@article{Rimal2024,
  author = "P. Rimal and S. K. Panday and W. Xu and Y. Peng and E. Alexov",
  title = "SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes",
  year = 2024,
  journal = "Bioinformatics",
  publisher = "Oxford University Press (OUP)",
  volume = 40,
  number = 9,
  month = "Sep",
  doi = "10.1093/bioinformatics/btae544",
  url = "http://dx.doi.org/10.1093/bioinformatics/btae544"
}


@article{aprigliano2020increased,
  author = "R. Aprigliano and S. Bradamante and B. Mihaljevic and W. Wang and S. L. F. Martin and D. L. Bordin and M. Bosshard and N. P. Montaldo and Y. Peng and E. Alexov and others",
  title = "Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities",
  year = 2021,
  journal = "Cell Reports Medicine",
  publisher = "Cold Spring Harbor Laboratory",
  volume = 2,
  pages = "100240",
  month = "Apr",
  doi = "https://doi.org/10.1016/j.xcrm.2021.100240",
  url = "https://www.cell.com/cell-reports-medicine/pdf/S2666-3791(21)00056-2.pdf"
}


@article{li2021sampdi,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.",
  year = 2021,
  journal = "Bioinformatics (Oxford, England)"
}


@article{Li2021c,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions",
  year = 2021,
  journal = "Bioinformatics",
  volume = 37,
  number = 21,
  pages = "3760-3765"
}


@article{lee2020mutations,
  author = "Y.-R. Lee and K. Khan and K. Armfield-Uhas and S. Srikanth and N. A. Thompson and M. Pardo and L. Yu and J. W. Norris and Y. Peng and K. W. Gripp and others",
  title = "Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy",
  year = 2020,
  journal = "Nature communications",
  publisher = "Nature Publishing Group",
  volume = 11,
  number = 1,
  pages = "1-17"
}


@article{peng2020ph,
  author = "Y. Peng and R. Kelle and C. Little and E. Michonova and K. G. Kornev and E. Alexov",
  title = "pH-dependent interactions of Apolipophorin-III with a lipid disk",
  year = 2020,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Publishing Company",
  pages = "1-12"
}


@article{panday2019modeling,
  author = "S. K. Panday and M. H. Shashikala and M. Koirala and S. Pahari and A. Chakvorty and Y. Peng and L. Li and Z. Jia and C. Li and E. Alexov",
  title = "Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]",
  year = 2019,
  journal = "Living Journal of Computational Molecular Science",
  publisher = "University of Colorado Boulder",
  volume = 1,
  number = 2,
  pages = "10841"
}


@article{wu2019novel,
  author = "B. Wu and Y. Peng and J. Eggert and E. Alexov",
  title = "Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women",
  year = 2019,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 20,
  number = 19,
  pages = "4828"
}


@article{peng2019dfmd,
  author = "Y. Peng and Y. Yang and L. Li and Z. Jia and W. Cao and E. Alexov",
  title = "DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme",
  year = 2019,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 6,
  pages = "74"
}


@article{li2019delphi,
  author = "C. Li and Z. Jia and A. Chakravorty and S. Pahari and Y. Peng and S. Basu and M. Koirala and S. K. Panday and M. Petukh and L. Li and others",
  title = "DelPhi suite: New developments and review of functionalities",
  year = 2019,
  journal = "Journal of computational chemistry",
  publisher = "John Wiley \& Sons, Inc. Hoboken, USA",
  volume = 40,
  number = 28,
  pages = "2502-2508"
}


@article{spellicy2019three,
  author = "C. J. Spellicy and Y. Peng and L. Olewiler and S. S. Cathey and R. C. Rogers and D. Bartholomew and J. Johnson and E. Alexov and J. A. Lee and M. J. Friez and others",
  title = "Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?",
  year = 2019,
  journal = "Journal of human genetics",
  publisher = "Nature Publishing Group",
  volume = 64,
  number = 6,
  pages = "561-572"
}


@article{wu2019investigating,
  author = "B. Wu and Y. Peng and J. A. Eggert and E. Alexov",
  title = "Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "192a"
}


@article{peng2019electrostatic,
  author = "Y. Peng and M. Koirala and E. Alexov",
  title = "Electrostatic Force Driven Molecular Dynamics Simulations",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "290a"
}


@article{peng2019structural,
  author = "Y. Peng and E. Alexov and S. Basu",
  title = "Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases",
  year = 2019,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 20,
  number = 3,
  pages = "548"
}


@article{peng2018structural,
  author = "Y. Peng and E. Alexov and S. Basu",
  title = "Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases",
  year = 2018
}


@article{tajielyato2018hooks,
  author = "N. Tajielyato and L. Li and Y. Peng and J. Alper and E. Alexov",
  title = "E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein",
  year = 2018,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 8,
  number = 1,
  pages = "1-10"
}


@article{chakravorty2018gaussian,
  author = "A. Chakravorty and Z. Jia and Y. Peng and N. Tajielyato and L. Wang and E. Alexov",
  title = "Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents",
  year = 2018,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 5,
  pages = "25"
}


@article{jia2018capricious,
  author = "Z. Jia and L. Li and Y. Peng and F. Ding and E. Alexov",
  title = "The capricious electrostatic force: Revealing the signaling pathway in integrin $\alpha$ 2-I domain",
  year = 2018,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 17,
  number = 3,
  pages = "1840001"
}


@article{spellicy2018key,
  author = "C. J. Spellicy and J. Norris and R. Bend and C. Bupp and P. Mester and T. Reynolds and J. Dean and Y. Peng and E. Alexov and C. E. Schwartz and others",
  title = "Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects",
  year = 2018,
  journal = "European Journal of Human Genetics",
  publisher = "Nature Publishing Group",
  volume = 26,
  number = 3,
  pages = "420-427"
}


@article{peng2018computational,
  author = "Y. Peng and R. Myers and W. Zhang and E. Alexov",
  title = "Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome",
  year = 2018,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 19,
  number = 1,
  pages = "141"
}


@article{peng2018predicting,
  author = "Y. Peng and L. Sun and Z. Jia and L. Li and E. Alexov",
  title = "Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver",
  year = 2018,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 34,
  number = 5,
  pages = "779-786"
}


@inproceedings{peng2017predicting,
  author = "Y. Peng and E. Alexov",
  title = "Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method",
  year = 2017,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 254
}


@article{li2017forces,
  author = "L. Li and Z. Jia and Y. Peng and S. Godar and I. Getov and S. Teng and J. Alper and E. Alexov",
  title = "Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations",
  year = 2017,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 7,
  number = 1,
  pages = "1-12"
}


@article{pengprotein,
  author = "Y. Peng and E. Alexov",
  title = "Protein Conformational Disease: Visit the Facts at a Glance",
  year = 2017,
  journal = "eLS",
  publisher = "American Cancer Society",
  pages = "1-7"
}


@article{li2017delphiforce,
  author = "L. Li and Z. Jia and Y. Peng and A. Chakravorty and L. Sun and E. Alexov",
  title = "DelPhiForce web server: electrostatic forces and energy calculations and visualization",
  year = 2017,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 33,
  number = 22,
  pages = "3661-3663"
}


@article{peng2017computational,
  author = "Y. Peng and E. Alexov",
  title = "Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes",
  year = 2017,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 85,
  number = 2,
  pages = "282-295"
}


@article{peng2016cofactors,
  author = "Y. Peng and E. Alexov",
  title = "Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model",
  year = 2016,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 84,
  number = 12,
  pages = "1797-1809"
}


@article{peng2016revealing,
  author = "Y. Peng and J. Norris and C. Schwartz and E. Alexov",
  title = "Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase",
  year = 2016,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 17,
  number = 1,
  pages = "77"
}


@article{peng2016investigating,
  author = "Y. Peng and E. Alexov",
  title = "Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding",
  year = 2016,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 84,
  number = 2,
  pages = "232-239"
}


@article{peng2015mutations,
  author = "Y. Peng and J. Suryadi and Y. Yang and T. G. Kucukkal and W. Cao and E. Alexov",
  title = "Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease",
  year = 2015,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 16,
  number = 11,
  pages = "27270-27287"
}