Publications – Center for Computational and Integrative Biology

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

2019

CM Hénault, C Govaerts, R Spurny, M Brams, A Estrada-Mondragon, J Lynch, D Bertrand, E Pardon, GL Evans, K Woods, BW Elberson, LG Cuello, G Brannigan, H Nury, J Steyaert, JE Baenziger, C Ulens. A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Nature chemical biology. 15(12):1156-1164. 2019
A McKinstry-Wu, KA Woll, T Joseph, W Bu, ER White, NV Bhanu, BA Garcia, G Brannigan, WP Dailey, RG Eckenhoff. Azi-medetomidine: Synthesis and Characterization of a Novel α2 Adrenergic Photoaffinity Ligand. ACS Chemical Neuroscience. 2019
K Woods, L Sharp, G Brannigan. Untangling direct and domain-mediated interactions between nicotinic acetylcholine receptors in DHA-rich membranes. The Journal of membrane biology. 252(4-5):385-396. 2019
S Murlidaran, J Henin, G Brannigan. Competitive dewetting underlies site-specific binding of general anesthetics to GABA(A) receptors. biorxiv
A Tong, JT Petroff, FF Hsu, PAM Schmidpeter, CM Nimigean, L Sharp, G Brannigan, WWL Cheng. Direct Binding of Phosphatidylglycerol at Specific Sites Modulates Desensitization of a Pentameric Ligand-Gated Ion Channel. eLife(8):e50766. 2019
SX Moffett, EA Klein, G Brannigan, JV Martin. L-3, 3’, 5-triiodothyronine and pregnenolone sulfate inhibit Torpedo nicotinic acetylcholine receptors. PloS one. 14(10)
R Lohia, R Salari G Brannigan. Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism shifts tertiary interactions in a long disordered protein. PLoS computational biology. 15(10). 2019
L Sharp, R Salari, G Brannigan. Boundary lipids of the nicotinic acetylcholine receptor: Spontaneous partitioning via coarse-grained molecular dynamics simulation. Biochim Biophys Acta Biomembr. 1861:887-896. 2019
O Dézerald, C Latorre, JL Betancourt, GAB Vera, AL González. Ecological fidelity and spatiotemporal resolution of arthropod death assemblages from rodent middens in the central Atacama Desert (northern Chile). Quaternary Science Reviews. 210:15-25. 2019
S Benavides‐Gordillo, VF Farjalla, AL González, GQ Romero. Changes in rainfall level and litter stoichiometry affect aquatic community and ecosystem processes in bromeliad phytotelmata. Freshwater Biology. 64(8):1357-1368. 2019
J Fu, SW Oh, AR Pereira. Dna logic-gated proximity assembly circuit for biochemical sensing (Patent).
T Zhang, J Nong, N Alzahrani, Z Wang, SW Oh, T Meier, DG Yang, Y Ke, Y Zhong, J Fu. Self-Assembly of DNA–Minocycline Complexes by Metal Ions with Controlled Drug Release. ACS applied materials & interfaces. 11(33):29512-29521
J Fu, SW Oh, K Monckton, G Arbuckle-Keil, Y Ke, T Zhang. Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures. Small. 18:e1900256. 2019
KD de Young, G Stankeviciute, EA Klein. Sugar-phosphate metabolism regulates stationary phase entry and stalk elongation in Caulobacter crescentus. Journal of bacteriology.
K Mandal, K Pogoda, S Nandi, S Mathieu, A Kasri, E Klein, F Radvanyi, B Goud, PA Janmey, JB Manneville. Role of a kinesin motor in cancer cell mechanics. Nano Letters. 19(11):7691-7702. 2019
G Stankeviciute, AV Miguel, A Radkov, S Chou, KC Huang, EA Klein. Differential modes of crosslinking establish spatially distinct regions of peptidoglycan in Caulobacter crescentus. Molecular Microbiology. 0(0):1-14. 2019
G Stankeviciute, Z Guan, H Goldfine, EA Klein. Caulobacter crescentus Adapts to Phosphate Starvation by Synthesizing Anionic Glycoglycerolipids and a Novel Glycosphingolipid. mBio. 10(2):e00107-19. 2019
JN Werner, H Shi, J Hsin, K Huang, Z Gitai, EA Klein. AimB is a small protein regulator of cell size and MreB assembly. bioRxiv:655720. 2019
N Bou-Rabee, M Holmes-Cerfon. Sticky Brownian Motion and its Numerical Solution. arxiv:1906.06803
JC Birget. New embeddings between the Higman-Thompson groups. arXiv:1902.09414
JL Rhodes, B Steinberg, JC Birget. Global local covers. arXiv:1904.01372
JC Birget. The word problem of the Brin-Thompson groups is coNP-complete. arXiv:1902.03852
J Dighton. Fungi and Remediation of Radionuclide Pollution. Fungal Bioremediation: Fundamentals and Applications (book chapter). 2019
J Dighton. The Roles of Macro Fungi (Basidomycotina) in Terrestrial Ecosystems. Advances in Macrofungi: Diversity, Ecology and Biotechnology (book chapter). 2019
J Nam. Multiplex cis-regulatory analysis. Methods in Cell Biology (book chapter). 159-176. 2019
B Piccoli. Measure differential equations. Archive for Rational Mechanics and Analysis. 233(3):1289-1317. 2019
T Liard, B Piccoli. Well-posedness for scalar conservation laws with moving flux constraints. SIAM Journal on Applied Mathematics. 79 (2), 641-667. 2019
M Chyba, B Piccoli. Special issue on mathematical methods in systems biology. Networks & Heterogeneous Media. 14(1):3081-3097. 2019
F Wu, RE Stern, S Cui, ML Delle Monache, R Bhadani, M Bunting, M Churchill, N Hamilton, B Piccoli, B Seibold, J Sprinkle, DB Work. Tracking vehicle trajectories and fuel rates in phantom traffic jams: Methodology and data. Transportation Research Part C: Emerging Technologies 99:82-10. 2019
RE Stern, Y Chen, M Churchill, F Wu, ML Delle Monache, B Piccoli, B Seibold, J Sprinkle, DB Work. Quantifying air quality benefits resulting from few autonomous vehicles stabilizing traffic. Transportation Research Part D: Transport and Environment. 67:351-365. 2019
R Bhadani, M Bunting, B Seibold, R Stern, S Cui, J Sprinkle, B Piccoli, DB Work. Real-time distance estimation and filtering of vehicle headways for smoothing of traffic waves. Proceedings of the 10th ACM/IEEE International Conference on Cyber-Physical Systems. 2019
B Piccoli, F Rossi, M Tournus. A Wasserstein norm for signed measures, with application to non local transport equation with source term. hal-01665244. 2019
F Camilli, G Cavagnari, R De Maio, B Piccoli. Superposition principle and schemes for Measure Differential Equations. arXiv:1902.05619. 2019
T Liard, B Piccoli. Existence of solutions for scalar conservation laws with moving flux constraints. hal-02149946. 2019
G Gunter, D Gloudemans, RE Stern, S McQuade, R Bhadani, M Bunting, ML Delle Monache, R Lysecky, B Seibold, J Sprinkle, B Piccoli, DB Work. Are commercially implemented adaptive cruise control systems string stable? arXiv:1905.02108. 2019
ML Delle Monache, T Liard, A Rat, R Stern, R Badhani, B Seibold, J Sprinkle, DB Work, B Piccoli. Feedback control algorithms for the dissipation of traffic waves with autonomous vehicles. hal-01930724. 2019
S Mcquade, B Piccoli, NP Duteil. Social dynamics models with time-varying influence. hal-02090560. 2019

2018

JC Birget. Polynomial-time right-ideal morphisms and congruences. International J of Algebra and Computation. 28(05):791-835. 2018
AL González, R Céréghino, O Dézerald, V Farjalla, C Leroy, BA Richardson, MJ Richardson, G Q Romero, D Srivatava. Ecological mechanisms and phylogeny shape invertebrate stoichiometry: a test using detritus-based communities across Central and South America. Functional Ecology. 2018
O Dézerald^, DS Srivastava, R Céréghino, JF Carrias, B Corbara, VF Farjalla, C Leroy, NA Marino, GC Piccoli, BA Richardson, MJ Richardson, GQ Romero, AL González. Functional traits and environmental conditions predict community isotopic niches and energy pathways across spatial scales. Functional Ecology. 2018. ^Postdoc advisee.
L Ludwig^#, MA Barbour, J Guevara, L Avilés, AL González. Caught in the web: spider web architectures affect prey specialization and spider-prey stoichiometric relationships. Ecology and Evolution. 8:6449-6462. 2018. ^#Undergrad student.
AL González, T Buttschardt. Agroforestry systems as alternative for conserving native plant species and improving agro-ecological knowledge. 4th European Agroforestry Conference. 2018
RA Marmion, N Yakoby. In locus analysis of patterning evolution in the BMPR2 Wishful thinking. Development. 145:161083. 2018
S Murlidaran, G Brannigan. Physical Accuracy Leads to Biological Relevance: Best Practices For Simulating Ligand-Gated Ion Channels Interacting With General Anesthetics. Methods in enzymology. 602:3-24. 2018
R Salari, T Joseph, R Lohia, J Henin, G Brannigan. A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol. J Chem Theory Comput. 14(12):6560-6573. 2018
SW Oh, A Pereira, T Zhang, T Li, A Lane, J Fu. DNA‐Mediated Proximity‐Based Assembly Circuit for Actuation of Biochemical Reactions. Angewandte Chemie. 130(40):13270-13274. 2018
S Huston, J Collins, F Sun, T Zhang, TD Vaden, YHP Zhang, J Fu. An activity transition from NADH dehydrogenase to NADH oxidase during protein denaturation. Biotechnology and Applied Biochemistry. 65(3):286-293. 2018
J Fu, Z Zhao, N Woodbury, H Yan. Nanocaged Enzymes with Enhanced Catalytic Activity and Increased Stability. US Patent App (patent). 15(649):351. 2018
YR Yang, J Fu, S Wootten, X Qi, M Liu, H Yan, Y Liu. 2D Enzyme Cascade Network with Efficient Substrate Channeling by Swinging Arms. ChemBioChem. 19(3):212-216. 2018
Z Ge, J Fu, M Liu, S Jiang, A Andreoni, X Zuo, Y Liu, H Yan, C Fan. Constructing Submonolayer DNA Origami Scaffold on Gold Electrode for Wiring of Redox Enzymatic Cascade Pathways. ACS applied materials & interfaces. 11(15):13881-13887. 2018
A Robinson, G Disalvo, S O’Malley, D Bubb, J Griepenburg. Nanoparticle mediated release of polymersomes under single pulsed femto second irradiation. Abstracts of Papers of the American Chemical Society 255. 2018
G Disalvo, A Robinson, J Griepenburg, D Bubb, S O’Malley. Temporal control of encapsulant release from polymersomes upon single pulse irradiation. Abstracts of Papers of the American Chemical Society 255. 2018
DE Culham, D Marom, R Boutin, J Garner, TN Ozturk, N Sahtout, L Tempelhagen, G Lamoureux, JM Wood. Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. Biophysical journal. 115(11):2152-2166. 2018
EA Orabi, G Lamoureux. Cation− π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. The Journal of Physical Chemistry B. 122(8):2251-2260. 2018
G Derevyanko, S Grudinin, Y Bengio, G Lamoureux. Deep convolutional networks for quality assessment of protein folds. arXiv:1801.06252. 2018
G Derevyanko, G Lamoureux. TorchProteinLibrary: A computationally efficient, differentiable representation of protein structure. arXiv:1812.01108. 2018
S Karkar, LE Alfonse, CM Grgicak, DS Lun. Statistical Modeling of Short-Tandem Repeat Capillary Electrophoresis Profiles. IEEE International Conference on Bioinformatics and Biomedicine(BIBM). 2018
H Swaminathan, MO Qureshi, CM Grgicak, K Duffy, DS Lun. Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting. PloS one. 13(11):e0207599. 2018
S Norsworthy, DS Lun, CM Grgicak. Determining the number of contributors to DNA mixtures in the low-template regime: Exploring the impacts of sampling and detection effects. Legal Medicine. 32:1-8. 2018
X Qian, Y Zhang, DS Lun, GC Dismukes. Rerouting of metabolism into desired cellular products by nutrient stress: Fluxes reveal the selected pathways in cyanobacterial photosynthesis. ACS synthetic biology. 7(5):1465-1476. 2018
L Harper, D Balasubramanian, EA Ohneck, WE Sause, J Chapman, B Mejia-Sosa, T Lhakhang, A Heguy, A Tsirigos, B Ueberheide, JM Boyd, DS Lun, VJ Torres. Staphylococcus aureus responds to the central metabolite pyruvate to regulate virulence. mBio. 9(1):e02272-17. 2018
A Krishnan, X Qian, G Ananyev, DS Lun, GC Dismukes. Rewiring of Cyanobacterial Metabolism for Hydrogen Production: Synthetic Biology Approaches and Challenges. Synthetic Biology of Cyanobacteria. 171-213. 2018
LE Alfonse, AD Garrett, DS Lun, KR Duffy, CM Grgicak. A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt. Forensic Science International: Genetics. 32:62-70. 2018
CL Guay, J Nam. Unbiased genome-scale identification of cis-regulatory modules in the human genome by GRAMc. bioRxiv:468405. 2018
M Chyba, B Piccoli. Special issue on mathematical methods in systems biology. Networks & Heterogeneous Media. 14(1):3081-3097. 2019
M Briani, B Piccoli. Fluvial to torrential phase transition in open canals. Networks & Heterogeneous Media. 13(4):663-690. 2018
B Piccoli, NP Duteil, E Trélat. Sparse control to prevent Black Swan clustering in collective dynamics. Annual American Control Conference (ACC). 955-960. 2018
ST McQuade, Z An, NJ Merrill, RE Abrams, K Azer, B Piccoli. Equilibria for large metabolic systems and the LIFE approach. Annual American Control Conference (ACC). 2005-2010. 2018
B Piccoli, M Tournus. A General BV Existence Result for Conservation Laws with Spatial Heterogeneities. SIAM Journal on Mathematical Analysis. 50(3):2901-2927. 2018
ML Delle Monache, S Hammond, B Piccoli. Riemann solver for a macroscopic double-lane roundabout model. Proceedings of the 15th IFAC Symposium on Control in Transportation Systems. 2018
RE Stern, S Cui, ML Delle Monache, R Bhadani, M Bunting, M Churchill, N Hamilton, H Pohlmann, F Wu, B Piccoli, B Seibold, J Sprinkle, DB Work. Dissipation of stop-and-go waves via control of autonomous vehicles: Field experiments. Transportation Research Part C: Emerging Technologies. 89:205-221. 2018
G Cavagnari, A Marigonda, B Piccoli. Averaged time-optimal control problem in the space of positive Borel measures. ESAIM: Control, Optimisation and Calculus of Variations. 24(2):721-740. 2018
M Caponigro, R Ghezzi, B Piccoli, E Trélat. Regularization of chattering phenomena via bounded variation controls. IEEE Transactions on Automatic Control. 2018
RK Bhadani, B Piccoli, B Seibold, J Sprinkle, D Work. Dissipation of Emergent Traffic Waves in Stop-and-Go Traffic Using a Supervisory Controller. IEEE Conference on Decision and Control (CDC). 3628-3633. 2018
B Piccoli, F Rossi. Measure-theoretic models for crowd dynamics. Crowd Dynamics. 1:137-165. 2018
B You, F Li, C Zhang, M Maier, D Margetis, M Luskin, H Liu, H Gao, M Briani, E Cristiani, E Iacomini, V Angulo-Castillo, LCF Ferreira, C Sun, M Li, MLD Monache, Pa Goatin, B Piccoli, E Davoli, P Liu, N Kajiwara, F Siddiqua, Z Wang, S Zhou, M Anguiano, FJ Suárez-Grau. Hamed Zakerzadeh and Sebastian Noelle. Communications in Mathematical Sciences. 16(1). 2018
NJ Merrill, Z An, ST McQuade, F Garin, K Azer, RE Abrams, B Piccoli. Stability of Metabolic Networks via Linear-In-Flux-Expressions. arXiv:1808.08263. 2018
B Piccoli, F Rossi. Measure dynamics with Probability Vector Fields and sources. arXiv:1809.03042. 2018
B Piccoli, NP Duteil, E Trélat. Sparse control of Hegselmann-Krause models: Black hole and declustering. arXiv:1802.00615. 2018
T Liard, B Piccoli. Well-posedness for scalar conservation laws with moving flux constraints. arXiv:1801.04814. 2018
M Briani, B Piccoli. Open canals flow with fluvial to torrential phase transitions on networks. arXiv:1805.06812. 2018
G Cavagnari, A Marigonda, B Piccoli. Generalized Dynamic Programming Principle and Sparse Mean-Field Control Problems. arXiv:1806.06119. 2018
G Bretti, E Cristiani, C Lattanzio, A Maurizi, B Piccoli. Two algorithms for a fully coupled and consistently macroscopic PDE-ODE system modeling a moving bottleneck on a road. arXiv:1807.07461. 2018
ML Delle Monache, T Liard, B Piccoli, R Stern, D Work. Traffic reconstruction using autonomous vehicles. hal-01882309. 2018
ML Delle Monache, K Chi, Y Chen, P Goatin, K Han, JM Qiu, B Piccoli. A three-phase fundamental diagram from three-dimensional traffic data. hal-01864628. 2018
B Piccoli, F Rossi, M Tournus. A Wasserstein norm for signed measures, with application to non local transport equation with source term. hal-01665244. 2018
S Hammond, A Rat, ML Delle Monache, B Piccoli. Operational Performance of a Double-Lane Roundabout with Additional Lane Length Design: Lighthill-Whitham-Richards Model Analysis. hal-01819238. Proceeding of the Transportation Research Board Annual Meeting. 2018

2017

Moffett,S.X., O’Malley, S.M., Man, S., Hong, D. Martin, J.V. (2017) Dynamics of high frequency brain activity. Scientific Reports, 7: 15758. doi:10.1038/s41598-017-15966-6
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
J. J. Kelley, A. Lane, X. Li, B. Mutthoju, S. Maor, D. Egen, and D. S. Lun. MOST: a software environment for constraint-based metabolic modeling and strain design. Bioinformatics, 31(4):610-611, February 2015. https://doi.org/10.1093/bioinformatics/btu685

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

R.A. Marmion, M. Jevtic, A. Springhorn, G. Pyrowolakis, and N. Yakoby. The Drosophila BMPRII, Wishful thinking, is required for eggshell patterning. 2013. Developmental Biology 375:45-53.
L. John Gagliardi and Daniel H. Shain, Is Intracellular pH a Clock for Mitosis?, Theoretical Biology and Medical modelling 2013, 10:8.

2012

General anesthetics predicted to block the GLIC pore with micromolar affinity, D. N. LeBard, J. Hénin, R. G. Eckenhoff, M.L. Klein, G. Brannigan PLoS Computational Biology 8(5): e1002532. (2012).
G. P. Bisson, C. Mehaffy, C. Broeckling, J. Prenni, D. Rifat, D. S. Lun, M. Burgos, D. Weissman, P. C. Karakousis, and K. Dobos. Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampicin-resistant, rpoB-mutant Mycobacterium tuberculosis. J. Bacteriol., 194(23):6441-6452, December 2012.
D. Egen and D. S. Lun. Truncated branch and bound achieves efficient constraint-based genetic design. Bioinformatics, 28(12):1619-1623, June 2012.
A. Brandes, D. S. Lun, K. Ip, J. Zucker, C. Colijn, B. Weiner, and J. E. Galagan. Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS ONE, 7(5):e36947, May 2012.
M. G. Niepielko, K. Ip, J. S. Kanodia, D. S. Lun, and N. Yakoby. Evolution of BMP signaling in Drosophila oogenesis: A receptor-based mechanism. Biophys. J., 102(8):1722-1730, April 2012.
B. Piccoli: Optimal syntheses for state constrained problems and optimization of cancer therapies, Mathematical Control and Related Fields, 2 (2012), 383-398.
N. Bellomo, B. Piccoli, A. Tosin: Modeling crowd dynamics from a complex system viewpoint, Mathematical Models and Methods in Applied Sciences, 22 (2012), DOI:10.1142/S0218202512300049.
B. Piccoli, F. Rossi: Transport equation with nonlocal velocity in Wasserstein spaces: convergence of numerical schemes, Acta Applicandae Mathematicae, (2012), DOI: 10.1007/s10440-012-9771-6.

2011

M. R. Golzarian, R. A. Frick, K. Rajendran, B. Berger, S. Roy, M. Tester, and D. S. Lun. Accurate inference of shoot biomass from high-throughput images of cereal plants. Plant Methods, 7:2, February 2011.
Can molecular cell biology explain chromosome motions?, Shain, D.H. and Gagliardi, L.J., Theoretical Biology and Medical Modelling., 8:15., May 2011.
Mycorrhiza, J. Dighton. In: M. Schaechter (ed) Eukaryotic Microbes, Academic Press. Pp. 73-83. 2011.
Analysis of complex metabolic behavior through pathway decomposition, K. Ip, C. Colijn, and D. S. Lun, BMC Syst. Biol., 5:91, June 2011.
Control of multi-hop communication networks for inter-session network coding, A. Eryilmaz, D. S. Lun, and B. T. Swapna, IEEE Trans. Inform. Theory, 57(2):1092-1110, February 2011.
Genetic and molecular characterization of a blue light photoreceptor MGWC-1 in Magnaporth oryzae, S. Kim, P. Singh, J. Park, S. Park, A. Friedman, T. Zheng, Y-H. Lee, K. Lee, .Fungal Genet. Biol. 48:400-407, 2011.
The Thompson-Higman monoids Mk,i : the J-order, the D-relation, and their complexity, J.C. Birget, International J. of Algebra and Computation 21(1-2) 1 – 34, March 2011.
An IR Study of Poly-1,4-Phenylenevinylene (PPV), the 2,5-Dimethoxy Derivative [(MeO)2-PPV], and their Corresponding Xanthate Precursor Polymers and Monomers, D.Michael Byler, Y. Patel, G. A. Arbuckle-Keil, Spectrochimica Acta Part A, 79, 118-126, 2011.
A computational model for signaling pathways in bounded small-world networks corresponding to brain size. S. Man, D. Hong, M.A. Palis, J.V. Martin, Neurocomputing 2011.
Pattern formation by a moving morphogen source, J. J. Zartman, L. S. Cheung, M. G. Niepielko, C. Bonini, B. Haley, N. Yakoby, and S. Y. Shvartsman. Physical Biology, 2011.
BMP signaling dynamics in the follicle cells of multiple Drosophila species, M. G. Niepielko, Y. Hernáiz-Hernández, and N. Yakoby. Developmental Biology, 354:151-159, 2011.
Nematic Nonocomposites with Enhanced Optical Birefringence , K. K. Vardanyan, E. D. Palazzo, and R. D. Walton, Liq. Cryst. 38 (6) 709-715, 2011.
Time-evolving measures and macroscopic modeling of pedestrian flow, B. Piccoli, A. Tosin, Archive for Rational Mechanics and Analysis, 199 (2011), 707-738.

2010

L. John Gagliardi, Review Article: Continuum Electrostatics in Cell Biology, NeuroQuantology, vol. 8, No. 3, 416-429 (2010).
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain, G. Brannigan, D. N. LeBard, J. Hénin, R. G. Eckenhoff, M. L. Klein, Proc. Natl. Acad. Sci. USA, 107(32), 14122-14127.
An atomistic model for simulations of the general anesthetic isoflurane, J. Hénin, G. Brannigan, W. Dailey, R. Eckenhoff, M. L. Klein, Journal of Physical Chemistry B, 114, 604-612.
Systems biology approaches to understanding mycobacterial survival mechanisms. H. I. M. Boshoff and D. S. Lun. Drug Discov. Today: Dis. Mech., 7(1):e75-e82, Spring 2010. Invited paper.
Sensitivity analysis of permeability parameters for flows on Barcelona networks, L. Rarita, C. D’Apice, B. Piccoli, D. Helbing, Journal of Differential Equations, 249 (2010), 3110-3131.
Neurospora, a potential fungal organism for experimental and evolutionary ecology, Lee, K. & Dighton, J. Fungal Biology Reviews 2010.