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Graduate Student Publications

Biological Sciences

Graduate Student Publications


The opportunity to author peer-reviewed publications is crucial for graduate students pursuing an advanced degree in biological sciences. 

This experience is invaluable as it mirrors the professional environment where peer feedback is a norm, thus preparing students for future collaborative and independent research endeavors. The ability to publish peer-reviewed work during graduate studies is not just a milestone but a foundational aspect of a successful academic and research career in biological sciences.

Below are examples of publications our students have authored over the years.

 

2022

  • Halloran, D.R.; Heubel, B.; MacMurray, C.; Root, D.; Eskander, M.; McTague, S.P.; Pelkey, H.; Nohe, A. Differentiation of Cells Isolated from Human Femoral Heads into Functional Osteoclasts. J. Dev. Biol. 2022, 10, 6. https://doi.org/10.3390/jdb10010006

  • Toney, N. J., Opdenaker, L. M., Cicek, K., Frerichs, L., Kennington, C. R., Oberly, S., Archinal, H., Somasundaram, R., & Sims-Mourtada, J. (2022). Tumor-B-cell interactions promote isotype switching to an immunosuppressive IgG4 antibody response through upregulation of IL-10 in triple negative breast cancers. Journal of translational medicine, 20(1), 112. 

  • Halloran, D.; Pandit, V.; Nohe, A. The Role of Protein Kinase CK2 in Development and Disease Progression: A Critical Review. J. Dev. Biol.

  • Halloran, D.; Pandit, V.; MacMurray, C.; Stone, V.; DeGeorge, K.; Eskander, M.; Root, D.; McTague, S.; Pelkey, H.; Nohe, A. Age-Related Low Bone Mineral Density in C57BL/6 Mice Is Reflective of Aberrant Bone Morphogenetic Protein-2 Signaling Observed in Human Patients Diagnosed with Osteoporosis. Int. J. Mol. Sci

  • Keown, R. A., Dums, J. T., Brumm, P. J., MacDonald, J., Mead, D. A., Ferrell, B. D., Moore, R. M., Harrison, A. O., Polson, S. W., & Wommack, K. E. (2022). Novel viral DNA polymerases from metagenomes suggest genomic sources of strand-displacing biochemical phenotypes. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.858366

  • "Clupper, M., Gill, R., Elsayyid, M., Touroutine, D., Caplan, J.L., Tanis, J.E., Kinesin-2 motors differentially impact biogenesis of extracellular vesicle subpopulations shed from sensory cilia, ISCIENCE (2022), doi: https://doi.org/10.1016/j.isci.2022.105262."

  • Yogeshwari Singh, Jeremy G. Bird, A gel electrophoresis-based assay for measuring enzymatic RNA decapping activity, Methods in Enzymology, Academic Press, 2022, ISSN 0076-6879, https://doi.org/10.1016/bs.mie.2022.07.014. (https://www.sciencedirect.com/science/article/pii/S007668792200252X)

  • Inguito KL, Schofield MM, Faghri AD, Bloom ET, Heino M, West VC, Ebron KMM, Elliott DM, Parreno J. Stress Deprivation of Tendon Explants or Tpm3.1 Inhibition in Tendon Cells Reduces F-actin to Promote a Tendinosis-like Phenotype. Mol Biol Cell. 2022 Sep 21:mbcE22020067. doi: 10.1091/mbc.E22-02-0067. Epub ahead of print. PMID: 36129771.

  • Asgin, N., Kal-Cakmakliogullari, E., Otlu, B., Ersoy, O. F., Celik, B., & Basustaoglu, A. (2022). Molecular Epidemiological Analysis of Bacillus Pseudo-Outbreak due to Contaminated Culture Tubes Containing Stuart Medium. Clinical Laboratory, 68(1), 115–120. https://doi.org/10.7754/CLIN.LAB.2021.210306

  • Ozbey, G., Otlu, B., Yakupogullari, Y., Celik, B., Tanriverdi, E. S., Kelestemur, N., Safak, T., Risvanli, A., Persad, A., & Sproston, E. (2022). Investigation of bacterial pathogens in milk from mastitic dairy cattle by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Thai Journal of Veterinary Medicine, 52(1), 63–73. https://doi.org/10.14456/TJVM.2022.7

  • Sabancı A, Eltas A, Celik B, Otlu B. The influence of diabetes mellitus on the peri-implant microflora: A cross-sectional study. J Oral Biol Craniofac Res. 2022 Jul-Aug;12(4):405-409. doi: 10.1016/j.jobcr.2022.05.007. Epub 2022 May 17. PMID: 35646552; PMCID: PMC9136106.

  • Celik, B.; Cicek, K.; Leal, A.F.; Tomatsu, S. Regulation of Molecular Targets in Osteosarcoma Treatment. Int. J. Mol. Sci. 2022, 23, 12583. https://doi.org/10.3390/ijms232012583

  • Xia P, Dutta A, Gupta K, et al. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines crosstalk between Type-III & Type-I CRISPR systems. J Biol Chem 2022;101591, doi:10.1016/j.jbc.2022.101591

  • Leal AF, Benincore-Flórez E, Rintz E, Herreño-Pachón AM, Celik B, Ago Y, Alméciga-Díaz CJ, Tomatsu S. Mucopolysaccharidoses: Cellular Consequences of Glycosaminoglycans Accumulation and Potential Targets. Int J Mol Sci. 2022 Dec 28;24(1):477. doi: 10.3390/ijms24010477. PMID: 36613919.

2021

  • "Holmes, L., Jr.; Rios, J.; Berice, B.; Benson, J.; Bafford, N.; Parson, K.; Halloran, D. Predictive Effect of Helicobacter pylori in Gastric Carcinoma Development: Systematic Review and Quantitative Evidence Synthesis. Medicines 2021, 8, 1."

  • Halakos EG, Connell AJ, Glazewski L, Wei S, Mason RW. Bottom up proteomics identifies neuronal differentiation pathway networks activated by cathepsin inhibition treatment in neuroblastoma cells that are enhanced by concurrent 13-cis retinoic acid treatment. J Proteomics. 2021;232:104068. doi:10.1016/j.jprot.2020.104068

  • Laurens Holmes, Malik A. Williams, Daniel R. Halloran, Jacqueline A. Benson, Nastocia T. Bafford, Kadedrah V. Parson, Kirk Dabney, Betyna N. Berice, Social gradient predicts survival disadvantage of African Americans/Black children with lymphoma, Journal of the National Medical Association

  • Sampilo, NF., Stepicheva, N. A., & Song, J. L. miR-31 regulates skeletogenesis by direct suppression of Eve and Wnt1. Developmental Biology. Jan 20;472:98-114. doi:10.1016/j.ydbio.2021.01.008

  • Roberts, R. J., Hallee, L., & Lam, C. K. (2021). The Potential of Hsp90 in Targeting Pathological Pathways in Cardiac Diseases. Journal of Personalized Medicine, 11(12), 1373. https://doi.org/10.3390/jpm11121373

  • Chen H, Khan S, Celik B, Suzuki Y, Ago Y, Tomatsu S. Activity of daily living in mucopolysaccharidosis IVA patients: Evaluation of therapeutic efficacy. Mol Genet Genomic Med. 2021 Nov;9(11):e1806. doi: 10.1002/mgg3.1806. Epub 2021 Oct 8. PMID: 34623762; PMCID: PMC8606213

  • Amendum PC, Khan S, Yamaguchi S, Kobayashi H, Ago Y, Suzuki Y, Celik B, Rintz E, Hossain J, Xiao W, Tomatsu S. Glycosaminoglycans as Biomarkers for Mucopolysaccharidoses and Other Disorders. Diagnostics (Basel). 2021 Aug 28;11(9):1563. doi: 10.3390/diagnostics11091563. PMID: 34573906; PMCID: PMC8468223.

  • Celik B, Tomatsu SC, Tomatsu S, Khan SA. Epidemiology of Mucopolysaccharidoses Update. Diagnostics (Basel). 2021 Feb 10;11(2):273. doi: 10.3390/diagnostics11020273. PMID: 33578874; PMCID: PMC7916572.

2020

  • Shaopeng Pei, Sucharitha Parthasarathy, Ashutosh Parjuli, Jerahme Martinez, Mengxi Lv, Sida Jiang, Danielle Wu, Shuo Wei, X Lucas Lu, Mary C. Farach-Carson, Catherine B. Kirn-Safrin, Liyun Wang - Perlecan/Hspg2 deficiency impairs bone's calcium signaling and associated transcriptome in response to mechanical loading

  • Daniel Halloran, Vrathasha Vrathasha, Hilary W. Durbano and Anja Nohe; Bone Morphogenetic Protein-2 Conjugated to Quantum Dot®s is Biologically Functional; Nanomaterials

  • Aryal, S., Viet J., Weatherbee, B.A., Siddam A.D., Hernandez, F.G., Gautier-Courteille, C., Paillard, L., Lachke, S.A. The cataract-linked RNA-binding protein Celf1 post-transcriptionally controls the spatiotemporal expression of the key homeodomain transcription factors Pax6 and Prox1 in lens development. Human Genetics (2020).

  • Halloran, D.; Durbano, H.W.; Nohe, A. Bone Morphogenetic Protein-2 in Development and Bone Homeostasis. J. Dev. Biol. 2020, 8, 19.

  • Durbano, H.W.; Halloran, D.; Nguyen, J.; Stone, V.; McTague, S.; Eskander, M.; Nohe, A. Aberrant BMP2 Signaling in Patients Diagnosed with Osteoporosis. Int. J. Mol. Sci. 2020, 21, 6909. doi: 10.3390/ijms21186909

  • Joglekar, P., Mesa, C. P., Richards, V. A., Polson, S. W., Wommack, K. E., & Fuhrmann, J. J. (2020). Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.). Systematic and applied microbiology, 43(3), 126073.

2019

  • Weatherbee, B.A.T., Barton, J.R., Siddam, A.D., Anand, D., Lachke, S.A.* Molecular characterization of the human lens epithelium-derived cell line SRA01/04.Experimental Eye Research 2019: accepted on August 30, 2019 *Corresponding Author

  • Barnum, C.E., Al Saai, S., Cheng, C., Anand, D., Patel, S.D., Dash, S., Siddam, A.D., Glazewski, L., Paglione, E., Polson, S., Chuma, S., Mason R.W., Batish, M., Fowler, V.M., Lachke, S.A.* The Tudor-domain family protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 and lens fiber cell morphology. Human Molecular Genetics 2019: in revision *Corresponding Author

  • "Dash, S., Brastrom, M.K., Patel, S.D., Scott, A.C., Slusarski, D.C., Lachke, S.A.* The master transcription factors SOX2, mutated in anophthalmia/microphthalmia, is regulated by the conserved RNA-binding protein RBM24 in vertebrate eye development. Human Molecular Genetics 2019: in minor revision *Corresponding Author"

  • Aryal, S., Hernandez, F.G., Anand, D., Weatherbee, B.A.T., Willmarth, P., Reddy, A., David, L.L., Lachke, S.A.* MS/MS in silico subtraction-based profiling of the developing lens to facilitate cataract gene discovery.  2019: submitted *Corresponding Author

  • Remsburg*, C., Konrad*, K, Sampilo*, NF. and J.L. Song (2019). Functional analysis of microRNAs. Methods in Cell Biology. Echinoderms part B, Volume 151.

  • Jiejing Li, Mark Perfetto, Christopher Materna, Rebecca Li, Hong Thi Tran, Kris Vleminckx, Melinda K. Duncan and Shuo Wei (2019), A new transgenic reporter line reveals Wnt-dependent Snail2 re-expression and cranial neural crest differentiation in Xenopus bioRxiv520726; Scientific Reports; 9(1) 11191

  • Mahbubul H. Shihan, Samuel G. Novo, and Melinda K. Duncan (2019) Cataract surgeon viewpoints on the need for novel preventative anti-inflammatory and anti-posterior capsular opacification therapies Current Medical Research and Opinion 35, 1971-1981

  • Gregory, G.S., D.P. Morreale, M.R. Carpenter, S.S. Kalburge, and E.F. Boyd. 2019. Quorum sensing regulator OpaR controls expression of the compatible solute ectoine. Applied and Environmental Microbiology, 85:

  • Regmi, A. and E.F. Boyd. 2019. Carbohydrate metabolism systems present on genomic islands that are lost and gained in Vibrio parahaemolyticus. BMC Microbiology, 19:112.

  • McDonald, N.D, Regmi, A., J.D. Borowski, D.P. Morreale, and Boyd, E.F. 2019. CRISPR-Cas systems are carried on mobile genetic elements in Vibrio species. BMC Genomics, 4;20(1):105. * co-first authors. *Undergraduate researcher

  • Yuhao Zhang, Cristian Coarfa, Xiaoyu Dong, Weiwu Jiang, Brielle Hayward-Piatkovskyi, Jason Gleghorn, and Krithika Lingappan (2019) MicroRNA-30a as a candidate underlying sex-specific differences in neonatal hyperoxic lung injury: Implications for BPD. American Journal of Physiology-Lung Cellular and Molecular Physiology 316(1):L144-L156. doi: 10.1152/ajplung.00372.2018.

  • Halakos EG, Connell AJ, Glazewski L, Wei S, Mason RW. Bottom up proteomics reveals novel differentiation proteins in neuroblastoma cells treated with 13-cis retinoic acid. J Proteomics. 2019;209:103491. doi:10.1016/j.jprot.2019.103491

  • Pike, C.M., Noll, R.R., and Neunuebel M.R. (2019). Exploitation of Phosphoinositides by the Intracellular Pathogen, Legionella pneumophila. Pathogenic Bacteria. IntechOpen. doi: 10.5772/intechopen.89158

2018

  • Yichen Wang, Priyha Mahesh, Yan Wang, Samuel G. Novo, Mahbubul H. Shihan, Brielle, Hayward-Piatkovskyi, and Melinda K. Duncan (2018) Spatiotemporal dynamics of canonical Wnt signaling during embryonic eye development and posterior capsular opacification (PCO). Experimental Eye Research 175, 148-158

  • Kakrana, A., Yang, A., Anand, D., Djordjevic, D., Ramachandruni, S.D., Singh, A., Huang, H., Ho, J.W.K.*, Lachke, S.A.*iSyTE 2.0: a developmental expression-based database for eye gene discovery. *Corresponding authors Nucleic Acids Research 2018: 46:D875-D885. View in: Pubmed

  • Budak, G., Dash, S., Srivastava, R., Lachke, S.A., Janga, S.C. Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. Experimental Eye Research 2018: 168:57-68. View in: Pubmed

  • Anand, D., Agrawal, S.A., Slavotinek, A., Lachke, S.A.* Mutation update of transcription factor genes HSF4, FOXE3, MAF and PITX3 cataracts and other developmental ocular defects.  Human Mutation 2018: 39:471-494. View in: Pubmed

  • Siddam, A.D., Gautier-Courteille, C., Perez-Campos, L., Anand, D., Kakrana, A., Dang, C.A., Legagneux, V., Méreau, A., Viet, J., Gross, J.M., Paillard, L.*, Lachke, S.A.* The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development. *Corresponding authors. PLoS Genetics 2018: 14(3):e1007278. View in: Pubmed

  • Anand, D., Kakrana, A., Siddam, A.D., Huang, H., Saadi, I., Lachke, S.A.* RNA-sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery. Human Genetics 2018: 137:941-954. View in: Pubmed

  • Sampilo*1, NF., Stepicheva*1,3, N.A., Zaidi*1, S.A.M., Wang2, L., Wu2, W.,Wikramanayake2, A., and J.L. Song1* (2018). Inhibition of microRNA suppression of Dishevelled results in Wnt pathway associated developmental defects. Development, Nov2. pii: dev.167130. doi: 10.1242/dev.167130.

  • Jian Jiang, Mahbubul Shihan, Yan Wang and Melinda K. Duncan (2018) Lens epithelial cells initiate the inflammatory response following cataract surgery. Investigative Ophthalmology and Visual Sciences 59, 4986-4997. Denoted a "hot topic" in ophthalmology at the 2018 ARVO meeting

  • Mc Donald, N.D., C. L. Grimes, K. Demeester, and E.F. Boyd. 2018. Structural and functional characterization of a modified legionaminic acid involved in glycosylation of the bacterial lipopolysaccharide. Journal Biological Chemistry, 7;293(49):19113-19126.

2017

  • "Wang, Y., Terrell, A.M., Riggio, B.A., Anand, D., Lachke, S.A., Duncan, M.K. Beta1-integrin deletion from the lens activates cellular stress responses leading to fibrosis and apoptosis. Investigative Ophthalmology and Visual Science 2017: 58:3896-3922. View in: Pubmed"

  • Srivastava, R., Budak, G., Dash, S., Lachke, S.A., Janga, S.C. Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. Scientific Reports 2017: 7:11572. View in: Pubmed

  • "Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management. Langwig KE, Wargo AR, Jones DR, Viss JR, Rutan BJ, Egan NA, Sá-Guimarães P, Kim MS, Kurath G, Gomes MGM, Lipsitch M. MBio. 2017 Nov 21;8(6). pii: e00796-17. doi: 10.1128/mBio.00796-17. PMID:29162706"

  • Stepicheva*, N., M. Dumas**, P. Kobi*, J. Donaldson, and J.L. Song (2017) The small GTPase Arf6 regulates sea urchin cellular morphogenesis. Differentiation. May - Jun;95:31-43. doi: 10.1016/j.diff.2017.01.003. PMID:28188999

  • Mallika Pathania, Yan Wang, Vladimir N. Simirskii, and Melinda K. Duncan (2016) b1-integrin controls cell fate specification in early lens development Differentiation, 92, 133-147.

  • Dylan S. Audette, David A. Scheiblin and Melinda K. Duncan (2017) The molecular mechanisms underlying lens fiber elongation. Experimental Eye Research-invited review, David Beebe memorial issue 156, 41-49.

  • Carpenter, M.R., S.S. Kalburge, J.D. Borowski, M. Peters*, R.R. Colwell, and E.F. Boyd. 2017. CRISPR-Cas and contact dependent secretion systems carried on excisable pathogenicity islands with conserved recombination modules. J. Bacteriology, 25;199(10). pii: e00842-16.

  • Kalburge, S.S., Carpenter, M.R., S. Rozovsky, and E.F. Boyd. 2017. Quorum sensing regulators are required for Vibrio parahaemolyticus metabolic fitness. Infection and Immunity, 23;85(3). pii: e00930-16.

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