, K. R., Osio, D., Ragge, N., Turton, S., Vogt, J., Williams, D., Bodek, S., Donaldson, A., Hills, A., Low, K., Newbury-Ecob, R., Norman, A. M., Roberts, E., Scurr, I., Smithson, S., Tooley, M., Abbs, S., Armstrong, R., Dunn, C., Holden, S., Park, S. M., Paterson, J., Raymond, L., Reid, E., Sandford, R., Simonic, I., Tischkowitz, M., Woods, G., Bradley, L., Comerford, J., Green, A., Lynch, S., McQuaid, S., Mullaney, B., Berg, J., Goudie, D., Mavrak, E., McLean, J., McWilliam, C., Reavey, E., Azam, T., Cleary, E., Jackson, A., Lam, W., Lampe, A., Moore, D., Porteous, M., Baple, E., Baptista, J., Brewer, C., Castle, B., Kivuva, E., Owens, M., Rankin, J., Shaw-Smith, C., Turner, C., Turnpenny, P., Tysoe, C., Bradley, T., Davidson, R., Gardiner, C., Joss, S., Kinning, E., Longman, C., McGowan, R., Murday, V., Pilz, D., Tobias, E., Whiteford, M., Williams, N., Barnicoat, A., Clement, E., Faravelli, F., Hurst, J., Jenkins, L., Jones, W., Ajith Kumar, V. K., Lees, M., Loughlin, S., Male, A., Morrogh, D., Rosser, E., Scott, R., Wilson, L., Beleza, A., Deshpande, C., Flinter, F., Holder, M., Irving, M., Izatt, L., Mohammed, S., Molenda, A., Robert, L., Roworth, W., Ruddy, D., Ryten, M., Yau, S., Bennett, C., Blyth, M., Campbell, J., Coates, A., Dobbie, A., Hewitt, S., Hobson, E., Jackson, E., Jewell, R., Kraus, A., Prescott, K., Sheridan, E., Thomson, J., Bradshaw, K., Dixit, A., Eason, J., Haines, R., Harrison, R., Mutch, S., Sarkar, A., Searle, C., Shannon, N., Sharif, A., Baldridge, D., Cole, F. S., Pak, S., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Feb 2024, In: Genetics in Medicine. 26, 2, 101023.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Brain malformations and seizures by impaired chaperonin function of TRiC

Kraft, F., Rodriguez-Aliaga, P., Yuan, W., Franken, L., Zajt, K., Hasan, D., Lee, T. T., Flex, E., Hentschel, A., Innes, A. M., Zheng, B., Suh, D. S. J., Knopp, C., Lausberg, E., Krause, J., Zhang, X., Trapane, P., Carroll, R., McClatchey, M. & Fry, A. E. & 67 others, Wang, L., Giesselmann, S., Hoang, H., Baldridge, D., Silverman, G., Radio, F. C., Bertini, E., Ciolfi, A., Blood, K. A., de Sainte Agathe, J. M., Charles, P., Bergant, G., Čuturilo, G., Peterlin, B., Diderich, K., Streff, H., Robak, L., Oegema, R., van Binsbergen, E., Herriges, J., Saunders, C. J., Maier, A., Wolking, S., Weber, Y., Lochmüller, H., Meyer, S., Aleman, A., Polavarapu, K., Nicolas, G., Goldenberg, A., Guyant, L., Pope, K., Hehmeyer, K. N., Monaghan, K. G., Quade, A., Smol, T., Caumes, R., Duerinckx, S., Depondt, C., Van Paesschen, W., Rieubland, C., Poloni, C., Guipponi, M., Arcioni, S., Meuwissen, M., Jansen, A. C., Rosenblum, J., Haack, T. B., Bertrand, M., Gerstner, L., Magg, J., Riess, O., Schulz, J. B., Wagner, N., Wiesmann, M., Weis, J., Eggermann, T., Begemann, M., Roos, A., Häusler, M., Schedl, T., Tartaglia, M., Bremer, J., Pak, S., Frydman, J., Elbracht, M. & Kurth, I., Nov 1 2024, In: Journal of Bio-X Research. 386, 6721, p. 516-525 10 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

The Critical Assessment of Genome Interpretation Consortium, Jain, S., Bakolitsa, C., Brenner, S. E., Radivojac, P., Moult, J., Repo, S., Hoskins, R. A., Andreoletti, G., Barsky, D., Chellapan, A., Chu, H., Dabbiru, N., Kollipara, N. K., Ly, M., Neumann, A. J., Pal, L. R., Odell, E., Pandey, G. & Peters-Petrulewicz, R. C. & 181 others, Srinivasan, R., Yee, S. F., Yeleswarapu, S. J., Zuhl, M., Adebali, O., Patra, A., Beer, M. A., Hosur, R., Peng, J., Bernard, B. M., Berry, M., Dong, S., Boyle, A. P., Adhikari, A., Chen, J., Hu, Z., Wang, R., Wang, Y., Miller, M., Wang, Y., Bromberg, Y., Turina, P., Capriotti, E., Han, J. J., Ozturk, K., Carter, H., Babbi, G., Bovo, S., Di Lena, P., Martelli, P. L., Savojardo, C., Casadio, R., Cline, M. S., De Baets, G., Bonache, S., Díez, O., Gutiérrez-Enríquez, S., Fernández, A., Montalban, G., Ootes, L., Özkan, S., Padilla, N., Riera, C., De la Cruz, X., Diekhans, M., Huwe, P. J., Wei, Q., Xu, Q., Dunbrack, R. L., Gotea, V., Elnitski, L., Margolin, G., Fariselli, P., Kulakovskiy, I. V., Makeev, V. J., Penzar, D. D., Vorontsov, I. E., Favorov, A. V., Forman, J. R., Hasenahuer, M., Fornasari, M. S., Parisi, G., Avsec, Z., Çelik, M. H., Nguyen, T. Y. D., Gagneur, J., Shi, F. Y., Edwards, M. D., Guo, Y., Tian, K., Zeng, H., Gifford, D. K., Göke, J., Zaucha, J., Gough, J., Ritchie, G. R. S., Frankish, A., Mudge, J. M., Harrow, J., Young, E. L., Yu, Y., Huff, C. D., Murakami, K., Nagai, Y., Imanishi, T., Mungall, C. J., Jacobsen, J. O. B., Kim, D., Jeong, C. S., Jones, D. T., Li, M. J., Guthrie, V. B., Bhattacharya, R., Chen, Y. C., Douville, C., Fan, J., Kim, D., Masica, D., Niknafs, N., Sengupta, S., Tokheim, C., Turner, T. N., Yeo, H. T. G., Karchin, R., Shin, S., Welch, R., Keles, S., Li, Y., Kellis, M., Corbi-Verge, C., Strokach, A. V., Kim, P. M., Klein, T. E., Mohan, R., Sinnott-Armstrong, N. A., Wainberg, M., Kundaje, A., Gonzaludo, N., Mak, A. C. Y., Chhibber, A., Lam, H. Y. K., Dahary, D., Fishilevich, S., Lancet, D., Lee, I., Bachman, B., Katsonis, P., Lua, R. C., Wilson, S. J., Lichtarge, O., Bhat, R. R., Sundaram, L., Viswanath, V., Bellazzi, R., Nicora, G., Rizzo, E., Limongelli, I., Mezlini, A. M., Chang, R., Kim, S., Lai, C., O’Connor, R., Topper, S., van den Akker, J., Zhou, A. Y., Zimmer, A. D., Mishne, G., Bergquist, T. R., Breese, M. R., Guerrero, R. F., Jiang, Y., Kiga, N., Li, B., Mort, M., Pagel, K. A., Pejaver, V., Stamboulian, M. H., Thusberg, J., Mooney, S. D., Teerakulkittipong, N., Cao, C., Kundu, K., Yin, Y., Yu, C. H., Kleyman, M., Lin, C. F., Stackpole, M., Mount, S. M., Eraslan, G., Mueller, N. S., Naito, T., Rao, A. R., Azaria, J. R., Brodie, A., Ofran, Y., Garg, A., Pal, D., Hawkins-Hooker, A., Kenlay, H., Reid, J. & Mucaki, E. J., Dec 2024, In: Genome biology. 25, 1, 53.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Catalytic isoforms of AMP-activated protein kinase differentially regulate IMPDH activity and photoreceptor neuron function

Lee, T. J., Sasaki, Y., Ruzycki, P. A., Ban, N., Lin, J. B., Wu, H. T., Santeford, A. & Apte, R. S., 2024, In: JCI Insight. 9, 4, e173707.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Characterization of early markers of disease in the mouse model of mucopolysaccharidosis IIIB

McCullough, K. B., Titus, A., Reardon, K., Conyers, S., Dougherty, J. D., Ge, X., Garbow, J. R., Dickson, P., Yuede, C. M. & Maloney, S. E., Dec 2024, In: Journal of neurodevelopmental disorders. 16, 1, 16.

Research output: Contribution to journal › Article › peer-review

Open Access

Cis-regulatory evolution of the recently expanded Ly49 gene family

Fan, C., Xing, X., Murphy, S. J. H., Poursine-Laurent, J., Schmidt, H., Parikh, B. A., Yoon, J., Choudhary, M. N. K., Saligrama, N., Piersma, S. J., Yokoyama, W. M. & Wang, T., Dec 2024, In: Nature communications. 15, 1, 4839.

Research output: Contribution to journal › Article › peer-review

Open Access

Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation

Foltz, J. A., Tran, J., Wong, P., Fan, C., Schmidt, E., Fisk, B., Becker-Hapak, M., Russler-Germain, D. A., Johnson, J., Marin, N. D., Cubitt, C. C., Pence, P., Rueve, J., Pureti, S., Hwang, K., Gao, F., Zhou, A., Foster, M., Schappe, T. & Marsala, L. & 9 others, Elliott, M., Cashen, A. F., Bednarski, J. J., Fertig, E., Griffith, O. L., Griffith, M., Wang, T., Petti, A. & Fehniger, T. A., Jun 28 2024, In: Science immunology. 9, 96, eadk4893.

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Deciphering the impact of genomic variation on function

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality

Ushiki, A., Sheng, R. R., Zhang, Y., Zhao, J., Nobuhara, M., Murray, E., Ruan, X., Rios, J. J., Wise, C. A. & Ahituv, N., Mar 26 2024, In: Cell Reports. 43, 3, 113907.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities

Undiagnosed Diseases Network, Ward, S. K., Wadley, A., Tsai, C. H., Benke, P. J., Emrick, L., Fisher, K., Houck, K. M., Dai, H., Acosta, M. T., Adam, M., Adams, D. R., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G. & Balasubramanyam, A. & 181 others, Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C. P., Chanprasert, S., Chao, H. T., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dickson, P., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A. S., Mahoney, R., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martínez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J., Nakano-Okuno, M., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Jan 2024, In: American Journal of Medical Genetics, Part A. 194, 1, p. 17-30 14 p.

Research output: Contribution to journal › Article › peer-review

De novo variants in DENND5B cause a neurodevelopmental disorder

Undiagnosed Diseases Network, Scala, M., Tomati, V., Ferla, M., Lena, M., Cohen, J. S., Fatemi, A., Brokamp, E., Bican, A., Phillips, J. A., Koziura, M. E., Nicouleau, M., Rio, M., Siquier, K., Boddaert, N., Musante, I., Tamburro, S., Baldassari, S., Iacomino, M. & Scudieri, P. & 181 others, Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Afzali, B., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Bernstein, J. A., Berry, G. T., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C. P., Chanprasert, S., Chao, H. T., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Delgado, M., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Fu, J., Gahl, W. A., Glass, I., Goddard, P. C., Godfrey, R. A., Grajewski, A., Gropman, A., Halley, M. C., Hamid, R., Hanchard, N., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A. S., Mahoney, R., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martínez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Morimoto, M., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Papp, J. C., Parker, N. H., Petcharet, L., Posey, J. E., Potocki, L., Swerdzewski, B. N. P., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Mar 7 2024, In: American journal of human genetics. 111, 3, p. 529-543 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end products using correlated meta-analyses: The Long Life Family Study

Feitosa, M. F., Lin, S. J., Acharya, S., Thyagarajan, B., Wojczynski, M. K., Kuipers, A. L., Kulminski, A., Christensen, K., Zmuda, J. M., Brent, M. R. & Province, M. A., Oct 2024, In: Aging Cell. 23, 10, e14261.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder

Undiagnosed Diseases Network, Forghani, I., Lang, S. H., Rodier, M. J., Bivona, S. A., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A. & Baldridge, D. & 181 others, Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennet, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T. C. P., Chanprasert, S., Chao, H. T., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kobren, S. N., Kohane, I. S., Kohler, J. N., Krakow, D., Krasnewich, D. M., Kravets, E., Korrick, S., Koziura, M., Krier, J. B., Lalani, S. R., Lam, B., Lam, C., LaMoure, G. L., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Mak, B. C., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martínez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Pak, S. C., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Jun 2024, In: American Journal of Medical Genetics, Part A. 194, 6, e63556.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Effect of genomic and cellular environments on gene expression noise

Hong, C. K. Y., Ramu, A., Zhao, S. & Cohen, B. A., Dec 2024, In: Genome biology. 25, 1, 137.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Environmental and genetic risk factors associated with total knee arthroplasty following cruciate ligament surgery

Inclan, P. M., Brophy, R. H., Saccone, N. L., Ma, Y., Pham, V. & Yanik, E. L., Mar 2024, In: Bone and Joint Journal. 106 B, 3, p. 249-255 7 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells

Jang, H. J., Shah, N. M., Maeng, J. H., Liang, Y., Basri, N. L., Ge, J., Qu, X., Mahlokozera, T., Tzeng, S. C., Williams, R. B., Moore, M. J., Annamalai, D., Chen, J. Y., Lee, H. J., DeSouza, P. A., Li, D., Xing, X., Kim, A. H. & Wang, T., Sep 2024, In: Nature Genetics. 56, 9, p. 1903-1913 11 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Examining Sex Differences in Autism Heritability

Sandin, S., Yip, B. H. K., Yin, W., Weiss, L. A., Dougherty, J. D., Fass, S., Constantino, J. N., Hailin, Z., Turner, T. N., Marrus, N., Gutmann, D. H., Sanders, S. J. & Christoffersson, B., Jul 3 2024, In: JAMA psychiatry. 81, 7, p. 673-680 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis

Undiagnosed Diseases Network, Pucel, J., Briere, L. C., Reuter, C., Gochyyev, P., Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D. & Bayrak-Toydemir, P. & 181 others, Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Peter Chang, T. C., Chanprasert, S., Chao, H. T., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Grajewski, A., Hadley, D., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A. S., Mahoney, R., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martínez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenthal, E., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Seto, E., Shashi, V., Shelkowitz, E., Sheppeard, S., Shin, J., Silverman, E. K., Solnica-Krezel, L. & Wambach, J., Jun 2024, In: Genetics in Medicine. 26, 6, 101115.

Research output: Contribution to journal › Article › peer-review

Factors associated with genetic markers for rotator cuff disease in patients with atraumatic rotator cuff tears

Yanik, E. L., Saccone, N. L., Aleem, A. W., Chamberlain, A. M., Zmistowski, B., Sefko, J. A. & Keener, J. D., May 2024, In: Journal of Orthopaedic Research. 42, 5, p. 934-941 8 p.

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Gene dosage of independent dynein arm motor preassembly factors influences cilia assembly in Chlamydomonas reinhardtii

Penny, G. M. & Dutcher, S. K., Mar 18 2024, In: PLoS genetics. 20, 3, 1011038.

Research output: Contribution to journal › Article › peer-review

Open Access

Genetic and multi-omic resources for Alzheimer disease and related dementia from the Knight Alzheimer Disease Research Center

Fernandez, M. V., Liu, M., Beric, A., Johnson, M., Cetin, A., Patel, M., Budde, J., Kohlfeld, P., Bergmann, K., Lowery, J., Flynn, A., Brock, W., Sanchez Montejo, B., Gentsch, J., Sykora, N., Norton, J., Gentsch, J., Valdez, O., Gorijala, P. & Sanford, J. & 24 others, Sun, Y., Wang, C., Western, D., Timsina, J., Mangetti Goncalves, T., Do, A. N., Sung, Y. J., Zhao, G., Morris, J. C., Moulder, K., Holtzman, D. M., Bateman, R. J., Karch, C., Hassenstab, J., Xiong, C., Schindler, S. E., Balls-Berry, J., Benzinger, T. L. S., Perrin, R. J., Denny, A., Snider, B. J., Stark, S. L., Ibanez, L. & Cruchaga, C., Dec 2024, In: Scientific data. 11, 1, 768.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

Biobank Japan Project, Penn Medicine BioBank, Regeneron Genetics Center, Genes & Health Research Team, eMERGE Consortium, International Consortium of Blood Pressure (ICBP), Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC), VA Million Veteran Program, AMED GRIFIN Diabetes Initiative Japan, Suzuki, K., Hatzikotoulas, K., Southam, L., Taylor, H. J., Yin, X., Lorenz, K. M., Mandla, R., Huerta-Chagoya, A., Melloni, G. E. M., Kanoni, S. & Rayner, N. W. & 189 others, Bocher, O., Arruda, A. L., Sonehara, K., Namba, S., Lee, S. S. K., Preuss, M. H., Petty, L. E., Schroeder, P., Vanderwerff, B., Kals, M., Bragg, F., Lin, K., Guo, X., Zhang, W., Yao, J., Kim, Y. J., Graff, M., Takeuchi, F., Nano, J., Lamri, A., Nakatochi, M., Moon, S., Scott, R. A., Cook, J. P., Lee, J. J., Pan, I., Taliun, D., Parra, E. J., Chai, J. F., Bielak, L. F., Tabara, Y., Hai, Y., Thorleifsson, G., Grarup, N., Sofer, T., Wuttke, M., Sarnowski, C., Gieger, C., Nousome, D., Trompet, S., Kwak, S. H., Long, J., Sun, M., Tong, L., Chen, W. M., Nongmaithem, S. S., Noordam, R., Lim, V. J. Y., Tam, C. H. T., Joo, Y. Y., Chen, C. H., Raffield, L. M., Prins, B. P., Nicolas, A., Yanek, L. R., Chen, G., Brody, J. A., Kabagambe, E., An, P., Xiang, A. H., Choi, H. S., Cade, B. E., Tan, J., Broadaway, K. A., Williamson, A., Kamali, Z., Cui, J., Thangam, M., Adair, L. S., Adeyemo, A., Aguilar-Salinas, C. A., Ahluwalia, T. S., Anand, S. S., Bertoni, A., Bork-Jensen, J., Brandslund, I., Buchanan, T. A., Burant, C. F., Butterworth, A. S., Canouil, M., Chan, J. C. N., Chang, L. C., Chee, M. L., Chen, J., Chen, S. H., Chen, Y. T., Chen, Z., Chuang, L. M., Cushman, M., Danesh, J., Das, S. K., de Silva, H. J., Dedoussis, G., Dimitrov, L., Doumatey, A. P., Du, S., Duan, Q., Eckardt, K. U., Emery, L. S., Evans, D. S., Evans, M. K., Fischer, K., Floyd, J. S., Ford, I., Franco, O. H., Frayling, T. M., Freedman, B. I., Genter, P., Gerstein, H. C., Giedraitis, V., González-Villalpando, C., González-Villalpando, M. E., Gordon-Larsen, P., Gross, M., Guare, L. A., Hackinger, S., Hakaste, L., Han, S., Hattersley, A. T., Herder, C., Horikoshi, M., Howard, A. G., Hsueh, W., Huang, M., Huang, W., Hung, Y. J., Hwang, M. Y., Hwu, C. M., Ichihara, S., Ikram, M. A., Ingelsson, M., Islam, M. T., Isono, M., Jang, H. M., Jasmine, F., Jiang, G., Jonas, J. B., Jørgensen, T., Kamanu, F. K., Kandeel, F. R., Kasturiratne, A., Katsuya, T., Kaur, V., Kawaguchi, T., Keaton, J. M., Kho, A. N., Khor, C. C., Kibriya, M. G., Kim, D. H., Kronenberg, F., Kuusisto, J., Läll, K., Lange, L. A., Lee, K. M., Lee, M. S., Lee, N. R., Leong, A., Li, L., Li, Y., Li-Gao, R., Ligthart, S., Lindgren, C. M., Linneberg, A., Liu, C. T., Liu, J., Locke, A. E., Louie, T., Luan, J., Luk, A. O., Luo, X., Lv, J., Lynch, J. A., Lyssenko, V., Maeda, S., Mamakou, V., Mansuri, S. R., Matsuda, K., Meitinger, T., Melander, O., Metspalu, A., Mo, H., Morris, A. D., Moura, F. A., Nadler, J. L., Nalls, M. A., Nayak, U., Ntalla, I., Okada, Y. & Province, M. A., Mar 14 2024, In: Nature. 627, 8003, p. 347-357 11 p.

Research output: Contribution to journal › Article › peer-review

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55 Scopus citations

Genetic Pleiotropy Between Pulmonary Function and Age-RelatedTraits:The Long Life Family Study

Feitosa, M. F., Wojczynski, M. K., Anema, J. A., WarwickDaw, E., Wang, L., Santanasto, A. J., Nygaard, M. & Province, M. A., Mar 1 2024, In: Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 79, 3, glac046.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Genetic risk accentuates dietary effects on hepatic steatosis, inflammation and fibrosis in a population-based cohort

Chen, V. L., Du, X., Oliveri, A., Chen, Y., Kuppa, A., Halligan, B. D., Province, M. A. & Speliotes, E. K., Sep 2024, In: Journal of Hepatology. 81, 3, p. 379-388 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Genome-Wide Epistatic Network Analyses of Semantic Fluency in Older Adults

Tan, Q., Li, W., Nygaard, M., An, P., Feitosa, M., Wojczynski, M. K., Zmuda, J., Arbeev, K., Ukraintseva, S., Yashin, A., Christensen, K. & Mengel-From, J., May 2024, In: International journal of molecular sciences. 25, 10, 5257.

Research output: Contribution to journal › Article › peer-review

Open Access

HAT: De novo variant calling for highly accurate short-read and long-read sequencing data

Ng, J. K. & Turner, T. N., Jan 1 2024, In: Bioinformatics. 40, 1, btad775.

Research output: Contribution to journal › Article › peer-review

Open Access

HIV-associated gut microbial alterations are dependent on host and geographic context

Rocafort, M., Gootenberg, D. B., Luévano, J. M., Paer, J. M., Hayward, M. R., Bramante, J. T., Ghebremichael, M. S., Xu, J., Rogers, Z. H., Munoz, A. R., Okello, S., Kim, J. H., Sentongo, R., Wagubi, R., Lankowski, A., Maruapula, S., Zhao, G., Handley, S. A., Mosepele, M. & Siedner, M. J. & 1 others, Kwon, D. S., Dec 2024, In: Nature communications. 15, 1, 1055.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Identification of direct connections between the dura and the brain

Smyth, L. C. D., Xu, D., Okar, S. V., Dykstra, T., Rustenhoven, J., Papadopoulos, Z., Bhasiin, K., Kim, M. W., Drieu, A., Mamuladze, T., Blackburn, S., Gu, X., Gaitán, M. I., Nair, G., Storck, S. E., Du, S., White, M. A., Bayguinov, P., Smirnov, I. & Dikranian, K. & 2 others, Reich, D. S. & Kipnis, J., Mar 7 2024, In: Nature. 627, 8002, p. 165-173 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

44 Scopus citations

Identification of plant transcriptional activation domains

Morffy, N., Van den Broeck, L., Miller, C., Emenecker, R. J., Bryant, J. A., Lee, T. M., Sageman-Furnas, K., Wilkinson, E. G., Pathak, S., Kotha, S. R., Lam, A., Mahatma, S., Pande, V., Waoo, A., Wright, R. C., Holehouse, A. S., Staller, M. V., Sozzani, R. & Strader, L. C., Aug 1 2024, In: Nature. 632, 8023, p. 166-173 8 p.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities

Jiang, Y. Z., Ma, D., Jin, X., Xiao, Y., Yu, Y., Shi, J., Zhou, Y. F., Fu, T., Lin, C. J., Dai, L. J., Liu, C. L., Zhao, S., Su, G. H., Hou, W., Liu, Y., Chen, Q., Yang, J., Zhang, N., Zhang, W. J. & Liu, W. & 16 others, Ge, W., Yang, W. T., You, C., Gu, Y., Kaklamani, V., Bertucci, F., Verschraegen, C., Daemen, A., Shah, N. M., Wang, T., Guo, T., Shi, L., Perou, C. M., Zheng, Y., Huang, W. & Shao, Z. M., 2024, (Accepted/In press) In: Nature Cancer.

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants

Undiagnosed Diseases Network, Lu, J., Toro, C., Adams, D. R., Moreno, C. A. M., Lee, W. P., Leung, Y. Y., Harms, M. B., Vardarajan, B., Heinzen, E. L., Acosta, M. T., Adam, M., Izumi, K., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A. & Bademci, G. & 181 others, Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C. P., Chanprasert, S., Chao, H. T., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D’Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell’Angelica, E. C., Dickson, P., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A. S., Mahoney, R., Malicdan, M. C. V., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martínez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J., Nakano-Okuno, M., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Swerdzewski, B. N. P., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Schedl, T., Shin, J., Solnica-Krezel, L. & Wambach, J., Dec 2024, In: BMC genomics. 25, 1, 115.

Research output: Contribution to journal › Article › peer-review

Open Access

LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD⁺ depletion

Terao, R., Lee, T. J., Colasanti, J., Pfeifer, C. W., Lin, J. B., Santeford, A., Hase, K., Yamaguchi, S., Du, D., Sohn, B. S., Sasaki, Y., Yoshida, M. & Apte, R. S., May 28 2024, In: Cell Reports. 43, 5, 114102.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Department of Genetics

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