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Employment (2)

Combinatics Inc.: Tokyo, JP

2020-04 to present | Founder, CEO
Employment
Source: Self-asserted source
Ashwini Patil

University of Tokyo: Tokyo, JP

2014-09 to 2019-08 | Lecturer (Institute of Medical Science)
Employment
Source: Self-asserted source
Ashwini Patil

Works (43)

Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model

Nature Communications
2024-06-10 | Journal article
DOI: 10.1038/s41467-024-48663-w
Contributors: Sudip Kumar Paul; Motohiko Oshima; Ashwini Patil; Masamitsu Sone; Hisaya Kato; Yoshiro Maezawa; Hiyori Kaneko; Masaki Fukuyo; Bahityar Rahmutulla; Yasuo Ouchi et al.
Source: check_circle
Crossref

A pairwise cytokine code explains the organism-wide response to sepsis

Nature Immunology
2024-02 | Journal article
DOI: 10.1038/s41590-023-01722-8
Contributors: Michihiro Takahama; Ashwini Patil; Gabriella Richey; Denis Cipurko; Katherine Johnson; Peter Carbonetto; Madison Plaster; Surya Pandey; Katerina Cheronis; Tatsuki Ueda et al.
Source: check_circle
Crossref

Organism-Wide Analysis of Sepsis Reveals Mechanisms of Systemic Inflammation

2023-02-02 | Preprint
DOI: 10.1101/2023.01.30.526342
Contributors: Michihiro Takahama; Ashwini Patil; Katherine Johnson; Denis Cipurko; Yoshimi Miki; Yoshitaka Taketomi; Peter Carbonetto; Madison Plaster; Gabriella Richey; Surya Pandey et al.
Source: Self-asserted source
Ashwini Patil

Enrichment patterns of intrinsic disorder in proteins

Biophysical Reviews
2022-12 | Journal article
DOI: 10.1007/s12551-022-01016-7
Contributors: Ashwini Patil
Source: check_circle
Crossref

Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer.

Nature communications
2022-07-13 | Journal article
DOI: 10.1038/s41467-022-31690-w
PMID: 35831322
PMC: PMC9279491
Contributors: Yuji Kubota; Yuko Fujioka; Patil A; Takagi Y; Matsubara D; Iijima M; Momose I; Naka R; Kenta Nakai; Nobuo N. Noda et al.
Source: Self-asserted source
Ashwini Patil

B cell–intrinsic TBK1 is essential for germinal center formation during infection and vaccination in mice

Journal of Experimental Medicine
2022-02-07 | Journal article
DOI: 10.1084/jem.20211336
Contributors: Michelle S.J. Lee; Takeshi Inoue; Wataru Ise; Julia Matsuo-Dapaah; James B. Wing; Burcu Temizoz; Kouji Kobiyama; Tomoya Hayashi; Ashwini Patil; Shimon Sakaguchi et al.
Source: check_circle
Crossref

FEATS: feature selection-based clustering of single-cell RNA-seq data.

Briefings in bioinformatics
2020-12-08 | Journal article
DOI: 10.1093/bib/bbaa306
PMID: 33285568
Source: Self-asserted source
Ashwini Patil

CellKb Immune: a manually curated database of mammalian hematopoietic marker gene sets for rapid cell type identification

2020-12-02 | Preprint
DOI: 10.1101/2020.12.01.389890
Contributors: Ajay Patil; Ashwini Patil
Source: check_circle
Crossref

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.

Life science alliance
2020-09-24 | Journal article
DOI: 10.26508/lsa.202000867
PMID: 32972997
PMC: PMC7536825
Source: Self-asserted source
Ashwini Patil

Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma.

PeerJ
2020-06-26 | Journal article
DOI: 10.7717/peerj.9294
PMID: 32617189
PMC: PMC7323713
Source: Self-asserted source
Ashwini Patil

Clustering of Small-Sample Single-Cell RNA-Seq Data via Feature Clustering and Selection

PRICAI 2019: Trends in Artificial Intelligence
2019 | Book chapter
DOI: 10.1007/978-3-030-29894-4_36
Part of ISBN: 9783030298937
Part of ISBN: 9783030298944
Part of ISSN: 0302-9743
Part of ISSN: 1611-3349
Contributors: Edwin Vans; Alok Sharma; Ashwini Patil; Daichi Shigemizu; Tatsuhiko Tsunoda
Source: Self-asserted source
Ashwini Patil

Protein–Protein Interaction Databases

Encyclopedia of Bioinformatics and Computational Biology
2019 | Book chapter
DOI: 10.1016/b978-0-12-809633-8.20660-2
Contributors: Ashwini Patil
Source: Self-asserted source
Ashwini Patil

Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions.

BMC bioinformatics
2019-02-04 | Journal article
DOI: 10.1186/s12859-018-2396-7
PMID: 30717652
PMC: PMC7653905
Source: Self-asserted source
Ashwini Patil

OPAL+: Length-Specific MoRF Prediction in Intrinsically Disordered Protein Sequences.

Proteomics
2018-11-02 | Journal article
DOI: 10.1002/pmic.201800058
PMID: 30324701
Source: Self-asserted source
Ashwini Patil

TimeXNet Web: identifying cellular response networks from diverse omics time-course data.

Bioinformatics (Oxford, England)
2018-11-01 | Journal article
DOI: 10.1093/bioinformatics/bty393
PMID: 29762638
Source: Self-asserted source
Ashwini Patil

OPAL: prediction of MoRF regions in intrinsically disordered protein sequences.

Bioinformatics (Oxford, England)
2018-06-01 | Journal article
DOI: 10.1093/bioinformatics/bty032
PMID: 29360926
Source: Self-asserted source
Ashwini Patil

Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing.

International immunology
2018-04-01 | Journal article
DOI: 10.1093/intimm/dxy006
PMID: 29617862
Source: Self-asserted source
Ashwini Patil

MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

Journal of theoretical biology
2017-10-16 | Journal article
DOI: 10.1016/j.jtbi.2017.10.015
PMID: 29042212
Source: Self-asserted source
Ashwini Patil

Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues.

Cell
2017-09-21 | Journal article
DOI: 10.1016/j.cell.2017.08.024
PMID: 28942919
PMC: PMC7895295
Source: Self-asserted source
Ashwini Patil

Predicting MoRFs in protein sequences using HMM profiles.

BMC bioinformatics
2016-12-22 | Journal article
DOI: 10.1186/s12859-016-1375-0
PMID: 28155710
PMC: PMC5259822
Source: Self-asserted source
Ashwini Patil

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

Database : the journal of biological databases and curation
2015-12-26 | Journal article
DOI: 10.1093/database/bav117
PMID: 26708988
PMC: PMC4691340
Source: Self-asserted source
Ashwini Patil

Discovery of Intermediary Genes between Pathways Using Sparse Regression.

PloS one
2015-09-08 | Journal article
DOI: 10.1371/journal.pone.0137222
PMID: 26348038
PMC: PMC4562633
Source: Self-asserted source
Ashwini Patil

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes.

FEBS letters
2015-04-23 | Journal article
DOI: 10.1016/j.febslet.2015.04.026
PMID: 25913176
Source: Self-asserted source
Ashwini Patil

TimeXNet: identifying active gene sub-networks using time-course gene expression profiles.

BMC systems biology
2014-12-08 | Journal article
DOI: 10.1186/1752-0509-8-s4-s2
PMID: 25522063
PMC: PMC4290689
Source: Self-asserted source
Ashwini Patil

Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function.

PloS one
2014-02-24 | Journal article
DOI: 10.1371/journal.pone.0089890
PMID: 24587103
PMC: PMC3933697
Source: Self-asserted source
Ashwini Patil

Innate immunity interactome dynamics.

Gene regulation and systems biology
2014-01-06 | Journal article
DOI: 10.4137/grsb.s12850
PMID: 24453478
PMC: PMC3885269
Source: Self-asserted source
Ashwini Patil

Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response.

PLoS computational biology
2013-11-07 | Journal article
DOI: 10.1371/journal.pcbi.1003323
PMID: 24244133
PMC: PMC3820512
Source: Self-asserted source
Ashwini Patil

Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.

BMC systems biology
2013-10-16 | Journal article
DOI: 10.1186/1752-0509-7-s3-s10
PMID: 24555803
PMC: PMC3852273
Source: Self-asserted source
Ashwini Patil

Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification.

Molecular bioSystems
2012-10-01 | Journal article
DOI: 10.1039/c2mb25202c
PMID: 23076520
Source: Self-asserted source
Ashwini Patil

Sequence- and species-dependence of proteasomal processivity.

ACS chemical biology
2012-06-28 | Journal article
DOI: 10.1021/cb3001155
PMID: 22716912
PMC: PMC3423507
Source: Self-asserted source
Ashwini Patil

Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
2012-01-01 | Journal article
PMID: 22174272
Source: Self-asserted source
Ashwini Patil

Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks.

BMC genomics
2011-11-30 | Journal article
DOI: 10.1186/1471-2164-12-s3-s19
PMID: 22369639
PMC: PMC3333178
Source: Self-asserted source
Ashwini Patil

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins.

BMC bioinformatics
2010-10-15 | Journal article
DOI: 10.1186/1471-2105-11-s7-s7
PMID: 21106129
PMC: PMC2957690
Source: Self-asserted source
Ashwini Patil

HitPredict: a database of quality assessed protein-protein interactions in nine species.

Nucleic acids research
2010-10-14 | Journal article
DOI: 10.1093/nar/gkq897
PMID: 20947562
PMC: PMC3013773
Source: Self-asserted source
Ashwini Patil

Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.

Protein science : a publication of the Protein Society
2010-08-01 | Journal article
DOI: 10.1002/pro.425
PMID: 20509167
PMC: PMC2923499
Source: Self-asserted source
Ashwini Patil

Hub promiscuity in protein-protein interaction networks.

International journal of molecular sciences
2010-04-26 | Journal article
DOI: 10.3390/ijms11041930
PMID: 20480050
PMC: PMC2871146
Source: Self-asserted source
Ashwini Patil

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks.

Biophysics (Nagoya-shi, Japan)
2007-07-21 | Journal article
DOI: 10.2142/biophysics.3.27
PMID: 27857564
PMC: PMC5036656
Source: Self-asserted source
Ashwini Patil

Use of transcriptional synergy to augment sensitivity of a splicing reporter assay.

RNA (New York, N.Y.)
2006-03-23 | Journal article
DOI: 10.1261/rna.8306
PMID: 16556940
PMC: PMC1440914
Source: Self-asserted source
Ashwini Patil

Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks.

FEBS letters
2006-03-10 | Journal article
DOI: 10.1016/j.febslet.2006.03.003
PMID: 16542654
Source: Self-asserted source
Ashwini Patil

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

BMC bioinformatics
2005-04-18 | Journal article
DOI: 10.1186/1471-2105-6-100
PMID: 15833142
PMC: PMC1127019
Source: Self-asserted source
Ashwini Patil

HINT: a database of annotated protein-protein interactions and their homologs.

Biophysics (Nagoya-shi, Japan)
2005-02-28 | Journal article
DOI: 10.2142/biophysics.1.21
PMID: 27857549
PMC: PMC5036632
Source: Self-asserted source
Ashwini Patil

PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery.

Genomics
2000-12-01 | Journal article
DOI: 10.1006/geno.2000.6359
PMID: 11161780
Source: Self-asserted source
Ashwini Patil

Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog.

Proceedings of the National Academy of Sciences of the United States of America
1998-06-01 | Journal article
DOI: 10.1073/pnas.95.13.7514
PMID: 9636181
PMC: PMC22669
Source: Self-asserted source
Ashwini Patil
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