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., 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., 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

Enhanced Notch3 signaling contributes to pulmonary emphysema in a Murine Model of Marfan syndrome

Jespersen, K., Liu, Z., Li, C., Harding, P., Sestak, K., Batra, R., Stephenson, C. A., Foley, R. T., Greene, H., Meisinger, T., Baxter, B. T. & Xiong, W., Dec 1 2020, In : Scientific reports. 10, 1, 10949.

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

Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana

Kuciński, J., Chamera, S., Kmera, A., Rowley, M. J., Fujii, S., Khurana, P., Nowotny, M. & Wierzbicki, A. T., Jun 1 2020, In : Plant & cell physiology. 61, 6, p. 1107-1119 13 p.

Research output: Contribution to journalArticle

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., 2020, (Accepted/In press) In : Journal of vascular surgery.

Research output: Contribution to journalArticle

Open Access

Fast transformation of 2D nanofiber membranes into pre-molded 3D scaffolds with biomimetic and oriented porous structure for biomedical applications

Chen, S., John, J. V., McCarthy, A., Carlson, M. A., Li, X. & Xie, J., Jun 1 2020, In : Applied Physics Reviews. 7, 2, 021406.

Research output: Contribution to journalArticle

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

High-risk cytogenetics in multiple myeloma: Further scrutiny of deletions within the IGH gene region enhances risk stratification

Smith, S. C., Althof, P. A., Dave, B. J. & Sanmann, J. N., 2020, (Accepted/In press) In : Genes Chromosomes and Cancer. 59, 10, p. 569-574 6 p.

Research output: Contribution to journalArticle

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., 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

Local and systemic immunosuppression in pancreatic cancer: Targeting the stalwarts in tumor's arsenal

Mundry, C. S., Eberle, K. C., Singh, P. K., Hollingsworth, M. A. & Mehla, K., Aug 2020, In : Biochimica et Biophysica Acta - Reviews on Cancer. 1874, 1, 188387.

Research output: Contribution to journalReview article

Open Access

Long non-coding RNA profiling of pediatric Medulloblastoma

Kesherwani, V., Shukla, M., Coulter, D. W., Sharp, J. G., Joshi, S. S., Chaturvedi, N. K. & Chaturvedi, N. K., Jun 26 2020, In : BMC Medical Genomics. 13, 1, 87.

Research output: Contribution to journalArticle

Open Access

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

Open Access

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

miRNA- and cytokine-associated extracellular vesicles mediate squamous cell carcinomas

Flemming, J. P., Hill, B. L., Haque, M. W., Raad, J., Bonder, C. S., Harshyne, L. A., Rodeck, U., Luginbuhl, A., Wahl, J. K., Tsai, K. Y., Wermuth, P. J., Overmiller, A. M. & Mahoney, M. Ỹ. G., Jan 1 2020, In : Journal of Extracellular Vesicles. 9, 1, 1790159.

Research output: Contribution to journalArticle

Open Access

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., 2020, In : PLoS pathogens. 16, 3, e1008354.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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

Nanoparticle Formulation of Indocyanine Green Improves Image-Guided Surgery in a Murine Model of Breast Cancer

Wojtynek, N. E., Olson, M. T., Bielecki, T. A., An, W., Bhat, A. M., Band, H., Lauer, S. R., Silva-Lopez, E. & Mohs, A. M., Aug 1 2020, In : Molecular Imaging and Biology. 22, 4, p. 891-903 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

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

Novel fibrin-fibronectin matrix accelerates mice skin wound healing

Jara, C. P., Wang, O., Paulino do Prado, T., Ismail, A., Fabian, F. M., Li, H., Velloso, L. A., Carlson, M. A., Burgess, W., Lei, Y., Velander, W. H. & Araújo, E. P., Dec 2020, In : Bioactive Materials. 5, 4, p. 949-962 14 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., 2020, (Accepted/In press) In : Journal of Maternal-Fetal and Neonatal Medicine.

Research output: Contribution to journalArticle

2 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

Recapitulating developmental mechanisms for retinal regeneration

Ahmad, I., Teotia, P., Erickson, H. & Xia, X., May 2020, In : Progress in Retinal and Eye Research. 76, 100824.

Research output: Contribution to journalReview article

1 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., 2020, (Accepted/In press) In : Science Bulletin. 65, 15, p. 1281-1296 16 p.

Research output: Contribution to journalArticle

Open Access

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 : Journal of Experimental Medicine. 217, 7, e20190745.

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., 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., 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
2 Scopus citations
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

3 Scopus citations

A microfluidic platform for stimulating chondrocytes with dynamic compression

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

Research output: Contribution to journalArticle