TimeXNet Web: Identifying cellular response networks from diverse omics time-course data.
Phit Ling Tan, Yosvany Lopez, Kenta Nakai and Ashwini Patil, Bioinformatics bty393, 2018. [Article]
Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing.
Yasuo Ouchi, Ashwini Patil, Yusuke Tamura, Hiroshi Nishimasu, Aina Negishi, Sudip Kumar Paul, Naoki Takemura, Takeshi Satoh, Yasumasa Kimura, Makoto Kurachi, Osamu Nureki, Kenta Nakai, Hiroshi Kiyono, Satoshi Uematsu, International Immunology 30(4):141-154, 2018, [Article]
OPAL: Prediction of MoRF regions in instrinsically disordered protein sequences.
Ronesh Sharma, Gaurav Raicar, Tatsuhiko Tsunoda, Ashwini Patil*, Alok Sharma*, Bioinformatics, 34(11):1850-1858, 2018. [Article]
Organism-level analysis of vaccination reveals networks of protection across tissues.
Motohiko Kadoki, Ashwini Patil, Cornelius C. Thaiss, Donald J. Brooks, Surya Pandey, Deeksha Deep, David Alvarez, Ulrich H. von Andrian, Amy J. Wagers, Kenta Nakai, Tarjei S. Mikkelsen, Magali Soumillon and Nicolas Chevrier, Cell 171:398-413, 2017. [Article]
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]
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]
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
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]
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]
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
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
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
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]