Laboratory of Functional Analysis in silico
Ashwini Patil
Senior Assistant Professor
Human Genome Center
Institute of Medical Science
University of Tokyo

Academic Background View Ashwini Patil's LinkedIn profile
Ph.D. Biosciences, Osaka University
M.S. Biomedical Engineering, University of Texas Southwestern Medical Center, Dallas
B.E. Electronics and Telecommunications, Government College of Engineering, Pune, India

Research Interests
  • Using computational methods to identify cellular response pathways
  • Role of intrinsic structural disorder in protein function
  • Single cell RNA-seq data analysis
Links
Publications View Ashwini Patil's LinkedIn profile
  • Predicting MoRFs in protein sequences using HMM profiles.
    Ronesh Sharma, Shiu Kumar, Tatsuhiko Tsunoda, Ashwini Patil* and Alok Sharma*, BMC Bioinformatics 17(Suppl 19):504, 2016.[PDF]
    (* joint corresponding author).

  • HitPredict version 4 - comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
    Yosvany Lopez, Kenta Nakai and Ashwini Patil, DATABASE 2015:bav117 , 2015.[PDF]

  • Discovery of intermediary genes between pathways using sparse regression.
    Kuo-ching Liang, Ashwini Patil and Kenta Nakai, PLOS ONE 10(9):e0137222, 2015. [PDF]

  • Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes.
    Sriganesh Srihari, Chern Han Yong, Ashwini Patil and Limsoon Wong, FEBS Letters, 589(19 Pt A):2590-602, 2015.[PDF]

  • TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles.
    Ashwini Patil and Kenta Nakai, BMC Systems Biology, 8(Suppl4), S2, 2014. [PDF]

  • Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function.
    Alok Sharma, Abdollah Dehzangi, James Lyons, Seiya Imoto, Satoru Miyano, Kenta Nakai and Ashwini Patil, PLOS ONE 9(2): e89890, 2014. [PDF] Access the recommendation on F1000Prime

  • Innate immunity interactome dynamics.
    Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki and Kenta Nakai, Gene Regulation and Systems Biology 2014:8 1-15, 2014. [PDF]

  • Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response.
    Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki and Kenta Nakai, PLOS Computational Biology 9(11):e1003323, 2013. [PDF] TimeXNet

  • Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.
    Yosvany Lopez, Ashwini Patil and Kenta Nakai, BMC Systems Biology 7(Suppl 2):S10, 2013. [PDF]

  • Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification.
    Harry Amri Moesa, Shunichi Wakabayashi, Kenta Nakai and Ashwini Patil, Molecular BioSystems 8(12):3262-3273, 2012. [PDF]

  • Sequence- and species-dependence of proteasomal processivity.
    Daniel A. Kraut, Eitan Israeli, Erin Schrader, Ashwini Patil, Kenta Nakai, Dhaval Nanavati, Tomonao Inobe and Andreas Matouschek, ACS Chemical Biology 7(8):1444-1453, 2012. [PDF]

  • Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator.
    Ashwini Patil*, Shunsuke Teraguchi*, Huy Dinh, Kenta Nakai and Daron M Standley, Pacific Symposium on Biocomputing 17:164-175, 2012. [PDF]
    (* joint first author).

  • Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks.
    Ashwini Patil, Kenta Nakai and Kengo Kinoshita, BMC Genomics 12 (Suppl 3):S19, 2011. [PDF]

  • HitPredict: a database of quality assessed protein-protein interactions in nine species.
    Ashwini Patil, Kenta Nakai and Haruki Nakamura, Nucleic Acids Research 39:D744:D749, 2011. [PDF] HitPredict

  • Intrinsically disordered domains deviate significantly from random sequences in innate immune and generic mammalian proteins.
    Shunsuke Teraguchi*, Ashwini Patil* and Daron Standley, BMC Bioinformatics 11(Suppl 7):S7, 2010. [PDF]
    (* joint first author).

  • Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.
    Ashwini Patil, Kengo Kinoshita and Haruki Nakamura, Protein Science 19:1461-1468, 2010. [PDF]

  • Hub promiscuity in protein-protein interaction networks.
    Ashwini Patil, Kengo Kinoshita and Haruki Nakamura, International Journal of Molecular Sciences 11(4):1930-1943, 2010. [PDF] One of 10 most cited papers in IJMS

  • The role of charged residues on the surfaces of small hubs in protein-protein interaction networks.
    Ashwini Patil and Haruki Nakamura, BIOPHYSICS 3:27-35, 2007. [PDF]

  • Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks.
    Ashwini Patil and Haruki Nakamura, FEBS Letters 580:2041-2045, 2006. [PDF]

  • Use of Transcriptional Synergy to Augment Sensitivity of a Splicing Reporter Assay.
    Noah Levinson, Rochelle Hinman, Ashwini Patil, Corey R. J. Stephenson, Stefan Werner, Grace H. C. Woo, Jingbo Xiao, Peter Wipf and Kristen W. Lynch, RNA 12(5):925, 2006. [PDF]

  • Filtering high-throughput protein-protein interaction data using a combination of genomic features.
    Ashwini Patil and Haruki Nakamura, BMC Bioinformatics 6:100, 2005. [PDF] HitPredict

  • HINT: a database of annotated protein-protein interactions and their homologs.
    Ashwini Patil and Haruki Nakamura, BIOPHYSICS 1:21-24, 2005. [PDF] HintDB

  • PANORAMA: An integrated web-based sequence analysis tool and its role in gene discovery.
    Alexander Pertsemlidis, Ashwini Pande, Brady Miller, Peter Schilling, Ming-Hui Wei, Michael I.Lerman, John D.Minna, Harold R.Garner, Genomics 70:300-306, 2000. [PDF]

  • Computerized Polymorphic Marker Identification: Experimental Validation and a Predicted Human Ploymorphism Catalog.
    John W.Fondon III, Gina M.Mele, Ruth I.Brezinschek, Donna Cummings, Ashwini Pande, Jonathan Wren, Kevin M.O'Brien, Kenneth C.Kupfer, Ming-Hui Wei, Micheal Lerman, John D.Minna, Harold R.Garner, Proceedings of the National Academy of Sciences 13:7514-7519, 1998. [PDF]

Contact
Institute of Medical Science
University of Tokyo
4-6-1, Shirokanedai,
Minato-ku, Tokyo 108-8639, Japan
Tel: +81-3-5449-5131 Fax: +81-3-5449-5133
Email:
Last update: 10 February 2017