Department of Biochemistry and Molecular Biology

  • United States

Research Output

2020

Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis

Li, Y., Liao, Z., Luo, H., Benyoucef, A., Kang, Y., Lai, Q., Dovat, S., Miller, B., Chepelev, I., Li, Y., Zhao, K., Brand, M. & Huang, S., Apr 6 2020, In : Nucleic acids research. 48, 6, p. 3119-3133 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A master regulator of bacteroides thetaiotaomicron gut colonization controls carbohydrate utilization and an alternative protein synthesis factor

Townsend, G. E., Han, W., Schwalm, N. D., Hong, X., Bencivenga-Barry, N. A., Goodman, A. L. & Groisman, E. A., Jan 1 2020, In : mBio. 11, 1, e03221-19.

Research output: Contribution to journalArticle

Open Access

Assessing constituent volumes and morphology of bovine casein micelles using cryo-electron tomography

Hettiarachchi, C. A., Swulius, M. T. & Harte, F. M., May 2020, In : Journal of dairy science. 103, 5, p. 3971-3979 9 p.

Research output: Contribution to journalArticle

Association analysis and meta-analysis of multiallelic variants for large-scale sequence data

Jiang, Y., Chen, S., Wang, X., Liu, M., Iacono, W. G., Hewitt, J. K., Hokanson, J. E., Krauter, K., Laakso, M., Li, K. W., Lutz, S. M., McGue, M., Pandit, A., Zajac, G. J. M., Boehnke, M., Abecasis, G. R., Vrieze, S. I., Jiang, B., Zhan, X. & Liu, D. J., May 2020, In : Genes. 11, 5, 585.

Research output: Contribution to journalArticle

Open Access
Open Access

Cellular signaling and epigenetic regulation of gene expression in leukemia

Gowda, C., Song, C., Ding, Y., Iyer, S., Dhanyamraju, P. K., McGrath, M., Bamme, Y., Soliman, M., Kane, S., Payne, J. L. & Dovat, S., Jan 2020, In : Advances in Biological Regulation. 75, 100665.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Clinical and Genetic Factors Associated With Complications After Crohn's Ileocolectomy

Kline, B. P., Weaver, T., Brinton, D. L., Deiling, S., Yochum, G. S., Berg, A. S. & Koltun, W. A., Mar 1 2020, In : Diseases of the colon and rectum. 63, 3, p. 357-364 8 p.

Research output: Contribution to journalArticle

Clinical features and haematological parameters among malaria patients in Mangaluru city area in the southwestern coastal region of India

Punnath, K., Dayanand, K. K., Chandrashekar, V. N., Achur, R. N., Kakkilaya, S. B., Ghosh, S. K., Mukhi, B., Midya, V., Kumari, S. N. & Gowda, D. C., Mar 1 2020, In : Parasitology Research. 119, 3, p. 1043-1056 14 p.

Research output: Contribution to journalArticle

De novo resonance assignment of the transmembrane domain of LR11/SorLA in E. coli membranes

Ding, X., Fu, R. & Tian, F., Jan 2020, In : Journal of Magnetic Resonance. 310, 106639.

Research output: Contribution to journalArticle

Design, synthesis characterization and biological evaluation of novel multi-isoform ALDH inhibitors as potential anticancer agents

Dinavahi, S. S., Gowda, R., Bazewicz, C. G., Battu, M. B., Lin, J. M., Chitren, R. J., Pandey, M. K., Amin, S., Robertson, G. P. & Gowda, K., Feb 1 2020, In : European Journal of Medicinal Chemistry. 187, 111962.

Research output: Contribution to journalArticle

Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

Dinavahi, S. S., Gowda, R., Gowda, K., Bazewicz, C. G., Chirasani, V. R., Battu, M. B., Berg, A., Dokholyan, N. V., Amin, S. & Robertson, G. P., Feb 1 2020, In : Molecular cancer therapeutics. 19, 2, p. 447-459 13 p.

Research output: Contribution to journalArticle

Differentiation and characterization of neural progenitors and neurons from mouse embryonic stem cells

Hanafiah, A., Geng, Z., Wang, Q. & Gao, Z., May 2020, In : Journal of Visualized Experiments. 2020, 159, e61446.

Research output: Contribution to journalArticle

Early-life stress impairs postnatal oligodendrogenesis and adult emotional behaviour through activity-dependent mechanisms

Teissier, A., Le Magueresse, C., Olusakin, J., Andrade da Costa, B. L. S., De Stasi, A. M., Bacci, A., Imamura Kawasawa, Y., Vaidya, V. A. & Gaspar, P., Jun 1 2020, In : Molecular Psychiatry. 25, 6, p. 1159-1174 16 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Environmental enrichment ameliorates perinatal brain injury and promotes functional white matter recovery

Forbes, T. A., Goldstein, E. Z., Dupree, J. L., Jablonska, B., Scafidi, J., Adams, K. L., Imamura, Y., Hashimoto-Torii, K. & Gallo, V., Dec 1 2020, In : Nature communications. 11, 1, 964.

Research output: Contribution to journalArticle

Open Access

Erratum: A master regulator of bacteroides thetaiotaomicron gut colonization controls carbohydrate utilization and an alternative protein synthesis factor(mBio 11, 1, e03221-19, 2020, 10.1128/mBio.03221-19)

Townsend, G. E., Han, W., Schwalm, N. D., Hong, X., Bencivenga-Barry, N. A., Goodman, A. L. & Groisman, E. A., Mar 1 2020, In : mBio. 11, 2, e00301-20.

Research output: Contribution to journalComment/debate

Open Access

Experimentally-driven protein structure modeling

Dokholyan, N. V., May 30 2020, In : Journal of Proteomics. 220, 103777.

Research output: Contribution to journalReview article

Gastrointestinal hypoalgesia in inflammatory bowel disease

Coates, M. D., Soriano, C., Dalessio, S., Stuart, A., Walter, V., Koltun, W., Bernasko, N., Tinsley, A., Clarke, K. & Williams, E. D., Jan 1 2020, In : Annals of Gastroenterology. 33, 1, p. 45-52 8 p.

Research output: Contribution to journalArticle

Open Access

Gut-resident CX3CR1hi macrophages induce tertiary lymphoid structures and IgA response in situ

Koscsó, B., Kurapati, S., Rodrigues, R. R., Nedjic, J., Gowda, K., Shin, C., Soni, C., Ashraf, A. Z., Purushothaman, I., Palisoc, M., Xu, S., Sun, H., Chodisetti, S. B., Lin, E., Mack, M., Imamura, Y., He, P., Rahman, Z. S. M., Aifantis, I., Shulzhenko, N. & 2 others, Morgun, A. & Bogunovic, M., Jan 1 2020, In : Science Immunology. 5, 46, eaax0062.

Research output: Contribution to journalArticle

Open Access

Hypermethylation of FOXA1 and allelic loss of PTEN drive squamous differentiation and promote heterogeneity in bladder cancer

Osei-Amponsa, V., Buckwalter, J. M., Shuman, L., Zheng, Z., Yamashita, H., Walter, V., Wildermuth, T., Ellis-Mohl, J., Liu, C., Warrick, J. I., Shantz, L. M., Feehan, R. P., Al-Ahmadie, H., Mendelsohn, C., Raman, J. D., Kaestner, K. H., Wu, X. R. & DeGraff, D. J., Feb 6 2020, In : Oncogene. 39, 6, p. 1302-1317 16 p.

Research output: Contribution to journalArticle

2 Scopus citations

Kcnn2 blockade reverses learning deficits in a mouse model of fetal alcohol spectrum disorders

Mohammad, S., Page, S. J., Wang, L., Ishii, S., Li, P., Sasaki, T., Basha, A., Salzberg, A., Quezado, Z., Imamura, F., Nishi, H., Isaka, K., Corbin, J. G., Liu, J. S., Kawasawa, Y. I., Torii, M. & Hashimoto-Torii, K., Apr 1 2020, In : Nature Neuroscience. 23, 4, p. 533-543 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

km23-1/DYNLRB1 regulation of MEK/ERK signaling and R-Ras in invasive human colorectal cancer cells

Raza, A., Pandey, M. S., Jin, Q. & Mulder, K. M., Jan 1 2020, In : Cell Biology International. 44, 1, p. 155-165 11 p.

Research output: Contribution to journalArticle

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations

Makepeace, K. A. T., Brodie, N. I., Popov, K. I., Gudavicius, G., Nelson, C. J., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Jan 16 2020, In : Journal of Proteomics. 211, 103544.

Research output: Contribution to journalArticle

Open Access

Loss of Skin Microbial Diversity and Alteration of Bacterial Metabolic Function in Hidradenitis Suppurativa

Schneider, A. M., Cook, L. C., Zhan, X., Banerjee, K., Cong, Z., Imamura-Kawasawa, Y., Gettle, S. L., Longenecker, A. L., Kirby, J. S. & Nelson, A. M., Mar 2020, In : Journal of Investigative Dermatology. 140, 3, p. 716-720 5 p.

Research output: Contribution to journalArticle

4 Scopus citations

Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn’s disease and regulate Th1/Th17 cell responses

Aguirre, J. E., Beswick, E. J., Grim, C., Uribe, G., Tafoya, M., Palma, G. C., Samedi, V., McKee, R., Villeger, R., Fofanov, Y., Cong, Y., Yochum, G., Koltun, W., Powell, D. & Pinchuk, I. V., Jan 1 2020, In : International immunology. 32, 1, p. 57-68 12 p.

Research output: Contribution to journalArticle

Methionine restriction delays aging-related urogenital diseases in male Fischer 344 rats

Komninou, D., Malloy, V. L., Zimmerman, J. A., Sinha, R. & Richie, J. P., Feb 1 2020, In : GeroScience. 42, 1, p. 287-297 11 p.

Research output: Contribution to journalArticle

Mice lacking the matrilin family of extracellular matrix proteins develop mild skeletal abnormalities and are susceptible to age-associated osteoarthritis

Li, P., Fleischhauer, L., Nicolae, C., Prein, C., Farkas, Z., Saller, M. M., Prall, W. C., Wagener, R., Heilig, J., Niehoff, A., Clausen-Schaumann, H., Alberton, P. & Aszodi, A., Jan 2 2020, In : International journal of molecular sciences. 21, 2, 666.

Research output: Contribution to journalArticle

Open Access

Mutational profile of endometrial hyperplasia and risk of progression to endometrioid adenocarcinoma

Russo, M., Newell, J. M., Budurlean, L., Houser, K. R., Sheldon, K., Kesterson, J., Phaeton, R., Hossler, C., Rosenberg, J., DeGraff, D., Shuman, L., Broach, J. R. & Warrick, J. I., Jun 15 2020, In : Cancer. 126, 12, p. 2775-2783 9 p.

Research output: Contribution to journalArticle

Pan-cancer mapping of differential protein-protein interactions

Gulfidan, G., Turanli, B., Beklen, H., Sinha, R. & Arga, K. Y., Dec 1 2020, In : Scientific reports. 10, 1, 3272.

Research output: Contribution to journalArticle

Open Access

Regulation of small GTPase Rab20 by ikaros in B-cell acute lymphoblastic leukemia

Payne, J. L., Song, C., Ding, Y., Dhanyamraju, P. K., Bamme, Y., Schramm, J. W., Desai, D., Sharma, A., Gowda, C. & Dovat, S., Mar 1 2020, In : International journal of molecular sciences. 21, 5, 1718.

Research output: Contribution to journalArticle

Open Access

Response to Ring et al. In Silico Predictive Metagenomic Analyses Highlight Key Metabolic Pathways Impacted in the Hidradenitis Suppurativa Skin Microbiome

Schneider, A. M., Cook, L. C., Zhan, X., Banerjee, K., Cong, Z., Imamura-Kawasawa, Y., Gettle, S. L., Longenecker, A. L., Kirby, J. S. & Nelson, A. M., Jan 1 2020, (Accepted/In press) In : Journal of Investigative Dermatology.

Research output: Contribution to journalArticle

RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1

Elcheva, I. A., Wood, T., Chiarolanzio, K., Chim, B., Wong, M., Singh, V., Gowda, C. P., Lu, Q., Hafner, M., Dovat, S., Liu, Z., Muljo, S. A. & Spiegelman, V. S., May 1 2020, In : Leukemia. 34, 5, p. 1354-1363 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Single-channel properties of skeletal muscle ryanodine receptor pore Δ4923FF4924 in two brothers with a lethal form of fetal akinesia

Xu, L., Harms, F. L., Chirasani, V. R., Pasek, D. A., Kortüm, F., Meinecke, P., Dokholyan, N. V., Kutsche, K. & Meissner, G., May 2020, In : Cell Calcium. 87, 102182.

Research output: Contribution to journalArticle

The Dopamine D2 Receptor Contributes to the Spheroid Formation Behavior of U87 Glioblastoma Cells

Weissenrieder, J. S., Reed, J. L., Green, M. V., Moldovan, G. L., Koubek, E. J., Neighbors, J. D. & Hohl, R. J., Jan 1 2020, In : Pharmacology. 105, 1-2, p. 19-27 9 p.

Research output: Contribution to journalArticle

Open Access

The native ORAI channel trio underlies the diversity of Ca2+ signaling events

Yoast, R. E., Emrich, S. M., Zhang, X., Xin, P., Johnson, M. T., Fike, A. J., Walter, V., Hempel, N., Yule, D. I., Sneyd, J., Gill, D. L. & Trebak, M., May 15 2020, In : Nature communications. 11, 1, 1 p.

Research output: Contribution to journalArticle

Open Access

The novel Isatin analog KS99 targets stemness markers in acute myeloid leukemia

Annageldiyev, C., Gowda, K., Patel, T., Bhattacharya, P., Tan, S. F., Iyer, S., Desai, D., Dovat, S., Feith, D. J., Loughran, T. P., Amin, S., Claxton, D. & Sharma, A., Mar 1 2020, In : Haematologica. 105, 3, p. 687-696 10 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Transient receptor potential ion channel TRPM2 promotes AML proliferation and survival through modulation of mitochondrial function, ROS, and autophagy

Chen, S. J., Bao, L., Keefer, K., Shanmughapriya, S., Chen, L., Lee, J., Wang, J. F., Zhang, X. Q., Hirschler-Laszkiewicz, I., Merali, S., Merali, C., Imamura, Y., Dovat, S., Madesh, M., Cheung, J. Y., Wang, H. G. & Miller, B. A., Apr 1 2020, In : Cell Death and Disease. 11, 4, 247.

Research output: Contribution to journalArticle

Open Access

Type II but not type I IFN signaling is indispensable for TLR7-promoted development of autoreactive B cells and systemic autoimmunity

Chodisetti, S. B., Fike, A. J., Domeier, P. P., Singh, H., Choi, N. M., Corradetti, C., Kawasawa, Y. I., Cooper, T. K., Caricchio, R. & Rahman, Z. S. M., Feb 15 2020, In : Journal of Immunology. 204, 4, p. 796-809 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Ubiquitinated-PCNA protects replication forks from DNA2-mediated degradation by regulating Okazaki fragment maturation and chromatin assembly

Thakar, T., Leung, W., Nicolae, C. M., Clements, K. E., Shen, B., Bielinsky, A. K. & Moldovan, G. L., Dec 1 2020, In : Nature communications. 11, 1, 2147.

Research output: Contribution to journalArticle

Open Access
2019

Abstracts of Presentations at the Association of Clinical Scientists 139th Meeting Hershey, PA, May 15-18, 2019

Donaldson, K., Buchanich, J. M., Grigson, P. S., Deneke, E., Vrana, K. E., Sacks, D. B., Kuehn, G. J., Cardamone, D., Pesce, A., Smiley, S., Nickley, J., Krock, K., Thomas, R., Wilkerson, M. L., Farag, H. A., Challa, S. R., Tice, A. M., Wolk, D. M., Prichard, J., Grant, M. L. & 102 others, Regmi, S., Kerbacher, B., Quinton, L. E., Tice, A. M., Olson, J., Haynes, A., Yu, E., McCully, K. S., Assi, J., Wong, M., Zarrin-Khameh, N., Nifong, T. P., Hawker, C. D., Carlton, G. T., Rivera, J. M., Foulis, P. R., Zuraw, A., Morlote, D., Peker, D., Reddy, V., Harada, S., Crutchfield, C., Zander, D., Barbhuiya, M. A., Pederson, E. C., Straub, M. L., Scott, S. C., Neibauer, T. L., Salter, W. F., Creer, M. H., Zhu, Y., Bornhorst, J. A., Theobald, J. P., Algeciras-Schimnich, A., Cao, L., Knox, J., Hardy, R., Texas, H. J., McGuire, M. F., Hunter, R. L., Brown, R. E., Hicks, J., Cai, Z., Brown, R. E., Ali, Y., Cheng, K. C., Katz, S. R., Ding, Y., Vanselow, D. J., Yakovlev, M. A., Lin, A. Y., Clark, D. P., Vargas, P., Xin, X., Copper, J. E., Canfield, V. A., Ang, K. C., Wang, Y., Xiao, X., De Carlo, F., van Rossum, D. B., La Rivière, P. J., Newell, J., Hossler, C., Roche, M., Warrick, J., Phaeton, R., Kesterson, J., Myers, C., Barrios, R., Mintz, P., Robyak, K., Hamilton, C., McGhee, P., Pederson, C., Straub, M., Scott, S., Neibauer, T., Salter, W., Robyak, K., Singh, N., Morlote, D., Vnencak-Jones, C., Yemelyanova, A., Harada, S., Shah, M., Moghadamtousi, S. Z., Lan, C., Duose, D., Hu, P., Esquenazi, Y., Luthra, R., Ballester, L. Y., Koenig, A. N., Liu, C. G., Zhang, J., Kalia, A., Al-Habib, A., Van Arsdall, M., Dhingra, S., Patel, K. & Tatevian, N., May 1 2019, In : Annals of clinical and laboratory science. 49, 3, p. 403-416 14 p.

Research output: Contribution to journalArticle

A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation

Chirasani, V. R., Xu, L., Addis, H. G., Pasek, D. A., Dokholyan, N. V., Meissner, G. & Yamaguchi, N., Aug 2019, In : American Journal of Physiology - Cell Physiology. 317, 2, p. C358-C365

Research output: Contribution to journalArticle

3 Scopus citations

Activation of Wnt signaling promotes olaparib resistant ovarian cancer

Yamamoto, T. M., McMellen, A., Watson, Z. L., Aguilera, J., Ferguson, R., Nurmemmedov, E., Thakar, T., Moldovan, G. L., Kim, H., Cittelly, D. M., Joglar, A. M., Brennecke, E. P., Wilson, H., Behbakht, K., Sikora, M. J. & Bitler, B. G., Oct 1 2019, In : Molecular Carcinogenesis. 58, 10, p. 1770-1782 13 p.

Research output: Contribution to journalArticle

8 Scopus citations

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J. P., Bolhuis, P. G., Vreede, J., Faccioli, P. & 19 others, Orioli, S., Ravasio, R., Yan, L., Brito, C., Wyart, M., Gkeka, P., Rivalta, I., Palermo, G., McCammon, J. A., Panecka-Hofman, J., Wade, R. C., Di Pizio, A., Niv, M. Y., Nussinov, R., Tsai, C. J., Jang, H., Padhorny, D., Kozakov, D. & McLeish, T., Apr 2 2019, In : Structure. 27, 4, p. 566-578 13 p.

Research output: Contribution to journalReview article

36 Scopus citations

An R package for model fitting, model selection and the simulation for longitudinal data with dropout missingness

Xu, C., Li, Z., Xue, Y., Zhang, L. & Wang, M., Oct 21 2019, In : Communications in Statistics: Simulation and Computation. 48, 9, p. 2812-2829 18 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Association between DNA methylation in obesity-related genes and body mass index percentile in adolescents

He, F., Berg, A., Imamura Kawasawa, Y., Bixler, E. O., Fernandez-Mendoza, J., Whitsel, E. A. & Liao, D., Dec 1 2019, In : Scientific reports. 9, 1, 2079.

Research output: Contribution to journalArticle

7 Scopus citations

Association between inflammatory cytokine levels and anemia during Plasmodium falciparum and Plasmodium vivax infections in Mangaluru: A Southwestern Coastal Region of India

Punnath, K., Dayanand, K. K., Chandrashekhar, V. N., Achur, R. N., Kakkilaya, S. B., Ghosh, S. K., Kumari, S. N. & Gowda, C., Jul 1 2019, In : Tropical Parasitology. 9, 2, p. 98-107 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

23andMe Research Team, HUNT All-In Psychiatry, Liu, M., Jiang, Y., Wedow, R., Li, Y., Brazel, D. M., Chen, F., Datta, G., Davila-Velderrain, J., McGuire, D., Tian, C., Zhan, X., Agee, M., Alipanahi, B., Auton, A., Bell, R. K., Bryc, K., Elson, S. L., Fontanillas, P. & 32 others, Furlotte, N. A., Hinds, D. A., Hromatka, B. S., Huber, K. E., Kleinman, A., Litterman, N. K., McIntyre, M. H., Mountain, J. L., Northover, C. A. M., Sathirapongsasuti, J. F., Sazonova, O. V., Shelton, J. F., Shringarpure, S., Tian, C., Tung, J. Y., Vacic, V., Wilson, C. H., Pitts, S. J., Mitchell, A., Skogholt, A. H., Winsvold, B. S., Sivertsen, B., Stordal, E., Morken, G., Kallestad, H., Heuch, I., Zwart, J. A., Fjukstad, K. K., Pedersen, L. M., Gabrielsen, M. E., Johnsen, M. B. & Liu, D., Feb 1 2019, In : Nature Genetics. 51, 2, p. 237-244 8 p.

Research output: Contribution to journalLetter

82 Scopus citations

Attraction of Likenesses: Mechanisms of Self-Association and Compartmentalization of Eukaryotic Chromatin

Grigoryev, S. A. & Popova, E. Y., Nov 1 2019, In : Molecular Biology. 53, 6, p. 820-837 18 p.

Research output: Contribution to journalReview article