Research Output

2020

Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. Elegans to mammals

Jordan Rowley, M., Poulet, A., Nichols, M. H., Bixler, B. J., Sanborn, A. L., Brouhard, E. A., Hermetz, K., Linsenbaum, H., Csankovszki, G., Aiden, E. L. & Corces, V. G., Jan 1 2020, In : Genome Research. 30, 3, p. 447-458 12 p.

Research output: Contribution to journalArticle

Open Access

A Novel Combination Approach Targeting an Enhanced Protein Synthesis Pathway in MYC-driven (Group 3) Medulloblastoma

Chaturvedi, N. K., Kling, M. J., Griggs, C. N., Kesherwani, V., Shukla, M., McIntyre, E. M., Ray, S., Liu, Y., McGuire, T. R., Sharp, J. G., Band, H., Joshi, S. S. & Coulter, D. W., Jun 1 2020, In : Molecular cancer therapeutics. 19, 6, p. 1351-1362 12 p.

Research output: Contribution to journalArticle

A TFAP2C gene signature is predictive of outcome in HER2-positive breast cancer

Wu, V. T., Kiriazov, B., Koch, K. E., Gu, V. W., Beck, A. C., Borcherding, N., Li, T., Addo, P., Wehrspan, Z. J., Zhang, W., Braun, T. A., Brown, B. J., Band, V., Band, H., Kulak, M. V. & Weigel, R. J., Jan 1 2020, In : Molecular Cancer Research. 18, 1, p. 46-56 11 p.

Research output: Contribution to journalArticle

Author Correction: Widespread long-range cis-regulatory elements in the maize genome (Nature Plants, (2019), 5, 12, (1237-1249), 10.1038/s41477-019-0547-0)

Ricci, W. A., Lu, Z., Ji, L., Marand, A. P., Ethridge, C. L., Murphy, N. G., Noshay, J. M., Galli, M., Mejía-Guerra, M. K., Colomé-Tatché, M., Johannes, F., Rowley, M. J., Corces, V. G., Zhai, J., Scanlon, M. J., Buckler, E. S., Gallavotti, A., Springer, N. M., Schmitz, R. J. & Zhang, X., Mar 1 2020, In : Nature Plants. 6, 3, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Collateral Development and Arteriogenesis in Hindlimbs of Swine After Ligation of Arterial Inflow

Gao, Y., Aravind, S., Patel, N. S., Fuglestad, M. A., Ungar, J. S., Mietus, C. J., Li, S., Casale, G. P., Pipinos, I. I. & Carlson, M. A., May 2020, In : Journal of Surgical Research. 249, p. 168-179 12 p.

Research output: Contribution to journalArticle

DNA polymerase δ proofreads errors made by DNA polymerase e

Bulock, C. R., Xing, X. & Shcherbakova, P. V., Mar 17 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 11, p. 6035-6041 7 p.

Research output: Contribution to journalArticle

Open Access

Effect of Doxycycline on Aneurysm Growth among Patients with Small Infrarenal Abdominal Aortic Aneurysms: A Randomized Clinical Trial

Baxter, B. T., Matsumura, J., Curci, J. A., McBride, R., Larson, L., Blackwelder, W., Lam, D., Wijesinha, M. & Terrin, M., May 26 2020, In : JAMA - Journal of the American Medical Association. 323, 20, p. 2029-2038 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

EHD1 and RUSC2 control basal epidermal growth factor receptor cell surface expression and recycling

Tom, E. C., Mushtaq, I., Mohapatra, B. C., Luan, H., Bhat, A. M., Zutshi, N., Chakraborty, S., Islam, N., Arya, P., Bielecki, T. A., Iseka, F. M., Bhattacharyya, S., Cypher, L. R., Goetz, B. T., Negi, S. K., Storck, M. D., Rana, S., Barnekow, A., Singh, P. K., Ying, G. & 4 others, Guda, C., Natarajan, A., Band, V. & Banda, H., Apr 1 2020, In : Molecular and cellular biology. 40, 7, e00434.

Research output: Contribution to journalArticle

1 Scopus citations

Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome

Roychoudhury, S., Pramanik, S., Harris, H. L., Tarpley, M., Sarkar, A., Spagnol, G., Sorgen, P. L., Chowdhury, D., Band, V., Klinkebiel, D. & Bhakat, K. K., May 26 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 21, A44.

Research output: Contribution to journalArticle

Open Access

Eradication of cancer stem cells in triple negative breast cancer using doxorubicin/pluronic polymeric micelles

Zhao, Y., Alakhova, D. Y., Zhao, X., Band, V., Batrakova, E. V. & Kabanov, A. V., Feb 2020, In : Nanomedicine: Nanotechnology, Biology, and Medicine. 24, 102124.

Research output: Contribution to journalArticle

3 Scopus citations

Ex vivo expansion of regulatory T cells from abdominal aortic aneurysm patients inhibits aneurysm in humanized murine model

Suh, M. K., Batra, R., Carson, J. S., Xiong, W., Dale, M. A., Meisinger, T., Killen, C., Mitchell, J. & Baxter, B. T., Jan 1 2020, (Accepted/In press) In : Journal of vascular surgery.

Research output: Contribution to journalArticle

Open Access

Global dna hypomethylation in epithelial ovarian cancer: Passive demethylation and association with genomic instability

Zhang, W., Klinkebiel, D., Barger, C. J., Pandey, S., Guda, C., Miller, A., Akers, S. N., Odunsi, K. & Karpf, A. R., Mar 2020, In : Cancers. 12, 3, 764.

Research output: Contribution to journalArticle

Open Access

Homologous Recombination Repair Truncations Predict Hypermutation in Microsatellite Stable Colorectal and Endometrial Tumors

Lee, M., Eng, G., Barbari, S. R., Deshpande, V., Shcherbakova, P. V. & Gala, M. K., Mar 1 2020, In : Clinical and translational gastroenterology. 11, 3, p. e00149

Research output: Contribution to journalArticle

Open Access

Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope

Vellichirammal, N. N., Albahrani, A., Li, Y. & Guda, C., Jan 1 2020, Methods in Molecular Biology. Humana Press Inc., p. 13-25 13 p. (Methods in Molecular Biology; vol. 2079).

Research output: Chapter in Book/Report/Conference proceedingChapter

Macrophages potentiate STAT3 signaling in skeletal muscles and regulate pancreatic cancer cachexia

Shukla, S. K., Markov, S. D., Attri, K. S., Vernucci, E., King, R. J., Dasgupta, A., Grandgenett, P. M., Hollingsworth, M. A., Singh, P. K., Yu, F. & Mehla, K., Aug 1 2020, In : Cancer Letters. 484, p. 29-39 11 p.

Research output: Contribution to journalArticle

MECOM rearrangement involving the MYC locus: Two additional patients with the rare translocation, t(3;8)(q26.2;q24), and molecular review

Smith, S. C., Qdaisat, T. Z. S., Althof, P. A., Dave, B. J. & Sanmann, J. N., Aug 2020, In : Leukemia Research. 95, 106387.

Research output: Contribution to journalArticle

Metabolic alterations in pancreatic cancer progression

Vernucci, E., Abrego, J., Gunda, V., Shukla, S. K., Dasgupta, A., Rai, V., Chaika, N., Buettner, K., Illies, A., Yu, F., Lazenby, A. J., Swanson, B. J. & Singh, P. K., Jan 2020, In : Cancers. 12, 1, 2.

Research output: Contribution to journalArticle

Open Access

Metabolic subtyping for novel personalized therapies against pancreatic cancer

Mehla, K. & Singh, P. K., Jan 1 2020, In : Clinical Cancer Research. 26, 1, p. 6-8 3 p.

Research output: Contribution to journalArticle

1 Scopus citations

Monocyte metabolic reprogramming promotes pro-inflammatory activity and Staphylococcus aureus biofilm clearance

Yamada, K. J., Heim, C. E., Xi, X., Attri, K. S., Wang, D., Zhang, W., Singh, P. K., Bronich, T. K. & Kielian, T., Jan 1 2020, In : PLoS pathogens. 16, 3, e1008354.

Research output: Contribution to journalArticle

Open Access

MUC1 oncoprotein mitigates ER stress via CDA-mediated reprogramming of pyrimidine metabolism

Olou, A. A., King, R. J., Yu, F. & Singh, P. K., Apr 16 2020, In : Oncogene. 39, 16, p. 3381-3395 15 p.

Research output: Contribution to journalArticle

Neutrophils are mediators of metastatic prostate cancer progression in bone

Costanzo-Garvey, D. L., Keeley, T., Case, A. J., Watson, G. F., Alsamraae, M., Yu, Y., Su, K., Heim, C. E., Kielian, T., Morrissey, C., Frieling, J. S. & Cook, L. M., Jun 1 2020, In : Cancer Immunology, Immunotherapy. 69, 6, p. 1113-1130 18 p.

Research output: Contribution to journalArticle

Open Access

Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts

Vellichirammal, N. N., Albahrani, A., Banwait, J. K., Mishra, N. K., Li, Y., Roychoudhury, S., Kling, M. J., Mirza, S., Bhakat, K. K., Band, V., Joshi, S. S. & Guda, C., Mar 6 2020, In : Molecular Therapy - Nucleic Acids. 19, p. 1379-1398 20 p.

Research output: Contribution to journalArticle

Open Access

Placental DNA methylation changes in detection of tetralogy of Fallot

Bahado-Singh, R., Vishweswaraiah, S., Mishra, N. K., Guda, C. & Radhakrishna, U., Jun 1 2020, In : Ultrasound in Obstetrics and Gynecology. 55, 6, p. 768-775 8 p.

Research output: Contribution to journalArticle

Precision cardiovascular medicine: artificial intelligence and epigenetics for the pathogenesis and prediction of coarctation in neonates

Bahado-Singh, R. O., Vishweswaraiah, S., Aydas, B., Yilmaz, A., Saiyed, N. M., Mishra, N. K., Guda, C. & Radhakrishna, U., Jan 1 2020, (Accepted/In press) In : Journal of Maternal-Fetal and Neonatal Medicine.

Research output: Contribution to journalArticle

1 Scopus citations

Prognostic and therapeutic implications of NHERF1 expression and regulation in colorectal cancer

Leiphrakpam, P. D., Lazenby, A. J., Chowdhury, S., Smith, L. M., Mathiesen, M., Brattain, M. G., Wang, J., Black, J. D. & Are, C., Mar 1 2020, In : Journal of Surgical Oncology. 121, 3, p. 547-560 14 p.

Research output: Contribution to journalArticle

Proximal tubule cyclophilin D regulates fatty acid oxidation in cisplatin-induced acute kidney injury

Jang, H. S., Noh, M. R., Jung, E. M., Kim, W. Y., Southekal, S., Guda, C., Foster, K. W., Oupicky, D., Ferrer, F. A. & Padanilam, B. J., Feb 2020, In : Kidney International. 97, 2, p. 327-339 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

Reprogramming of ovarian granulosa cells by YAP1 leads to development of high-grade cancer with mesenchymal lineage and serous features

Lv, X., He, C., Huang, C., Hua, G., Chen, X., Timm, B. K., Maclin, V. M., Haggerty, A. A., Aust, S. K., Golden, D. M., Dave, B. J., Tseng, Y. A., Chen, L., Wang, H., Chen, P., Klinkebiel, D. L., Karpf, A. R., Dong, J., Drapkin, R. I., Rueda, B. R. & 2 others, Davis, J. S. & Wang, C., Jan 1 2020, (Accepted/In press) In : Science Bulletin.

Research output: Contribution to journalArticle

Role of Small Intestine and Gut Microbiome in Plant-Based Oral Tolerance for Hemophilia

Kumar, S. R. P., Wang, X., Avuthu, N., Bertolini, T. B., Terhorst, C., Guda, C., Daniell, H. & Herzog, R. W., May 20 2020, In : Frontiers in immunology. 11, 844.

Research output: Contribution to journalArticle

Open Access

SIRT1-NOX4 signaling axis regulates cancer cachexia

Dasgupta, A., Shukla, S. K., Vernucci, E., King, R. J., Abrego, J., Mulder, S. E., Mullen, N. J., Graves, G., Buettner, K., Thakur, R., Murthy, D., Attri, K. S., Wang, D., Chaika, N. V., Pacheco, C. G., Rai, I., Engle, D. D., Grandgenett, P. M., Punsoni, M., Reames, B. N. & 10 others, Teoh-Fitzgerald, M., Oberley-Deegan, R., Yu, F., Klute, K. A., Hollingsworth, M. A., Zimmerman, M. C., Mehla, K., Sadoshima, J., Tuveson, D. A. & Singh, P. K., Jul 6 2020, In : The Journal of experimental medicine. 217, 7

Research output: Contribution to journalArticle

Sterile α-motif domain requirement for cellular signaling and survival

Ray, S., Chee, L., Matson, D. R., Palermo, N. Y., Bresnick, E. H. & Hewitt, K. J., May 15 2020, In : Journal of Biological Chemistry. 295, 20, p. 7113-7125 13 p.

Research output: Contribution to journalArticle

Open Access

Symbiotic prodrugs (SymProDs) dual targeting of NFkappaB and CDK

Rana, S., Kour, S., Sonawane, Y. A., Robb, C. M., Contreras, J. I., Kizhake, S., Zahid, M., Karpf, A. R. & Natarajan, A., Jan 1 2020, (Accepted/In press) In : Chemical Biology and Drug Design.

Research output: Contribution to journalArticle

Targeting histone chaperone FACT complex overcomes 5-fluorouracil resistance in colon cancer

Song, H., Zeng, J., Roychoudhury, S., Biswas, P., Mohapatra, B., Ray, S., Dowlatshahi, K., Wang, J., Band, V., Talmon, G. & Bhakat, K. K., Jan 1 2020, In : Molecular cancer therapeutics. 19, 1, p. 258-269 12 p.

Research output: Contribution to journalArticle

The proteomic landscape of pancreatic ductal adenocarcinoma liver metastases identifies molecular subtypes and associations with clinical response A C

Law, H. C. H., Lagundzin, D., Clement, E. J., Qiao, F., Wagner, Z. S., Krieger, K. L., Costanzo-Garvey, D., Caffrey, T. C., Grem, J. L., DiMaio, D. J., Grandgenett, P. M., Cook, L. M., Fisher, K. W., Yu, F., Hollingsworth, M. A. & Woods, N. T., Mar 1 2020, In : Clinical Cancer Research. 26, 5, p. 1065-1076 12 p.

Research output: Contribution to journalArticle

Open Access
2019

Accuracy of ultrasound-guided localization of the peripatellar plexus for knee pain management

McCumber, T. L., Cassidy, K. M., Latacha, K. S., Simet, S. M., Vilburn, M. J., Urban, N. D., Vogt, C. M. & Urban, J. A., Dec 2019, In : Journal of Clinical Anesthesia. 58, p. 1-2 2 p.

Research output: Contribution to journalLetter

Alcohol potentiates RSV-mediated injury to ciliated airway epithelium

Wyatt, T. A., Bailey, K. L., Simet, S. M., Warren, K. J., Sweeter, J. M., DeVasure, J. M., Pavlik, J. A. & Sisson, J. H., Nov 2019, In : Alcohol. 80, p. 17-24 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

A microfluidic platform for stimulating chondrocytes with dynamic compression

Lee, D., Erickson, A., Dudley, A. T. & Ryu, S., Jan 1 2019, In : Journal of Visualized Experiments. 2019, 151, e59676.

Research output: Contribution to journalArticle

A mitotic CDK5-PP4 phospho-signaling cascade primes 53BP1 for DNA repair in G1

Zheng, X. F., Acharya, S. S., Choe, K. N., Nikhil, K., Adelmant, G., Satapathy, S. R., Sharma, S., Viccaro, K., Rana, S., Natarajan, A., Sicinski, P., Marto, J. A., Shah, K. & Chowdhury, D., Dec 1 2019, In : Nature communications. 10, 1, 4252.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Animal models of cancer-associated cachexia

Shukla, S. K. & Singh, P. K., Apr 17 2019, Animal Models in Cancer Drug Discovery. Elsevier, p. 59-74 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

A novel approach to eliminate therapy-resistant mantle cell lymphoma: synergistic effects of Vorinostat with Palbociclib

Chaturvedi, N. K., Hatch, N. D., Sutton, G. L., Kling, M., Vose, J. M. & Joshi, S. S., Apr 16 2019, In : Leukemia and Lymphoma. 60, 5, p. 1214-1223 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Antioxidant properties of citric acid interfere with the uricase-based measurement of circulating uric acid

Ryan, E. M., Duryee, M. J., Hollins, A., Dover, S. K., Pirruccello, S. J., Sayles, H., Real, K. D., Hunter, C. D., Thiele, G. M. & Mikuls, T. R., Feb 5 2019, In : Journal of Pharmaceutical and Biomedical Analysis. 164, p. 460-466 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme

Xing, X., Kane, D. P., Bulock, C. R., Moore, E. A., Sharma, S., Chabes, A. & Shcherbakova, P. V., Dec 1 2019, In : Nature communications. 10, 1, 374.

Research output: Contribution to journalArticle

7 Scopus citations

Artificial intelligence analysis of newborn leucocyte epigenomic markers for the prediction of autism

Bahado-Singh, R. O., Vishweswaraiah, S., Aydas, B., Mishra, N. K., Yilmaz, A., Guda, C. & Radhakrishna, U., Dec 1 2019, In : Brain Research. 1724, 146457.

Research output: Contribution to journalArticle

1 Scopus citations

A simple fluorescent assay for the discovery of protein-protein interaction inhibitors

Al-Mugotir, M., Kolar, C., Vance, K., Kelly, D. L., Natarajan, A. & Borgstahl, G. E. O., Mar 15 2019, In : Analytical Biochemistry. 569, p. 46-52 7 p.

Research output: Contribution to journalArticle

Betaglycan drives the mesenchymal stromal cell osteogenic program and prostate cancer-induced osteogenesis

Cook, L. M., Frieling, J. S., Nerlakanti, N., McGuire, J. J., Stewart, P. A., Burger, K. L., Cleveland, J. L. & Lynch, C. C., Oct 31 2019, In : Oncogene. 38, 44, p. 6959-6969 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Biochemical and cellular assays to assess the effects of acetylation on base excision repair enzymes

Roychoudhury, S., Pramanik, S., Harris, H. L. & Bhakat, K. K., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 191-206 16 p. (Methods in Molecular Biology; vol. 1983).

Research output: Chapter in Book/Report/Conference proceedingChapter

Brain changes in a maternal immune activation model of neurodevelopmental brain disorders

Bergdolt, L. & Dunaevsky, A., Apr 2019, In : Progress in Neurobiology. 175, p. 1-19 19 p.

Research output: Contribution to journalReview article

14 Scopus citations

Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions

Nowialis, P., Lopusna, K., Opavska, J., Haney, S. L., Abraham, A., Sheng, P., Riva, A., Natarajan, A., Guryanova, O., Simpson, M. A., Hlady, R., Xie, M. & Opavsky, R., Dec 1 2019, In : Nature communications. 10, 1, 4374.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

CD95-ligand contributes to abdominal aortic aneurysm progression by modulating inflammation

Liu, Z., Fitzgerald, M., Meisinger, T., Batra, R., Suh, M., Greene, H., Penrice, A. J., Sun, L., Baxter, B. T. & Xiong, W., Mar 15 2019, In : Cardiovascular research. 115, 4, p. 807-818 12 p.

Research output: Contribution to journalArticle

1 Scopus citations