• A pairwise cytokine code explains the organism-wide response to sepsis.
  Michihiro Takahama, Ashwini Patil, Gabriella Richey, Denis Cipurko, Katherine Johnson, Peter Carbonetto, Madison Plaster, Surya Pandey, Katerina Cheronis, Tatsuki Ueda, Adam Gruenbaum, Tadafumi Kawamoto, Matthew Stephens, Nicolas Chevrier, Nature Immunology, 25:226, 2024. [Article]
• Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model.
  Sudip Kumar Paul, Motohiko Oshima, Ashwini Patil, Masamitsu Sone, Hisaya Kato, Yoshiro Maezawa, Hiyori Kaneko, Masaki Fukuyo, Bahityar Rahmutulla, Yasuo Ouchi, Kyoko Tsujimura, Mahito Nakanishi, Atsushi Kaneda, Atsushi Iwama, Koutaro Yokote, Koji Eto, Naoya Takayama, Nature Communications, 15:4772, 2024. [Article]

• CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
  Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, CAID predictors, Silvio C E Tosatto, Damiano Piovesan, Nucleic Acids Research, 51(W1):W62-W69, 2023. [Article]
• Investigating how glioblastoma tumor cells exploit their metabolic microenvironment.
  Chloe Shard, Rebecca Ormsby, Santosh Poonnoose, John Toubia, Paul Trim, Lisa Ebert, Ashwini Patil, Guillermo Gomez, Neuro-Oncology, 25(Supplement_5):v274, 2023. [Article]

• Enrichment patterns of intrinsic disorder in proteins.
  Ashwini Patil*, Biophysical Reviews, 14:1487, 2022. [PDF]
• Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer.
  Yuji Kubota, Yuko Fujioka, Ashwini Patil, Yusuke Takagi, Daisuke Matsubara, Masatomi Iijima, Isao Momose, Ryosuke Naka, Kenta Nakai, Nobuo N Noda, Mutsuhiro Takekawa, Nature Communications, 13(1):4063, 2022. [Article]
• B cell–intrinsic TBK1 is essential for germinal center formation during infection and vaccination in mice.
  Michelle S.J. Lee, Takeshi Inoue, Wataru Ise, Julia Matsuo-Dapaah, James B. Wing, Burcu Temizoz, Kouji Kobiyama, Tomoya Hayashi, Ashwini Patil, Shimon Sakaguchi, A. Katharina Simon, Jelena S. Bezbradica, Satoru Nagatoishi, Kouhei Tsumoto, Jun-Ichiro Inoue, Shizuo Akira, Tomohiro Kurosaki, Ken J. Ishii, Cevayir Coban, Journal of Experimental Medicine, 219(2):e20211336, 2022. [Article]

• FEATS: Feature selection based clustering of single-cell RNA-seq data.
  Edwin Vans, Ashwini Patil*, Alok Sharma*, Briefings in Bioinformatics, bbaa306, 2021. [Article]

• CellKb Immune: a manually curated database of mammalian hematopoietic marker gene sets for rapid cell type identification.
  Ajay Patil, Ashwini Patil*, bioRxiv, 2020. [Preprint]
• Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
  Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, et al., DREAM SCTC Consortium, Life Science Alliance, 3(11), 2020. [Article]
• Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma.
  Munmee Dutta, Hidewaki Nakagawa, Hiroaki Kato, Kazuhiro Maejima, Shota Sasagawa, Kaoru Nakano, Aya Sasaki-Oku, Akihiro Fujimoto, Raúl Nicolás Mateos, Ashwini Patil, Hiroko Tanaka, Satoru Miyano, Takushi Yasuda, Kenta Nakai, Masashi Fujita, PeerJ e9294, 2020. [Article]

• Clustering of small-sample single-cell RNA-seq data via feature clustering and selection.
  Edwin Vans, Alok Sharma, Ashwini Patil, Daichi Shigemizu, Tatsuhiko Tsunoda, Pacific Rim International Conference on Artificial Intelligence 445-456, 2019. [PDF]
• OPAL+: length‐specific MoRF prediction in intrinsically disordered protein sequences.
  Ronesh Sharma, Alok Sharma, Gaurav Raicar, Tatsuhiko Tsunoda, Ashwini Patil*, Proteomics 19(6):1800058, 2019. [PDF]
• Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions.
  Ronesh Sharma, Alok Sharma, Ashwini Patil, Tatsuhiko Tsunoda, BMC Bioinformatics 19(13):155-163, 2019. [Article]
• Protein-protein interaction databases.
  Ashwini Patil*, Encyclopedia of Bioinformatics and Computational Biology 2:849-855, 2019. [Book chapter]

• TimeXNet Web: Identifying cellular response networks from diverse omics time-course data.
  Phit Ling Tan, Yosvany Lopez, Kenta Nakai and Ashwini Patil*, Bioinformatics 34(21):3764-3765, 2018. [Article] TimeXNet
• 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]
• MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.
  Ronesh Sharma, Maitsetseg Bayarjargal, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma, Journal of Theoretical Biology 437:9-19, 2018. [PDF]

• 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]

• 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]

• 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] TimeXNet
• 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]
• 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]

• 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]
• Domain distribution and intrinsic disorder in hubs in the human protein–protein interaction network.
  Ashwini Patil*, Kengo Kinoshita and Haruki Nakamura, Protein Science 19(8):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 is now a part of HitPredict)

• 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]
• On the optimal selection of portfolios under limited diversification.
  Jayaram K. Sankaran, Ajay Patil, Journal of Banking and Finance 23(11):1655-1666, 1999. [PDF]
• Computerized Polymorphic Marker Identification: Experimental Validation and a Predicted Human Polymorphism 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]

* Corresponding author, # Joint first/last author