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List of works by Xin Gao

A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus

scientific article

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

scientific article

A Slice-based 13C-detected NMR Spin System Forming and Resonance Assignment Method

scientific article published on 25 June 2018

A deep learning framework to predict binding preference of RNA constituents on protein surface

scientific article published on 30 October 2019

A fast fiducial marker tracking model for fully automatic alignment in electron tomography

scientific article published on 23 October 2017

A framework for scalable parameter estimation of gene circuit models using structural information.

scientific article published on July 2013

A joint method for marker-free alignment of tilt series in electron tomography

scientific article published on 01 July 2019

A novel constrained reconstruction model towards high-resolution sub-tomogram averaging

scientific article published on 16 October 2019

A novel method for improved accuracy of transcription factor binding site prediction

scientific article published on 2 April 2018

A protein-dependent side-chain rotamer library.

scientific article

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

scientific article published in August 2013

Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning

scientific article published on 19 March 2022

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming.

scientific article

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.

scientific article published on 18 August 2015

Approximate Kernel Selection via Matrix Approximation

scientific article published on 14 January 2020

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

scientific article

AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis

scientific article published on 23 September 2020

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction

scientific article published on 01 January 2019

AuTom: A novel automatic platform for electron tomography reconstruction.

scientific article

Automatic peak selection by a Benjamini-Hochberg-based algorithm

scientific article

Bag-of-features based medical image retrieval via multiple assignment and visual words weighting.

scientific article

Bayesian peak picking for NMR spectra.

scientific article

Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression

scientific article published on 13 November 2015

Bioinformatics clouds for big data manipulation

scientific article

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

scientific article

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

scientific article

CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming

scientific article published on 25 February 2020

Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility

scientific article published in 2024

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY.

scientific article

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

scientific article published on 17 December 2019

Computer-aided drug repurposing for cancer therapy: Approaches and opportunities to challenge anticancer targets

scientific article published on 25 September 2019

Condensing Raman spectrum for single-cell phenotype analysis

scientific article published on 9 December 2015

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis.

scientific article

DCE-MRI texture analysis with tumor subregion partitioning for predicting Ki-67 status of estrogen receptor-positive breast cancers.

scientific article published on 8 December 2017

DEEPre: sequence-based enzyme EC number prediction by deep learning

scientific article published on 23 October 2017

DESM: portal for microbial knowledge exploration systems

scientific article

DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning

scientific article published on 22 September 2021

DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques

scientific article published on 29 June 2020

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification

scientific article published on 01 July 2019

Deep Learning Deepens the Analysis of Alternative Splicing

scientific article published on 01 April 2019

Deep learning in bioinformatics

scientific article published on 08 June 2019

Deep learning in bioinformatics: Introduction, application, and perspective in the big data era

scientific article published on 22 April 2019

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing

scientific article published on 08 January 2020

Diffusion-weighted imaging features of breast tumours and the surrounding stroma reflect intrinsic heterogeneous characteristics of molecular subtypes in breast cancer.

scientific article

Distinct profiling of antimicrobial peptide families

scientific article published on 10 November 2014

Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

scientific article published in January 2017

Error tolerant NMR backbone resonance assignment and automated structure generation

scientific article

Estimating heritability and genetic correlations from large health datasets in the absence of genetic data

scientific article published on 03 December 2019

Facile Synthesis of NH-Free 5-(Hetero)Aryl-Pyrrole-2-Carboxylates by Catalytic C-H Borylation and Suzuki Coupling

scientific article published on 30 April 2020

Feature selection and multi-kernel learning for sparse representation on a manifold.

scientific article

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms

scientific article published on 11 November 2020

Finding optimal interaction interface alignments between biological complexes

scientific article published on June 2015

Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization

scientific article published on 28 August 2019

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data

scientific article published on 01 April 2020

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

scientific article published on 4 January 2018

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment

scientific article published on 14 August 2017

Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data

scientific article

H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing ⬇️

article

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes

scientific article

Harnessing Multi-Role Capabilities of Large Language Models for Open-Domain Question Answering

scientific article published on 08 May 2024

Hologenome analysis of two marine sponges with different microbiomes

scientific article

How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine-aspartic acid (LD) motifs

scientific article published on June 2014

Identification and characterization of SSE15206, a microtubule depolymerizing agent that overcomes multidrug resistance

scientific article published on 19 February 2018

Improving consensus contact prediction via server correlation reduction

scientific article

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

scientific article published on 22 May 2018

In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.

scientific article

Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli

scientific article published on 08 September 2020

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC

scientific article published on 18 June 2020

Integration of dynamic contrast-enhanced magnetic resonance imaging and T2-weighted imaging radiomic features by a canonical correlation analysis-based feature fusion method to predict histological grade in ductal breast carcinoma

scientific article published on 23 October 2019

Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate

scientific article published on 11 February 2019

Joint prediction of breast cancer histological grade and Ki-67 expression level based on DCE-MRI and DWI radiomics

scientific article published on 28 November 2019

Large capillary hemangioma of the temporal bone with a dural tail sign: A case report

scientific article

Learning from Weak and Noisy Labels for Semantic Segmentation

scientific article published on 08 April 2016

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

scientific article

Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms

scientific article published on 22 December 2017

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.

scientific article published on 29 April 2016

Machine Learning To Predict Standard Enthalpy of Formation of Hydrocarbons

scientific article published on 16 September 2019

Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2.

scientific article published on 7 March 2017

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

scientific article published on 16 July 2015

Max-min distance nonnegative matrix factorization.

scientific article published on 26 October 2014

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra.

scientific article

MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data

scientific article published on 09 August 2021

MiR-196a exerts its oncogenic effect in glioblastoma multiforme by inhibition of IκBα both in vitro and in vivo.

scientific article published on 23 January 2014

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

scientific article published on 12 December 2014

Multi-instance dictionary learning via multivariate performance measure optimization

scientific article published in June 2017

Multiple graph regularized protein domain ranking ⬇️

scientific article published on November 19, 2012

NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding

scientific article published on 20 October 2021

Neural Functions Play Different Roles in Triple Negative Breast Cancer (TNBC) and non-TNBC

scientific article published on 20 February 2020

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing

scientific article published on 01 March 2020

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

scientific article published in 2022

Origin and evolution of the bread wheat D genome

scientific article published in 2024

PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes

scientific article published on 16 November 2020

PERK silence inhibits glioma cell growth under low glucose stress by blockage of p-AKT and subsequent HK2's mitochondria translocation.

scientific article

PICKY: a novel SVD-based NMR spectra peak picking method.

scientific article

Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis

scientific article published on 26 May 2022

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

scientific article

Poly(A) motif prediction using spectral latent features from human DNA sequences

scientific article published on July 2013

Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species

scientific article published on 05 November 2020

Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models

scientific article published on 10 November 2021

ProClusEnsem: predicting membrane protein types by fusing different modes of pseudo amino acid composition

scientific article published on 3 March 2012

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.

scientific article

Prolificacy Assessment of Spermatozoan via State-of-the-Art Deep Learning Frameworks

scientific article published on 26 January 2022

Promoter analysis and prediction in the human genome using sequence-based deep learning models

scientific article published on 01 August 2019

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

scientific article

Protein domain recurrence and order can enhance prediction of protein functions

scientific article

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs

scientific article published on 01 February 2020

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.

scientific article published on 26 April 2018

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

scientific article published on 07 September 2021

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis

scientific article

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine.

scientific article published on 12 February 2018

Rise and fall of the global conversation and shifting sentiments during the COVID-19 pandemic

scholarly article by Xiangliang Zhang published in 2021

SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification

scientific article

Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

scientific article published on 27 July 2017

SupportNet: a novel incremental learning framework through deep learning and support data

scholarly article published 8 May 2018

Synthesis and evaluation of modified chalcone based p53 stabilizing agents.

scientific article published on 15 July 2017

Synthesis and identification of novel pyridazinylpyrazolone based diazo compounds as inhibitors of human islet amyloid polypeptide aggregation

scientific article published on 28 November 2018

Synthesis of Fluoroalkoxy Substituted Arylboronic Esters by Iridium-Catalyzed Aromatic C-H Borylation

scientific article published on 17 August 2015

Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions

scientific article published on 01 August 2019

The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins.

scientific article

The Emerging Facets of Non-Cancerous Warburg Effect.

scientific article published on 23 October 2017

Towards Fully Automated Structure-Based NMR Resonance Assignment of15N-Labeled Proteins From Automatically Picked Peaks ⬇️

scientific article published on March 1, 2011

Towards artificial general intelligence via a multimodal foundation model

scientific article published on 02 June 2022

Tumour heterogeneity revealed by unsupervised decomposition of dynamic contrast-enhanced magnetic resonance imaging is associated with underlying gene expression patterns and poor survival in breast cancer patients

scientific article published on 17 October 2019

Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

scientific article published on 27 December 2018

Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes.

scientific article

WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering ⬇️

scientific article published on February 10, 2012

Write Summary Step-by-Step: A Pilot Study of Stepwise Summarization

scholarly article

gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles

scientific article published on 24 October 2019

iPAC: A genome-guided assembler of isoforms via phasing and combing paths

scientific article published on 27 January 2020

mir-300 promotes self-renewal and inhibits the differentiation of glioma stem-like cells

scientific article published on 28 January 2014

msRepDB: a comprehensive repetitive sequence database of over 80 000 species

scientific article published on 01 January 2022

scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means

scientific article published in 2023

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