Xiaowen Liu

11 papers in the catalog · USA, Indianapolis, Canada

Xiaowen Liu: 11 papers in the catalog · USA, Indianapolis, Canada · Indiana University Indianapolis, Indiana University School of Medicine · Works on AI proteomics perspective, Champs, Deep learning protein scaffold filling

Affiliations

Indiana University Indianapolis
Indiana University School of Medicine · Center for Computational Biology and Bioinformatics
Indiana University-Purdue University Indianapolis · Department of BioHealth Informatics
Tulane University · Deming Department of Medicine, School of Medicine
University of Waterloo · David R. Cheriton School of Computer Science

Elsewhere

ORCID 0000-0003-4139-1127 · OpenAlex

Papers

AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
Generative AI Models for the Protein Scaffold Filling Problem (2025, Journal of Computational Biology)
Deep Learning Approaches for the Protein Scaffold Filling Problem (2022, 2022 IEEE 34th International Conference on Tools with Artificial Intelligence (ICTAI))
De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods (2017, PROTEOMICS)
Filling a Protein Scaffold With a Reference (2017, IEEE Transactions on NanoBioscience)
Top-down analysis of protein samples by de novo sequencing techniques (2016, Bioinformatics)
Filling a Protein Scaffold with a Reference (2016, Lecture Notes in Computer Science)
De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015, Journal of Proteome Research)
De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014, Journal of Proteome Research)
Better score function for peptide identification with ETD MS/MS spectra (2010, BMC Bioinformatics)
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009, Bioinformatics)

Methods and tools

AI proteomics perspective, Champs, Deep learning protein scaffold filling, Generative AI protein scaffold filling, PEAKS, Protein scaffold filling with a reference, T-Bruijn graph top-down de novo sequencing, Top-down plus bottom-up de novo protein sequencing, Top-down protein analysis from de novo strings

Co-authors (85)

Ranked by Newman fractional collaboration strength, so a pair on a two-author paper counts for more than a pair on a 50-author consortium paper.

Binhai Zhu (Montana State University) strength 1.07, 4 shared
Letu Qingge strength 1.07, 4 shared
Bin Ma strength 0.67, 2 shared
Farong Zhong strength 0.67, 2 shared
Kira Vyatkina strength 0.46, 4 shared
Lennard J. M. Dekker strength 0.46, 4 shared
Ljiljana Paša-Tolić strength 0.46, 4 shared
Martijn M. VanDuijn strength 0.46, 4 shared
Nikola Tolić strength 0.46, 4 shared
Si Wu strength 0.46, 4 shared
Theo M. Luider strength 0.46, 4 shared
Jordan Sturtz strength 0.40, 2 shared
Baozhen Shan strength 0.33, 1 shared
Denis Yuen strength 0.33, 1 shared
Lei Xin strength 0.33, 1 shared
Yonghua Han strength 0.33, 1 shared
Pavel A. Pevzner strength 0.32, 3 shared
Kushal Badal strength 0.20, 1 shared
Richard Annan strength 0.20, 1 shared
Xiaohong Yuan strength 0.20, 1 shared
Xingang Fu strength 0.20, 1 shared
Mikhail Dvorkin strength 0.19, 2 shared
Sonya Alexandrova strength 0.19, 2 shared
Qiang Kou strength 0.09, 1 shared
Asif Khan strength 0.02, 1 shared
Benjamin Boyang Sun strength 0.02, 1 shared
Bing Zhang strength 0.02, 1 shared
Chao Liu strength 0.02, 1 shared
Chen Li strength 0.02, 1 shared
Cheng Chang strength 0.02, 1 shared
Chris Sander strength 0.02, 1 shared
Christopher M. Overall strength 0.02, 1 shared
Eric W. Deutsch strength 0.02, 1 shared
Fuchu He strength 0.02, 1 shared
Gilbert S. Omenn strength 0.02, 1 shared
Haixu Tang strength 0.02, 1 shared
Henning Hermjakob strength 0.02, 1 shared
Huanhuan Gao strength 0.02, 1 shared
Huilin Jin strength 0.02, 1 shared
Jiangning Song strength 0.02, 1 shared

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