Publications

Listed below is a selection of some of our faculty’s recent publications.

2017

  • N. Revaitis, R.A. Marmion, M. Farhat, V. Ekiz, W. Wang, N. Yakoby. Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis. G3 2017 Jun 20. pii: g3.117.043810. doi: 10.1534/g3.117.043810.
  • G. Pyrowolakis, V. Veikkolainen, N. Yakoby, S.Y. Shvartsman. Gene regulation during Drosophila eggshell patterning. PNAS  2017 Jun 6;114(23):5808-5813. doi: 10.1073/pnas.1610619114.

  • Dighton J. & White, J. W. Jr Eds. (2017) The Fungal Community: its Organization and Role in the Ecosystem. 4th Edition CRC Taylor and Francis.

  • Malcolm, K. and Dighton, J. (2017) Ecology of Fungal Phylloplane Epiphytes In: The Fungal Community: its Organization and Role in the Ecosystem. 4th Edition, ed. J. Dighton & J. W. White Jr., CRC Taylor and Francis pp. 159-168.

  • Dighton, J. (2017) Fungal degradation of our cultural heritage In: The Fungal Community: its Organization and Role in the Ecosystem. 4th Edition, ed. J. Dighton & J. W. White Jr., CRC Taylor and Francis pp. 501-508.

  • Luo, J., Walsh, E., Miller, S., Blystone, D. Dighton, J., Zhang, Nl. (2017) Root endophytic fungal communities associated with pitch pine, switchgrass and rosette grass in the pine barrens ecosystem, Fungal Biology 121: 478-487.

  • Dinamarca, O. Levitan, G. K. Kumaraswamy, D. S. Lun, and P. Falkowski. Overexpression of a diacylglycerol acyltransferase gene in Phaeodactylum tricornutum directs carbon towards lipid biosynthesis. J. Phycology, 53(2):405-414, April 2017.

  • Qian, M. K. Kim, G. K. Kumaraswamy, A. Agarwal, D. S. Lun, and G. C. Dismukes. Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis. BBA – Bioenergetics, 1858(4):276-287, April 2017.

  • E. Alfonse, G. Tejada, H. Swaminathan, D. S. Lun, and C. M. Grgicak. Inferring the number of contributors to complex DNA mixtures using three methods: Exploring the limits of low-template DNA interpretation. J. Forensic Sci., 62(2):308-316, March 2017.

  • Guay*, C. L., McQuade*, S. T., Nam, J., 2017. Single embryo-resolution quantitative analysis of reporters permits multiplex spatial cis-regulatory analysis. Developmental Biology. 422, 92-104. (* = equal contribution) https://www.sciencedirect.com/science/article/pii/S0012160616306601

  • Lori Ludwig#, Matthew Barbour, Jennifer Guevara, Leticia Avilés & Angélica L. González. Caught in the web: spider web architectures affect prey specialization and spider-prey stoichiometric relationships. Accepted Ecology & Evolution. #Undergraduate student.

  • J. Gagliardi and D.H. Shain, Electrostatic forces drive poleward chromosome motions at kinetochores, Cell Division 2016, 11:14.

  • Hideyuki Doi, Fumikazu Akamatsu & Angélica L. González. 2017. Starvation effect on nitrogen and carbon isotope values of animals: an insight from meta-analysis of feeding experiments. R. Soc. open sci. 4: 170633. *Collaborative paper. 

  • Stilianos Louca, Saulo M.S. Jacques, Aliny P.F. Pires, Juliana S. Leal, Angélica L. González, Michael Doebeli & Vinicius F. Farjalla. 2017. Structure and function of bacterial and archaeal communities in bromeliad tanks. Environmental Microbiology 19:3132–3151.

  • Liu Y, Su G, Wang F, Jia J, Li S, Zhao L, Shi Y, Cai Y, Zhu H, Zhao B, Jiang G, Zhou H, Yan B Elucidation of the Molecular Determinants for Optimal Perfluorooctanesulfonate Adsorption Using a Combinatorial Nanoparticle Library Approach. Sci. Technol., 2017; (51) 7120-7127. https://www.ncbi.nlm.nih.gov/pubmed/28537376

  • Zhao L, Wang W, Sedykh A, Zhu H* Experimental Errors in QSAR Modeling Sets: What We Can Do and What We Cannot Do. ACS Omega, 2017; (2) 2805-2812. https://pubs.acs.org/doi/full/10.1021/acsomega.7b00274

  • Bai X, Liu F, Liu Y, Li C, Wang S, Zhou H, Wang W, Zhu H, Winkler D, Yan B Toward A Systematic Exploration of Nano-Bio Interactions. Appl. Pharmacol. 2017; (323) 66-73. https://www.ncbi.nlm.nih.gov/pubmed/28344110

  • Hamm J, Sullivan K, Clippinger A J, Strickland J, Bell S, Bhhatarai B, Blaauboer B, Casey W, Dorman D, Forsby A, Garcia-Reyero N, Gehen S, Graepel R, Hotchkiss J, Lowit A, Matheson J, Reaves E, Scarano L, Sprankle C, Tunkel J, Wilson D, Xia M, Zhu H, Allen D Alternative approaches for identifying acute systemic toxicity: Moving from research to regulatory testing. in Vitro, 2017; (41) 245-259. https://www.ncbi.nlm.nih.gov/pubmed/28069485

  • Russo D P, Kim M, Wang W, Pinolini D, Shende S, Strickland J, Hartung T, Zhu H* CIIPro: A new read-across portal to fill data gaps using public large scale chemical and biological data. Bioinformatics, 2017; (33) 464-466. https://www.ncbi.nlm.nih.gov/pubmed/28172359

  • Kelley, J. J., Maor, S., Kim, M. K., Lane, A., & Lun, D. S. (2017). MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks. Bioinformatics, btx240.

  • Waters, J. C., Nixon, A., Dwyer, M., Biffinger, J. C., & Lee, K. (2017). Developing elite Neurospora crassa strains for cellulosic ethanol production using fungal breeding. J Ind Microbiol Biotechnol. doi:10.1007/s10295-017-1941-0.

  • Ratti, M., Naddeo, J.J., Griepenburg, O’Malley, S.M., Bubb, D.M., Klein, E.A. Production of Metal Nanoparticles by Pulsed Laser-ablation in Liquids: A Tool for Studying the Antibacterial Properties of Nanoparticles. Vis. Exp. (2017), 124: e55416. 

  • Smith SD, Kawash JK, Karaiskos S, Biluck I, Grigoriev A. (2017) Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants. DNA Research 24(4): 359-369. Link:  https://academic.oup.com/dnaresearch/article-lookup/doi/10.1093/dnares/dsx007

  • Choudhari, S., Grigoriev, A. (2017) Phylogenetic Heatmaps Highlight
    Composition Biases in Sequenced Reads    .  Microorganisms, 5(1), 4. Link: https://www.mdpi.com/2076-2607/5/1/4

  • Angélica L. González, Olivier Dézerald, Pablo A. Marquet, Gustavo Q. Romero & Diane S. Srivastava. 2017. The multidimensional biogeochemical niche: a demonstration using terrestrial and aquatic communities. Front. Ecol. Evol. 5:110. *Invited paper to Research Topic: Progress in Ecological Stoichiometry.

2016

  • Webb, P., Whitlow, J.W., Jr. & Venter, D. (2016, in press).  From exploratory talk to abstract reasoning: A case for far transfer?  Educational Psychology Review
  • Zhao Zhao+, Jinglin Fu*+, Soma Dhakal, Alexander Johnson-Buck, Minghui Liu, Ting Zhang, Neal Woodbury, Yan Liu, Nils G. Walter and Hao Yan* “Nano-caged Enzymes with Enhanced Activity and Increased Stability against Protease Digestion”, Nature Communications 2016, 7, 10619.
  • Ratti, M., Naddeo, J.J., Tan, Y., Griepenburg, J.C., Tomko, J., Trout, T., OMalley, S.M., Bubb, D.M., Klein, E.A. Irradiation with visible light enhances the antibacterial toxicity of silver nanoparticles produced by laser ablation. Applied Physics A (2016), 122(4):346.
  • Moorthy, S., Keklak, J., Klein, E.A. Perspective: Adhesion Mediated Signal Transduction in Bacterial Pathogens. Pathogens (2016), 5(1):23.

  • Hong, D., Man, S., Martin, J.V. (2016) A stochastic mechanism for signal propagation in the brain: Force of rapid random fluctuations in membrane potentials of individual neurons, Journal of Theoretical Biology, 389: 225-236.

  • “A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of GABAA Receptor Subunit Binding Selectivity in Synaptosomes”, K.A. Woll, S. Murlidaran, B. J. Pinch, J. Hénin, X. Wang, R. Salari, M. Covarrubias, W. P. Dailey, G. Brannigan, B. A. Garcia, and R. G. Eckenhoff, J Biol Chem, DOI 10.1074/jbc.M116.736975.
  • “Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands.“, K.A. Woll,W. P. Dailey, G. Brannigan, and R. G. Eckenhoff, Anesthesia & Analgesia, 10.1213/ANE.0000000000001365 .
  • D. Balasubramanian, E. A. Ohneck, J. Chapman, A. Weiss, M. K. Kim, T. Reyes-Robles, J. Zhong, L. N. Shaw, D. S. Lun, B. Ueberheide, B. Shopsin, and V. J. Torres. Staphylococcus aureus coordinates leukocidin expression and pathogenesis by sensing metabolic fluxes via RpiRc. mBio, 7(3):e00818-16, June 2016.
  • M. K. Kim, A. Lane, J. J. Kelley, and D. S. Lun. E-Flux2 and SPOT: Validated methods for inferring intracellular metabolic flux distributions from transcriptomic data. PLoS ONE, 11(6):e0157101, June 2016.
  • H. Swaminathan, A. Garg, C. M. Grgicak, M. Medard, and D. S. Lun. CEESIt: A computational tool for the interpretation of STR mixtures. Forensic Sci. Int. Genet., 22:149-160, May 2016.
  • J. Kim, M. Fabris, G. Baart, M. K. Kim, A. Goossens, W. Vyverman, P. G. Falkowski, and D. S. Lun. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. Plant J., 85(1):161-176, January 2016.

  • Dighton, J. (2016) Fungi in Ecosystem Processes, 2nd Edition, CRC Taylor and Francis, 408pp.

  • Caplan, J. S. et al. (2016) Nutrient foraging strategies of forest shrubs Correspond to interspecific differences in productivity and population growth. Ann. Bot. doi:10.1093/aob/mcw271.

  • J.C. Birget, “Infinitely generated semigroups and polynomial complexity”, International J. of Algebra and Computation 26.04 (2016) pp. 727-750.

  • Xiang J, Zhang Z, Mu Y, Xu X, Guo S, Liu Y, Russo D, Zhu H, Yan B, Bai X Discovery of Novel Tricyclic Thiazepine Derivatives as Anti-Drug-Resistant Cancer Agents by Combining Diversity-Oriented Synthesis and Converging Screening Approach. ACS Comb.Sci. 2016; (18) 230–235. https://www.ncbi.nlm.nih.gov/pubmed/27082930

  • Ribay K, Kim M, Wang W, Pinolini D, Zhu H* Hybrid Modeling of Estrogen Receptor Binding Agents Using Advanced Cheminformatics Tools and Massive Public Data. Front. Environ. Sci. 2016; (4) 12. PMCID: PMC5023020. https://www.ncbi.nlm.nih.gov/pubmed/27642585

  • Kim M, Huang R, Sedykh A, Zhang J, Xia M, Zhu H* Mechanism profiling liver toxicants by using antioxidant response element assay data model and public big data. Environ. Health Perspect. 2016; (124) 634-641. PMCID: PMC4858396 https://www.ncbi.nlm.nih.gov/pubmed/26383846

  • Mu Y, Liu Y, Xiang J, Zhang Q, Zhai S, Russo D P, Zhu H, Bai X, Yan B From fighting depression to conquering tumors: a novel tricyclic thiazepine compound as a tubulin polymerization inhibitor Cell Death and Disease. 2016; (7) e2143.

  • Zhu H, Bouhifd M, Kleinstreuer N, Kroese ED, Liu Z, Luechtefeld T, Pamies D, Shen J, Strauss V, Wu S, Hartung T Supporting read-across using biological data. ALTEX. 2016; (33) 167-182. (ALTEX cover paper. Featured together with following 5 ALTEX papers by Science Feb 12, 2016 “A crystal ball for chemical safety” and Nature Feb 11, 2016 “Legal tussle delays launch of huge toxicity database”) PMCID: PMC4834201 https://www.ncbi.nlm.nih.gov/pubmed/26863516

  • Ball N, Cronin M T, Shen J, Adenuga M D, Blackburn K, Booth E D, Bouhifd M, Donley E, Egnash L, Freeman J J, Hastings C, Juberg D R, Kleensang A, Kleinstreuer N, Kroese E D, Luechtefeld T, Maertens A, Marty S, Naciff J M, Palmer J, Pamies D, Penman M, Richarz A N, Russo D P, Stuard S B, Patlewicz G, van Ravenzwaay B, Wu S, Zhu H, Hartung T Toward Good Read-Across Practice (GRAP) guidance. ALTEX. 2016; (33) 149-166. https://www.ncbi.nlm.nih.gov/pubmed/26863606

  • Luechtefeld T, Maertens A, Russo D P, Rovida C, Zhu H, Hartung T Analysis of publically available skin sensitization data from REACH registrations 2008-2014. ALTEX. 2016; (33) 135-148. https://www.ncbi.nlm.nih.gov/pubmed/26863411

  • Luechtefeld T, Maertens A, Russo D P, Rovida C, Zhu H, Hartung T Analysis of Draize eye irritation testing and its prediction by mining publicly available 2008-2014 REACH data. ALTEX. 2016; (33) 123-134. https://www.ncbi.nlm.nih.gov/pubmed/26863293

  • Luechtefeld T, Maertens A, Russo D P, Rovida C, Zhu H, Hartung T Analysis of public oral toxicity data from REACH registrations 2008-2014. ALTEX. 2016; (33) 111-122. https://www.ncbi.nlm.nih.gov/pubmed/26863198

  • Luechtefeld T, Maertens A, Russo D P, Rovida C, Zhu H, Hartung T Global analysis of publicly available safety data for 9,801 substances registered under REACH from 2008-2014. ALTEX. 2016; (33) 95-109. https://www.ncbi.nlm.nih.gov/pubmed/26863090

  • Zhang Y, Wang Y, Liu A, Xu S L, Zhao B, Zhang Y, Zou H, Wang W, Zhu H, Yan B Modulation of Carbon Nanotube’s Perturbation to the Metabolic Activity of CYP3A4 in the Liver. Advanced Functional Materials. 2016; (26) 841-850. (Advanced Functional Materials cover paper)

  • Huggins T.M., Whiteley J.M., Love, C.T., Lee K., Lee S-H.,Ren Z.J., Biffinger, J.C. 2016. Controlled Growth of Nanostructured Biotemplates with Cobalt and Nitrogen Codoping as a Binderless Lithium-Ion Battery Anode. DOI: 10.1021/acsami.6b09300

  • Ratti, M.#*, Naddeo, J.J.#*, Tan, Y.#, Griepenburg, J.C., Tomko, J.#, Trout, T.#, O’Malley, S.M., Bubb, D.M., Klein, E.A. Irradiation with visible light enhances the antibacterial toxicity of silver nanoparticles produced by laser ablation. Applied Physics A (2016), 122(4):346. 

  • Moorthy,S., Keklak, J., Klein, E.A. Perspective: Adhesion Mediated Signal Transduction in Bacterial Pathogens. Pathogens (2016), 5(1):23. 

  • Karaiskos, S., Grigoriev, A. (2016) Dynamics of tRNA fragments and their targets in aging mammalian brain. F1000Research, 5(ISCB Comm J):2758.  Link: https://f1000research.com/articles/5-2758/

  • Balasubramanian, E. A. Ohneck, J. Chapman, A. Weiss, M. K. Kim, T. Reyes-Robles, J. Zhong, L. N. Shaw, D. S. Lun, B. Ueberheide, B. Shopsin, and V. J. Torres. Staphylococcus aureus coordinates leukocidin expression and pathogenesis by sensing metabolic fluxes via RpiRc. mBio, 7(3):e00818-16, June 2016.

  • Zhu H*, Menghang Xia High throughput screening in toxicology. Springer Science+Business Media LLC, 2016, New York, ISBN 978-1-4939-6344-7. https://www.springer.com/us/book/9781493963447

  • K. Kim, A. Lane, J. J. Kelley, and D. S. Lun. E-Flux2 and SPOT: Validated methods for inferring intracellular metabolic flux distributions from transcriptomic data. PLoS ONE, 11(6):e0157101, June 2016.

  • Swaminathan, A. Garg, C. M. Grgicak, M. Medard, and D. S. Lun. CEESIt: A computational tool for the interpretation of STR mixtures. Forensic Sci. Int. Genet., 22:149-160, May 2016.

  • Kim, M. Fabris, G. Baart, M. K. Kim, A. Goossens, W. Vyverman, P. G. Falkowski, and D. S. Lun. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. Plant J., 85(1):161-176, January 2016.

2015

  • M. Caponigro, M. Fornasier, B. Piccoli, E. Trelat: Sparse stabilization and control of alignment models, Mathematical Models and Methods in Applied Sciences, 25 (2015), 521{564.
  • N. Swaminathan, C. M. Grgicak, M. Medard, and D. S. Lun. NOCIt: A computational method to infer the number of contributors to DNA samples analyzed by STR genotyping. Forensic Sci. Int. Genet., 16:172-180, May 2015.
  • John Collins, Ting Zhang, Scott Huston, Fangfang Sun, Percival Zhang and Jinglin Fu* “A Hidden Transhydrogen Activity of A FMN-Bound Diaphorase under Anaerobic Conditions” PLoS One, accepted.
  • Minghui Liu, Jinglin Fu, Xiaodong Qi, Shaun Wootten, Neal W. Woodbury, Yan Liu, Hao Yan* “A three-enzyme pathway with an optimized geometric arrangement to facilitate substrate transfer” ChemBioChem, accepted.
  • Whitlow, J.W., Jr. & Loatman, P.A. (2015).  When patterning discriminations are harder than biconditional ones: A cue constellation approach.  Journal of Experimental Psychology: Animal Learning and Cognition, 41, 354-370.
  • Naddeo, J.J., Ratti, M., OMalley, S.M., Griepenburg, J.C., Bubb, D.M., Klein, E.A. Antibacterial properties of nanoparticles: a comparative review of chemically synthesized and laser-generated particles. Advanced Science, Engineering, and Medicine (2015), 7(12):1044-1057.
  • Interactions of  L-3,5,3?-triiodothyronine, Allopregnanolone, and Ivermectin with the GABA(A) receptor: Evidence for Overlapping Intersubunit Binding Modes, T. Westergard, R. Salari, J.V. Martin, G. Brannigan, PLOS ONE,  DOI: 10.1371/journal.pone.0139072 (2015). (Link)
  • Role of the fourth transmembrane-helix in the allosteric modulation of pentameric ligand-gated ion channels, C. Carswell, C.M Hénault, S. Murlidaran, J.P.D Therien, P.F. Juranka, J.A Surujballi, G. Brannigan, J. E. Baenziger,Structure, DOI:10.1016/j.str.2015.06.020 (2015). (Link)
  • Membrane protein structure, function, and dynamics: a perspective from experiments and theory, Z. Cournia…G. Brannigan…A-N. Bondar, Journal of Membrane Biology DOI:10.1007/s00232-015-9802-0 (2015). (Link)
  • Karaiskos, S., Naqvi, A., Swanson, K., Grigoriev, A. (2015) Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biology Direct, 10 (1), 51.
  • Smith SD, Kawash JK, Grigoriev A: GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ, 2015, 3:e836

2014

  • N. Bou-Rabee, A. Donev, E. Vanden-Eijnden. Metropolized Integration Schemes for Self-Adjoint Diffusions. Multiscale Modeling and Simulation, 12, 781–831, 2014.
  • N. Bou-Rabee. Time Integrators for Molecular Dynamics. Entropy, 16, 138–162, 2014.
  • B. Piccoli, F. Rossi: Generalized Wasserstein distance and its application to transport equation with source, Archive for Rational Mechanics and Analysis, 211 (2014), 335{358.
  • B. Weiser, R. Salari, R.G. Eckenhoff, G. Brannigan. Computational Investigation of Cholesterol Binding Sites on Mitochondrial VDAC ,  J Phys Chem B., 118 (33) 9852-9860, 2014. 
  • J. Hénin, R. Salari, S. Murlidaran, G. Brannigan. A Predicted binding site for cholesterol on the GABA(A) receptor ,  Biophys J, 106 (9) 1938–1949, 2014. 
  • R. Salari, S. Murlidaran, G. Brannigan, Pentameric ligand-gated ion channels : Insights from Computation , Mol Sim, DOI:10.1080/08927022.2014.896462, 2014.
  • H. Zhu H, J. Zhang, M. Kim, A. Boison, A. Sedykh, K. Moran. Big Data in Chemical Toxicity Research: the Use of High-Throughput Screening Assays to Identify Potential Toxicants. Chem. Res. Tox. 27(10): 1643-1651, October 2014
  • J. Zhang, J-H. Hsieh, H. Zhu. Profiling animal toxicants by automatically mining public bioassay data: a big data approach for computational toxicology. PLoS One 9(6): e99863, June 2014
  • M.G. Niepielko, R. A. Marmion, K. Kim, D. Luor, C. Ray, N. Yakoby. Chorion Patterning: A window into gene regulation and Drosophila species-relatedness. 2014. Molecular Biology & Evolution. 31 (1):154-164.
  • M.G. Niepielko and N. Yakoby. Evolutionary changes in TGF-alpha distribution underlie morphological diversity in Drosophila eggshells. 2014. Development 15;141(24):4710-4715.
  • E.W. Gachomo, T. Kefela, P. Houngnandan, L. Baba-Moussa and, S.O. Kotchoni. Bradyrhizobium japonicum IRAT FA3 increases biomass, yield and drought tolerance in plants. Journal of Biology and Nature, 1(1):12-23, December 2014.
  • Grigoriev, A.*, & Bonini, N. M.* Age-dependent patterns of microRNA RISC loading (2014) Aging, 6(9), 705–706.
  • Choudhari S.^, Lohia R.^, Grigoriev A. (2014) Comparative Metagenome Analysis of an Alaskan Glacier. J. Bioinform. Comput. Biol.
  • Jinglin Fu*, Yuhe Renee Yang, Alexander Johnson-Buck, Minghui Liu, Yan Liu, Nils G. Walter, Neal W. Woodbury and Hao Yan* “Multi-enzyme complexes on DNA scaffolds capable of substrate channeling with an artificial swinging arm” Nature Nanotechnology 2014, 9, 531–536.
  • H. Harikrishnan, V. Shanmugaiah, N. Balasubramanian, M.P. Sharma, S.O. Kotchoni, S. Huang, D.B. Szymanski and, C.J. Staiger. Antagonistic potential of native strain Streptomyces aurantiogriseus VSMGT1014 against sheath blight of rice disease. World Journal of Microbiology and Biotechnology, 30:3149-3161, December 2014.
  • Choi, Y. Ye, D. Salas de la Cruz, W. Liu, K. I. Winey, Y. A. Elabd, J. Runt, R. H. Colby, Macromolecules, 47 (2), 777-790, 2014.“Dielectric and viscoelastic responses of imidazolium-based ionomers with different counterions and side chain lengths.”
  • K. Ip, N. Donoghue, M. K. Kim, and D. S. Lun. Constraint-based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids inEscherichia coli. Biotechol. Bioeng., 111(10):2056-2066, October 2014.

2013

2012

2011

2010