Neda Bagheri, PhD - Publications

Chemical and Biological Engineering Northwestern University, Evanston, IL 
Computational biology and control theory

32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Xue AY, Yu AM, Lucks JB, Bagheri N. DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Bioinformatics (Oxford, England). PMID 31389563 DOI: 10.1093/bioinformatics/btz449  1
2019 Finkle JD, Bagheri N. Hybrid analysis of gene dynamics predicts context specific expression and offers regulatory insights. Bioinformatics (Oxford, England). PMID 30994899 DOI: 10.1093/bioinformatics/btz256  1
2019 Yamankurt G, Berns EJ, Xue A, Lee A, Bagheri N, Mrksich M, Mirkin CA. Exploration of the nanomedicine-design space with high-throughput screening and machine learning. Nature Biomedical Engineering. 3: 318-327. PMID 30952978 DOI: 10.1038/s41551-019-0351-1  0.6
2018 Finkle JD, Wu JJ, Bagheri N. Windowed Granger causal inference strategy improves discovery of gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 29440433 DOI: 10.1073/pnas.1710936115  1
2017 Xue AY, Szymczak LC, Mrksich M, Bagheri N. Machine learning on SAMDI mass spectrometry signal to noise ratio improves peptide array designs. Analytical Chemistry. PMID 28719743 DOI: 10.1021/acs.analchem.7b01728  1
2016 Yu JS, Bagheri N. Multi-class and multi-scale models of complex biological phenomena. Current Opinion in Biotechnology. 39: 167-173. PMID 27115496 DOI: 10.1016/j.copbio.2016.04.002  1
2015 Ciaccio MF, Chen VC, Jones RB, Bagheri N. The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integrative Biology : Quantitative Biosciences From Nano to Macro. 7: 776-91. PMID 26057728 DOI: 10.1039/c5ib00065c  1
2014 Duncan MT, Shin S, Wu JJ, Mays Z, Weng S, Bagheri N, Miller WM, Shea LD. Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnology and Bioengineering. 111: 2082-94. PMID 24853077 DOI: 10.1002/bit.25262  1
2014 Ciaccio MF, Finkle JD, Xue AY, Bagheri N. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture. Integrative and Comparative Biology. 54: 296-306. PMID 24813462 DOI: 10.1093/icb/icu037  1
2014 Bagheri N, Azadegan-Dehkordi F, Sanei H, Taghikhani A, Rahimian G, Salimzadeh L, Hashemzadeh-Chaleshtori M, Rafieian-kopaei M, Shirzad M, Shirzad H. Associations of a TLR4 single-nucleotide polymorphism with H.pylori associated gastric diseases in iranian patients Clinics and Research in Hepatology and Gastroenterology. 38: 366-371. PMID 24508388 DOI: 10.1016/j.clinre.2013.12.004  0.01
2014 Safkhani M, Peris-Lopez P, Hernandez-Castro JC, Bagheri N. Cryptanalysis of the Cho et al. protocol: A hash-based RFID tag mutual authentication protocol Journal of Computational and Applied Mathematics. 259: 571-577. DOI: 10.1016/  0.04
2014 Bagheri N, Safkhani M, Peris-Lopez P, Tapiador JE. Weaknesses in a new ultralightweight RFID authentication protocol with permutation-RAPP Security and Communication Networks. 7: 945-949. DOI: 10.1002/sec.803  0.04
2013 Dehkordi FA, Rashki A, Bagheri N, Chaleshtori MH, Memarzadeh E, Salehi A, Ghatreh H, Zandi F, Yazdanpanahi N, Tabatabaiefar MA, Chaleshtori MH. Study of VSX1 mutations in patients with keratoconus in southwest Iran using PCR-single-strand conformation polymorphism/heteroduplex analysis and sequencing method. Acta Cytologica. 57: 646-51. PMID 24107477 DOI: 10.1159/000353297  0.01
2013 Bagheri N, Taghikhani A, Rahimian G, Salimzadeh L, Azadegan Dehkordi F, Zandi F, Chaleshtori MH, Rafieian-Kopaei M, Shirzad H. Association between virulence factors of helicobacter pylori and gastric mucosal interleukin-18 mRNA expression in dyspeptic patients Microbial Pathogenesis. 65: 7-13. PMID 24036181 DOI: 10.1016/j.micpath.2013.08.005  0.01
2013 Yazdanpanahi N, Tabatabaiefar MA, Farrokhi E, Abdian N, Bagheri N, Shahbazi S, Noormohammadi Z, Chaleshtori MH. Compound heterozygosity for two novel SLC26A4 mutations in a large Iranian pedigree with Pendred syndrome Clinical and Experimental Otorhinolaryngology. 6: 201-208. DOI: 10.3342/ceo.2013.6.4.201  0.01
2013 Bagheri N, Safkhani M, Peris-Lopez P, Tapiador JE. Comments on security improvement of an RFID security protocol of ISO/IEC WD 29167-6 Ieee Communications Letters. 17: 805-807. DOI: 10.1109/LCOMM.2013.021213.122837  0.04
2013 Picazo-Sanchez P, Bagheri N, Peris-Lopez P, Tapiador JE. Two RFID standard-based security protocols for healthcare environments Journal of Medical Systems. 37. DOI: 10.1007/s10916-013-9962-3  0.04
2013 Yu J, Bagheri N. Agent based models of heterogeneous tumor cell populations Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 925.  1
2012 Han Q, Bagheri N, Bradshaw EM, Hafler DA, Lauffenburger DA, Love JC. Polyfunctional responses by human T cells result from sequential release of cytokines. Proceedings of the National Academy of Sciences of the United States of America. 109: 1607-12. PMID 22160692 DOI: 10.1073/pnas.1117194109  1
2012 Safkhani M, Bagheri N, Peris-Lopez P, Mitrokotsa A, Hernandez-Castro JC. Weaknesses in another Gen2-based RFID authentication protocol 2012 Ieee International Conference On Rfid-Technologies and Applications, Rfid-Ta 2012. 80-84. DOI: 10.1109/RFID-TA.2012.6404572  0.04
2012 Safkhani M, Bagheri N, Peris-Lopez P, Mitrokotsa A. On the traceability of tags in SUAP RFID authentication protocols 2012 Ieee International Conference On Rfid-Technologies and Applications, Rfid-Ta 2012. 292-296. DOI: 10.1109/RFID-TA.2012.6404532  0.04
2012 Hernandez-Castro JC, Peris-Lopez P, Safkhani M, Bagheri N, Naderi M. Another fallen hash-based RFID authentication protocol Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7322: 29-37. DOI: 10.1007/978-3-642-30955-7_4  0.04
2011 Bagheri N, Shiina M, Lauffenburger DA, Korn WM. A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition. Plos Computational Biology. 7: e1001085. PMID 21379332 DOI: 10.1371/journal.pcbi.1001085  1
2011 Ghotbi MY, Bagheri N, Sadrnezhaad SK. Large pore volume mesoporous copper particles and scaffold microporous carbon material obtained from an inorganic-organic nanohybrid material, copper-succinate-layered hydroxide Journal of Colloid and Interface Science. 362: 89-93. DOI: 10.1016/j.jcis.2011.05.086  0.01
2010 Hildebrandt S, Bagheri N, Gunawan R, Mirsky H, Shoemaker J, Taylor S, Petzold L, Doyle FJ. Systems Analysis for Systems Biology Systems Biomedicine. 249-272. DOI: 10.1016/B978-0-12-372550-9.00010-9  1
2008 Bagheri N, Lawson MJ, Stelling J, Doyle FJ. Modeling the Drosophila melanogaster circadian oscillator via phase optimization. Journal of Biological Rhythms. 23: 525-37. PMID 19060261 DOI: 10.1177/0748730408325041  1
2008 Bagheri N, Stelling J, Doyle FJ. Circadian phase resetting via single and multiple control targets. Plos Computational Biology. 4: e1000104. PMID 18795146 DOI: 10.1371/journal.pcbi.1000104  1
2008 Bagheri N, Taylor SR, Meeker K, Petzold LR, Doyle FJ. Synchrony and entrainment properties of robust circadian oscillators. Journal of the Royal Society, Interface / the Royal Society. 5: S17-28. PMID 18426774 DOI: 10.1098/rsif.2008.0045.focus  1
2007 Bagheri N, Stelling J, Doyle FJ. Quantitative performance metrics for robustness in circadian rhythms. Bioinformatics (Oxford, England). 23: 358-64. PMID 17158515 DOI: 10.1093/bioinformatics/btl627  1
2007 Bagheri N, Stelling J, Doyle FJ. Circadian phase entrainment via nonlinear model predictive control International Journal of Robust and Nonlinear Control. 17: 1555-1571. DOI: 10.1002/rnc.1209  1
2006 Doyle FJ, Gunawan R, Bagheri N, Mirsky H, To TL. Circadian rhythm: A natural, robust, multi-scale control system Computers and Chemical Engineering. 30: 1700-1711. DOI: 10.1016/j.compchemeng.2006.05.029  1
2005 Bagheri N, Stelling J, Doyle FJ. Optimal phase-tracking of the nonlinear circadian oscillator Proceedings of the American Control Conference. 5: 3235-3240.  1
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