Xin Gao

  • King Abdullah University of Science and Technology, Computer, Electrical and Mathematical Sciences and Engineering Division, Thuwal, Saudi Arabia
  • Carnegie Mellon University, School of Computer Science, Pittsburgh, PA, USA (2009 - 2010)
  • University of Waterloo, ON, Canada (PhD 2009)

According to our database1, Xin Gao authored at least 214 papers between 2007 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports.
CoRR, 2024

Cross-Parametric Generative Adversarial Network-Based Magnetic Resonance Image Feature Synthesis for Breast Lesion Classification.
IEEE J. Biomed. Health Informatics, November, 2023

RPI-CapsuleGAN: Predicting RNA-protein interactions through an interpretable generative adversarial capsule network.
Pattern Recognit., September, 2023

Spatom: a graph neural network for structure-based protein-protein interaction site prediction.
Briefings Bioinform., September, 2023

Graph Neural Network and Spatiotemporal Transformer Attention for 3D Video Object Detection From Point Clouds.
IEEE Trans. Pattern Anal. Mach. Intell., August, 2023

Spectrum-irrelevant fine-grained representation for visible-infrared person re-identification.
Comput. Vis. Image Underst., July, 2023

DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape.
Briefings Bioinform., July, 2023

miProBERT: identification of microRNA promoters based on the pre-trained model BERT.
Briefings Bioinform., May, 2023

End-to-end interpretable disease-gene association prediction.
Briefings Bioinform., May, 2023

A universal framework for single-cell multi-omics data integration with graph convolutional networks.
Briefings Bioinform., May, 2023

Multi-modality attribute learning-based method for drug-protein interaction prediction based on deep neural network.
Briefings Bioinform., May, 2023

TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides.
Patterns, March, 2023

Efficient locality-sensitive hashing over high-dimensional streaming data.
Neural Comput. Appl., February, 2023

Follow the Timeline! Generating an Abstractive and Extractive Timeline Summary in Chronological Order.
ACM Trans. Inf. Syst., January, 2023

scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

CryoAlign: feature-based method for global and local 3D alignment of EM density maps.
CoRR, 2023

Automated Bioinformatics Analysis via AutoBA.
CoRR, 2023

Path to Medical AGI: Unify Domain-specific Medical LLMs with the Lowest Cost.
CoRR, 2023

Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR, 2023

A Topic-aware Summarization Framework with Different Modal Side Information.
CoRR, 2023

SkinGPT: A Dermatology Diagnostic System with Vision Large Language Model.
CoRR, 2023

Efficient automatic segmentation for multi-level pulmonary arteries: The PARSE challenge.
CoRR, 2023

Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.
CoRR, 2023

Audit to Forget: A Unified Method to Revoke Patients' Private Data in Intelligent Healthcare.
CoRR, 2023

Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning.
CoRR, 2023

Follow the Timeline! Generating Abstractive and Extractive Timeline Summary in Chronological Order.
CoRR, 2023

Interpretable Research Interest Shift Detection with Temporal Heterogeneous Graphs.
Proceedings of the Sixteenth ACM International Conference on Web Search and Data Mining, 2023

A Topic-aware Summarization Framework with Different Modal Side Information.
Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2023

Topology-Preserving Computed Tomography Super-Resolution Based on Dual-Stream Diffusion Model.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

Counterfactual Learning on Heterogeneous Graphs with Greedy Perturbation.
Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023

Learn to Encode Heterogeneous Data: A Heterogeneous Aware Network for Multi-Future Trajectory Prediction.
Proceedings of the International Joint Conference on Neural Networks, 2023

A Distribution Preserving Model for Molecular Graph Generation.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Improving the Robustness of Summarization Systems with Dual Augmentation.
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 2023

Learning towards Selective Data Augmentation for Dialogue Generation.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

Towards Efficient and Domain-Agnostic Evasion Attack with High-Dimensional Categorical Inputs.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS.
Genom. Proteom. Bioinform., October, 2022

SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information.
Bioinform., October, 2022

Preventing Sensitive Information Leakage From Mobile Sensor Signals via Integrative Transformation.
IEEE Trans. Mob. Comput., 2022

A Framework for Deep Multitask Learning With Multiparametric Magnetic Resonance Imaging for the Joint Prediction of Histological Characteristics in Breast Cancer.
IEEE J. Biomed. Health Informatics, 2022

Person Re-Identification by Context-Aware Part Attention and Multi-Head Collaborative Learning.
IEEE Trans. Inf. Forensics Secur., 2022

Special issue on computational biology and bioinformatic applications to the COVID-19 pandemic.
Quant. Biol., 2022

An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.
Nat. Mach. Intell., 2022

msRepDB: a comprehensive repetitive sequence database of over 80 000 species.
Nucleic Acids Res., 2022

<i>iFeatureOmega: </i> an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.
Nucleic Acids Res., 2022

PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms.
J. Chem. Inf. Model., 2022

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.
Genom. Proteom. Bioinform., 2022

Identification of DNA modification sites based on elastic net and bidirectional gated recurrent unit with convolutional neural network.
Biomed. Signal Process. Control., 2022

Supervised graph co-contrastive learning for drug-target interaction prediction.
Bioinform., 2022

Deep learning identifies and quantifies recombination hotspot determinants.
Bioinform., 2022

NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks.
Briefings Bioinform., 2022

Protein-RNA interaction prediction with deep learning: structure matters.
Briefings Bioinform., 2022

RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.
Briefings Bioinform., 2022

Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies.
Briefings Bioinform., 2022

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.
Briefings Bioinform., 2022

Accelerating bioactive peptide discovery via mutual information-based meta-learning.
Briefings Bioinform., 2022

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.
Briefings Bioinform., 2022

Discovering trends and hotspots of biosafety and biosecurity research via machine learning.
Briefings Bioinform., 2022

RPI-MDLStack: Predicting RNA-protein interactions through deep learning with stacking strategy and LASSO.
Appl. Soft Comput., 2022

Prolificacy Assessment of Spermatozoan via State-of-the-Art Deep Learning Frameworks.
IEEE Access, 2022

Target-aware Abstractive Related Work Generation with Contrastive Learning.
Proceedings of the SIGIR '22: The 45th International ACM SIGIR Conference on Research and Development in Information Retrieval, Madrid, Spain, July 11, 2022

Towards Improving Faithfulness in Abstractive Summarization.
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Rolling Bearing Fault Diagnosis Based on Deep Adversarial Networks with Convolutional Layer and Wasserstein Distance.
Proceedings of the 27th International Conference on Automation and Computing, 2022

Unsupervised Multi-Task Learning for 3D Subtomogram Image Alignment, Clustering and Segmentation.
Proceedings of the 2022 IEEE International Conference on Image Processing, 2022

Scientific Paper Extractive Summarization Enhanced by Citation Graphs.
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 2022

DEMO: Disentangled Molecular Graph Generation via an Invertible Flow Model.
Proceedings of the 31st ACM International Conference on Information & Knowledge Management, 2022

AdvCat: Domain-Agnostic Robustness Assessment for Cybersecurity-Critical Applications with Categorical Inputs.
Proceedings of the IEEE International Conference on Big Data, 2022

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
PLoS Comput. Biol., 2021

Introduction of Progress in Education under Recent Technology Revolution.
Mob. Networks Appl., 2021

DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning.
J. Cheminformatics, 2021

Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach.
J. Cheminformatics, 2021

QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
Genom. Proteom. Bioinform., 2021

Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors.
Genom. Proteom. Bioinform., 2021

WenLan 2.0: Make AI Imagine via a Multimodal Foundation Model.
CoRR, 2021

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.
Bioinform., 2021

A novel constrained reconstruction model towards high-resolution subtomogram averaging.
Bioinform., 2021

Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints.
Bioinform., 2021

Semantic similarity and machine learning with ontologies.
Briefings Bioinform., 2021

Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species.
PLoS Comput. Biol., November, 2020

Approximate Kernel Selection via Matrix Approximation.
IEEE Trans. Neural Networks Learn. Syst., 2020

A Rapid, Accurate and Machine-Agnostic Segmentation and Quantification Method for CT-Based COVID-19 Diagnosis.
IEEE Trans. Medical Imaging, 2020

Joint Prediction of Breast Cancer Histological Grade and Ki-67 Expression Level Based on DCE-MRI and DWI Radiomics.
IEEE J. Biomed. Health Informatics, 2020

Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis.
Sensors, 2020

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.
PLoS Comput. Biol., 2020

A unified linear convergence analysis of k-SVD.
Memetic Comput., 2020

DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques.
J. Cheminformatics, 2020

SenWave: Monitoring the Global Sentiments under the COVID-19 Pandemic.
CoRR, 2020

Multichannel Deep Attention Neural Networks for the Classification of Autism Spectrum Disorder Using Neuroimaging and Personal Characteristic Data.
Complex., 2020

Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data.
BMC Bioinform., 2020

Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation.
BMC Bioinform., 2020

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads.
BMC Bioinform., 2020

iPAC: a genome-guided assembler of isoforms via phasing and combing paths.
Bioinform., 2020

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Bioinform., 2020

gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles.
Bioinform., 2020

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing.
Bioinform., 2020

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.
Bioinform., 2020

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.
Bioinform., 2020

PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation.
Algorithms, 2020

Automated Counting of Colony Forming Units Using Deep Transfer Learning From a Model for Congested Scenes Analysis.
IEEE Access, 2020

Automatic and Interpretable Model for Periodontitis Diagnosis in Panoramic Radiographs.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020

Learning To Stop While Learning To Predict.
Proceedings of the 37th International Conference on Machine Learning, 2020

RNA Secondary Structure Prediction By Learning Unrolled Algorithms.
Proceedings of the 8th International Conference on Learning Representations, 2020

When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores.
Neural Comput. Appl., 2019

Accelerating flash calculation through deep learning methods.
J. Comput. Phys., 2019

Deep Learning Deepens the Analysis of Alternative Splicing.
Genom. Proteom. Bioinform., 2019

In Memory of Vladimir B. Bajic (1952-2019).
Genom. Proteom. Bioinform., 2019

Deep learning in bioinformatics: introduction, application, and perspective in big data era.
CoRR, 2019

Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization.
BMC Bioinform., 2019

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.
Bioinform., 2019

PredMP: a web server for de novo prediction and visualization of membrane proteins.
Bioinform., 2019

Promoter analysis and prediction in the human genome using sequence-based deep learning models.
Bioinform., 2019

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.
Bioinform., 2019

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.
Bioinform., 2019

A joint method for marker-free alignment of tilt series in electron tomography.
Bioinform., 2019

Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions.
Bioinform., 2019

GCN-MF: Disease-Gene Association Identification By Graph Convolutional Networks and Matrix Factorization.
Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 2019

Domain Randomization for Macromolecule Structure Classification and Segmentation in Electron Cyro-tomograms.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

Confidence Weighted Multitask Learning.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Approximate Kernel Selection with Strong Approximate Consistency.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Multiscale and Multimodal Analysis for Computational Biology.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

A Slice-based <sup>13</sup>C-detected NMR Spin System Forming and Resonance Assignment Method.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets.
Quant. Biol., 2018

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.
PLoS Comput. Biol., 2018

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
PLoS Comput. Biol., 2018

PromID: human promoter prediction by deep learning.
CoRR, 2018

On the Decision Boundary of Deep Neural Networks.
CoRR, 2018

SupportNet: solving catastrophic forgetting in class incremental learning with support data.
CoRR, 2018

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.
Bioinform., 2018

DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.
Bioinform., 2018

DEEPre: sequence-based enzyme EC number prediction by deep learning.
Bioinform., 2018

DeepSimulator: a deep simulator for Nanopore sequencing.
Bioinform., 2018

A fast fiducial marker tracking model for fully automatic alignment in electron tomography.
Bioinform., 2018

An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.
Bioinform., 2018

Robust Asymmetric Recommendation via Min-Max Optimization.
Proceedings of the 41st International ACM SIGIR Conference on Research & Development in Information Retrieval, 2018

Robust Cost-Sensitive Learning for Recommendation with Implicit Feedback.
Proceedings of the 2018 SIAM International Conference on Data Mining, 2018

Bandit Online Learning on Graphs via Adaptive Optimization.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Convergence Analysis of Gradient Descent for Eigenvector Computation.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Randomized Kernel Selection With Spectra of Multilevel Circulant Matrices.
Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence, 2018

Robust Online Multi-Task Learning with Correlative and Personalized Structures.
IEEE Trans. Knowl. Data Eng., 2017

Multi-instance dictionary learning via multivariate performance measure optimization.
Pattern Recognit., 2017

Learning from Weak and Noisy Labels for Semantic Segmentation.
IEEE Trans. Pattern Anal. Mach. Intell., 2017

Learning gene regulatory networks from gene expression data using weighted consensus.
Neurocomputing, 2017

K-nearest uphill clustering in the protein structure space.
Neurocomputing, 2017

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.
Bioinform., 2017

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.
Bioinform., 2017

Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data.
Bioinform., 2017

Deep Asymmetric Pairwise Hashing.
Proceedings of the 2017 ACM on Multimedia Conference, 2017

FeaBoost: Joint Feature and Label Refinement for Semantic Segmentation.
Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence, 2017

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

DESM: portal for microbial knowledge exploration systems.
Nucleic Acids Res., 2016

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
Nucleic Acids Res., 2016

Large margin classification with indefinite similarities.
Mach. Learn., 2016

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.
Bioinform., 2016

Optimizing Multivariate Performance Measures from Multi-View Data.
Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016

Condensing Raman spectrum for single-cell phenotype analysis.
BMC Bioinform., December, 2015

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.
PLoS Comput. Biol., 2015

Max-min distance nonnegative matrix factorization.
Neural Networks, 2015

Sparse structure regularized ranking.
Multim. Tools Appl., 2015

Regularized maximum correntropy machine.
Neurocomputing, 2015

Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization.
Expert Syst. Appl., 2015

Maximum mutual information regularized classification.
Eng. Appl. Artif. Intell., 2015

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.
Bioinform., 2015

Distinct profiling of antimicrobial peptide families.
Bioinform., 2015

Finding optimal interaction interface alignments between biological complexes.
Bioinform., 2015

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.
Briefings Bioinform., 2015

Social Image Parsing by Cross-Modal Data Refinement.
Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, 2015

Partially Labeled Data Tuple Can Optimize Multivariate Performance Measures.
Proceedings of the 24th ACM International Conference on Information and Knowledge Management, 2015

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Compare local pocket and global protein structure models by small structure patterns.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Noise-Robust Semi-Supervised Learning by Large-Scale Sparse Coding.
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015

Efficient Active Learning of Halfspaces via Query Synthesis.
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015

Feature selection and multi-kernel learning for sparse representation on a manifold.
Neural Networks, 2014

Bayesian Peak Picking for NMR Spectra.
Genom. Proteom. Bioinform., 2014

Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization.
Eng. Appl. Artif. Intell., 2014

Learning manifold to regularize nonnegative matrix factorization.
CoRR, 2014

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels.
BMC Syst. Biol., 2014

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone.
BMC Bioinform., 2014

Semi-supervised sparse coding.
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014

Large margin image set representation and classification.
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014

Minimum Information Loss Based Multi-kernel Learning for Flagellar Protein Recognition in Trypanosoma Brucei.
Proceedings of the 2014 IEEE International Conference on Data Mining Workshops, 2014

Quick Mining of Isomorphic Exact Large Patterns from Large Graphs.
Proceedings of the 2014 IEEE International Conference on Data Mining Workshops, 2014

Adding Robustness to Support Vector Machines Against Adversarial Reverse Engineering.
Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management, 2014

Support vector machines with indefinite kernels.
Proceedings of the Sixth Asian Conference on Machine Learning, 2014

Supervised Transfer Sparse Coding.
Proceedings of the Twenty-Eighth AAAI Conference on Artificial Intelligence, 2014

Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification.
Pattern Recognit., 2013

Multiple graph regularized nonnegative matrix factorization.
Pattern Recognit., 2013

Discriminative sparse coding on multi-manifolds.
Knowl. Based Syst., 2013

Recent Advances in Computational Methods for Nuclear Magnetic Resonance Data Processing.
Genom. Proteom. Bioinform., 2013

Non-negative matrix factorization by maximizing correntropy for cancer clustering.
BMC Bioinform., 2013

Poly(A) motif prediction using spectral latent features from human DNA sequences.
Bioinform., 2013

A framework for scalable parameter estimation of gene circuit models using structural information.
Bioinform., 2013

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles.
Briefings Bioinform., 2013

ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition.
Comput. Biol. Medicine, 2012

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.
BMC Bioinform., 2012

Multiple graph regularized protein domain ranking.
BMC Bioinform., 2012

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from <sup>15</sup>N-NOESY.
BMC Bioinform., 2012

Protein domain recurrence and order can enhance prediction of protein functions.
Bioinform., 2012

WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering.
Bioinform., 2012

Adaptive graph regularized Nonnegative Matrix Factorization via feature selection.
Proceedings of the 21st International Conference on Pattern Recognition, 2012

Towards Fully Automated Structure-Based NMR Resonance Assignment of <sup>15</sup>N-Labeled Proteins From Automatically Picked Peaks.
J. Comput. Biol., 2011

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation.
J. Bioinform. Comput. Biol., 2011

A protein-dependent side-chain rotamer library.
BMC Bioinform., 2011

An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems.
Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from <sup>15</sup>N-NOESY.
Proceedings of the ACM International Conference on Bioinformatics, 2011

Towards Automated Structure-Based NMR Resonance Assignment.
Proceedings of the Research in Computational Molecular Biology, 2010

Towards Automating Protein Structure Determination from NMR Data.
PhD thesis, 2009

Predicting Local Quality of a Sequence-Structure Alignment.
J. Bioinform. Comput. Biol., 2009

PICKY: a novel SVD-based NMR spectra peak picking method.
Bioinform., 2009

Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information.
Proceedings of the Research in Computational Molecular Biology, 2008

Designing succinct structural alphabets.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

New Algorithms for the Spaced Seeds.
Proceedings of the Frontiers in Algorithmics, First Annual International Workshop, 2007