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Network analysis of the proteome and peptidome sheds light on human milk as a biological system
- Pieter M. Dekker
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Enhancing coevolutionary signals in protein–protein interaction prediction through clade-wise alignment integration
- Tao Fang
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Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti
- Murali Aarthy
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Immunoinformatics-guided approach for designing a pan-proteome multi-epitope subunit vaccine against African swine fever virus
- Alea Maurice Simbulan
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Plasma proteome profiling reveals the therapeutic effects of the PPAR pan-agonist chiglitazar on insulin sensitivity, lipid metabolism, and inflammation in type 2 diabetes
- Xingyue Wang
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- & Tao Xu
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Protein–protein interaction network module changes associated with the vertebrate fin-to-limb transition
- Pasan C. Fernando
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- & Erliang Zeng
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PACT - Prediction of amyloid cross-interaction by threading
- Jakub W. Wojciechowski
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- & Malgorzata Kotulska
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DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle
- Hideki Maehara
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- & Shinya Kuroda
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Comparative proteomic analysis of edible bird’s nest from different origins
- Xianyang Wang
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Proteomic and phosphoproteomic analyses of myectomy tissue reveals difference between sarcomeric and genotype-negative hypertrophic cardiomyopathy
- Ramin Garmany
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- & Michael J. Ackerman
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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter
- Tzu-Yun Kuo
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- & Ching-Tai Chen
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Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework
- Vikram Singh
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Plasma proteome of growing tumors
- Shashi Gupta
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Proteomic analysis of the effect of hemin in breast cancer
- G. P. Coló
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Large scale proteomic studies create novel privacy considerations
- Andrew C. Hill
- , Claire Guo
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A blood and bronchoalveolar lavage protein signature of rapid FEV1 decline in smoking-associated COPD
- Katarina M. DiLillo
- , Katy C. Norman
- & Kelly B. Arnold
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Integrative Mendelian randomization reveals the soluble receptor for advanced glycation end products as protective in relation to rheumatoid arthritis
- Gha Young Lee
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Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics
- Qiang Zhang
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The amniotic fluid proteome changes with term labor and informs biomarker discovery in maternal plasma
- Gaurav Bhatti
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Proteomics reveals unique identities of human TGF-β-induced and thymus-derived CD4+ regulatory T cells
- Mark Mensink
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Assessment of variability in the plasma 7k SomaScan proteomics assay
- Julián Candia
- , Gulzar N. Daya
- & Keenan A. Walker
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Identification of key candidate genes for IgA nephropathy using machine learning and statistics based bioinformatics models
- Md. Al Mehedi Hasan
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- & Jungpil Shin
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Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.)
- Mahantesha B. N. Naika
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- & Ramanathan Sowdhamini
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Resolving missing protein problems using functional class scoring
- Bertrand Jern Han Wong
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- & Wilson Wen Bin Goh
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iTRAQ-based quantitative proteomic analysis provides insight into the drought-stress response in maize seedlings
- Wen Ren
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Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function
- Raju Dash
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Proteomic profiling of concurrently isolated primary microvascular endothelial cells, pericytes, and vascular smooth muscle cells from adult mouse heart
- Zhiping Cao
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- & Catherine M. Davis
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Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics
- Jen-Hung Wang
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Comparative assessment and novel strategy on methods for imputing proteomics data
- Minjie Shen
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The amniotic fluid proteome changes with gestational age in normal pregnancy: a cross-sectional study
- Gaurav Bhatti
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Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale
- Theodore G. Smith
- , Anuli C. Uzozie
- & Philipp F. Lange
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| Open Access
Computational identification of multiple lysine PTM sites by analyzing the instance hardness and feature importance
- Sabit Ahmed
- , Afrida Rahman
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Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes
- Kalyani B. Karunakaran
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Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)
- Bin Huang
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Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities
- Dvison de Melo Pacífico
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Venom duct origins of prey capture and defensive conotoxins in piscivorous Conus striatus
- S. W. A. Himaya
- , Ai-Hua Jin
- & Richard J. Lewis
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| Open Access
A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry
- Heyi Yang
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Continual proteomic divergence of HepG2 cells as a consequence of long-term spheroid culture
- Andrea Antonio Ellero
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- & Tracey Hurrell
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Improved methods for RNAseq-based alternative splicing analysis
- Rebecca F. Halperin
- , Apurva Hegde
- & Nicholas J. Schork
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Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses
- Takayuki Amemiya
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- & Kazuhiko Fukui
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PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions
- Sonia T. Nicolaou
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- & Jim Warwicker
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Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids
- Yue Wang
- & Paul M. Harrison
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Assessing the degradation of ancient milk proteins through site-specific deamidation patterns
- Abigail Ramsøe
- , Mia Crispin
- & Camilla Speller
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Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds
- Eleni Voukali
- , Nithya Kuttiyarthu Veetil
- & Michal Vinkler
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Proteome-wide profiling and mapping of post translational modifications in human hearts
- Navratan Bagwan
- , Henrik H. El Ali
- & Alicia Lundby
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Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
- Ching-Tai Chen
- , Jen-Hung Wang
- & Ting-Yi Sung
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A comparative study of evaluating missing value imputation methods in label-free proteomics
- Liang Jin
- , Yingtao Bi
- & Yu Tian
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Regulators of TNFα mediated insulin resistance elucidated by quantitative proteomics
- Rodrigo Mohallem
- & Uma K. Aryal
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Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools
- Marek Prachar
- , Sune Justesen
- & Frederik Otzen Bagger
Enhancing missense variant pathogenicity prediction with protein language models using VariPred