Publications

January 2021 PRICAI 2021: Trends in Artificial Intelligence: 18th Pacific Rim International Conference on Artificial Intelligence, PRICAI 2021, Hanoi, Vietnam, November 8–12, 2021, Proceedings, Part III

kldm: Inferring multiple metagenomic association networks based on the variation of environmental factors

Yuqing Yang, Xin Wang, Kaikun Xie, Congmin Zhu, Ning Chen, Ting Chen

January 2021 Genomics, Proteomics & Bioinformatics

Explainable dynamic multimodal variational autoencoder for the prediction of patients with suspected central precocious puberty

Yimin Xu, Xiaohong Liu, Liyan Pan, Xiaojian Mao, Huiying Liang, Guangyu Wang, Ting Chen

January 2021 IEEE Journal of Biomedical and Health Informatics

Deep-learning models for the detection and incidence prediction of chronic kidney disease and type 2 diabetes from retinal fundus images

Kang Zhang, Xiaohong Liu, Jie Xu, Jin Yuan, Wenjia Cai, Ting Chen, Kai Wang, Yuanxu Gao, Sheng Nie, Xiaodong Xu, others

January 2021 Nature Biomedical Engineering

Deep Active Learning For Fibrosis Segmentation Of Chest CT Scans From Covid-19 Patients

Xiaohong Liu, Kai Wang, Ting Chen

January 2021 2021 IEEE International Conference on Image Processing (ICIP)

Automatic emergency diagnosis with knowledge-based tree decoding

Ke Wang, Xuyan Chen, Ning Chen, Ting Chen

January 2021 Proceedings of the Twenty-Ninth International Conference on International Joint Conferences on Artificial Intelligence

An Adversarial Collaborative-Learning Approach for Corneal Scar Segmentation with Ocular Anterior Segment Photography

Ke Wang, Guangyu Wang, Kang Zhang, Ting Chen

January 2021 2021 IEEE International Conference on Image Processing (ICIP)

A qualitative transcriptional signature of recurrence risk for stages II--III gastric cancer patients after surgical resection

Huarong Zhang, Xiangyu Li, Junling Wu, Jiahui Zhang, Haiyan Huang, Yawei Li, Meifeng Li, Shanshan Wang, Jie Xia, Lishuang Qi, others

January 2021 Journal of Gastroenterology and Hepatology

A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images

Guangyu Wang, Xiaohong Liu, Jun Shen, Chengdi Wang, Zhihuan Li, Linsen Ye, Xingwang Wu, Ting Chen, Kai Wang, Xuan Zhang, others

January 2021 Nature biomedical engineering

2020

Svqn: Sequential variational soft q-learning networks

Shiyu Huang, Hang Su, Jun Zhu, Ting Chen

January 2020

scAIDE: clustering of large-scale single-cell RNA-seq data reveals putative and rare cell types

Kaikun Xie, Yu Huang, Feng Zeng, Zehua Liu, Ting Chen

January 2020 NAR genomics and bioinformatics

Kiseg: A three-stage segmentation framework for multi-level acceleration of chest ct scans from covid-19 patients

Xiaohong Liu, Kai Wang, Ke Wang, Ting Chen, Kang Zhang, Guangyu Wang

January 2020 Medical Image Computing and Computer Assisted Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru, October 4–8, 2020, Proceedings, Part IV 23

Joint Medical Ontology Representation Learning for Healthcare Predictions

Ke Wang, Ning Chen, Ting Chen

January 2020 2020 International Joint Conference on Neural Networks (IJCNN)

Clinically applicable AI system for accurate diagnosis, quantitative measurements, and prognosis of COVID-19 pneumonia using computed tomography

Kang Zhang, Xiaohong Liu, Jun Shen, Zhihuan Li, Ye Sang, Xingwang Wu, Yunfei Zha, Wenhua Liang, Chengdi Wang, Ke Wang, others

January 2020 Cell

Attention u-net for interpretable classification on chest x-ray image

Xuan Zhang, Ting Chen

January 2020 2020 IEEE international conference on bioinformatics and biomedicine (BIBM)

Anterior segment eye lesion segmentation with advanced fusion strategies and auxiliary tasks

Ke Wang, Xiaohong Liu, Kang Zhang, Ting Chen, Guangyu Wang

January 2020 Medical Image Computing and Computer Assisted Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru, October 4–8, 2020, Proceedings, Part V 23

Ambient fine particulate matter and hospital admissions for ischemic and hemorrhagic strokes and transient ischemic attack in 248 Chinese cities

Jiangshao Gu, Ying Shi, Ning Chen, Haibo Wang, Ting Chen

January 2020 Science of the Total Environment

Ambient air pollution and cause-specific risk of hospital admission in China: A nationwide time-series study

Jiangshao Gu, Ying Shi, Yifang Zhu, Ning Chen, Haibo Wang, Zongjiu Zhang, Ting Chen

January 2020 PLoS Medicine

2019

Seasonal succession and spatial distribution of bacterial community structure in a eutrophic freshwater Lake, Lake Taihu

Congmin Zhu, Junyi Zhang, Muhammad Zohaib Nawaz, Shahid Mahboob, Khalid A Al-Ghanim, Iqrar Ahmad Khan, Zuhong Lu, Ting Chen

January 2019 Science of the Total Environment

How Robust is Your Automatic Diagnosis Model?

Ke Wang, Guangyu Wang, Ning Chen, Ting Chen

January 2019 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Deeptriager: A neural attention model for emergency triage with electronic health records

Guangyu Wang, Xiaohong Liu, Ken Xie, Ning Chen, Ting Chen

January 2019 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data

Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen

January 2019 BMC bioinformatics

Dcmn: Double core memory network for patient outcome prediction with multimodal data

Yujuan Feng, Zhenxing Xu, Lin Gan, Ning Chen, Bin Yu, Ting Chen, Fei Wang

January 2019 2019 IEEE International Conference on Data Mining (ICDM)

Computer-aided Diagnosis of Ambulatory Electrocardiograms via ASRS: Active-Selection-Random-Selection

Xuan Zhang, Guangyu Wang, Ning Chen, Ting Chen

January 2019 2019 IEEE International Conference on Healthcare Informatics (ICHI)

Combo-action: Training agent for fps game with auxiliary tasks

Shiyu Huang, Hang Su, Jun Zhu, Ting Chen

January 2019 Proceedings of the AAAI Conference on Artificial Intelligence

Bone age assessment by deep convolutional neural networks combined with clinical TW3-RUS

Xiaohong Liu, Guangyu Wang, Yimin Xu, Ning Chen, Ting Chen

January 2019 2019 IEEE international conference on bioinformatics and biomedicine (BIBM)

Automatic Diagnosis with 12-Lead ECG Signals

Ke Wang, Xuan Zhang, Haoxi Zhong, Ting Chen

January 2019 Machine Learning and Medical Engineering for Cardiovascular Health and Intravascular Imaging and Computer Assisted Stenting: First International Workshop, MLMECH 2019, and 8th Joint International Workshop, CVII-STENT 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13, 2019, Proceedings 1

Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathways

Cong-Min Zhu, Jun-Yi Zhang, Rui Guan, Lauren Hale, Ning Chen, Ming Li, Zu-Hong Lu, Qin-Yu Ge, Yun-Feng Yang, Ji-Zhong Zhou, others

January 2019 Science of the Total Environment

2018

Ontology-based venous thromboembolism risk factors mining and model developing from medical records

Yuqing Yang, Xin Wang, Yu Huang, Ning Chen, Juhong Shi, Ting Chen

January 2018 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning

Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Hairong Lv, Ting Chen, Rui Jiang

January 2018 Methods

Identifying group-specific sequences for microbial communities using long k-mer sequence signatures

Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun

January 2018 Frontiers in microbiology

GePMI: A statistical model for personal intestinal microbiome identification

Zicheng Wang, Huazhe Lou, Ying Wang, Ron Shamir, Rui Jiang, Ting Chen

January 2018 npj Biofilms and Microbiomes

Dropout training for SVMs with data augmentation

Ning Chen, Jun Zhu, Jianfei Chen, Ting Chen

January 2018 Frontiers of Computer Science

Approximation Algorithms for the Selection of Robust Tag SNPs

Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao

January 2018 Handbook of Approximation Algorithms and Metaheuristics

2017

Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks

Mengmeng Wu, Zhixiang Lin, Shining Ma, Ting Chen, Rui Jiang, Wing Hung Wong

January 2017 Journal of Molecular Cell Biology

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen

January 2017 Nature communications

Patient outcome prediction via convolutional neural networks based on multi-granularity medical concept embedding

Yujuan Feng, Xu Min, Ning Chen, Hu Chen, Xiaolei Xie, Haibo Wang, Ting Chen

January 2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data

Mengmeng Wu, Ting Chen, Rui Jiang

January 2017 Scientific Reports

Large-scale 16S gene assembly using metagenomics shotgun sequences

Feng Zeng, Zicheng Wang, Ying Wang, Jizhong Zhou, Ting Chen

January 2017 Bioinformatics

Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes

Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Yijia Zhang, Ting Chen, Rui Jiang

January 2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

Nathan A Ahlgren, Yangyang Chen, David M Needham, Alma E Parada, Rohan Sachdeva, Vickie Trinh, Ting Chen, Jed A Fuhrman

January 2017 Environmental microbiology

DACE: a scalable DP-means algorithm for clustering extremely large sequence data

Linhao Jiang, Yichao Dong, Ning Chen, Ting Chen

January 2017 Bioinformatics

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

Yang Young Lu, Ting Chen, Jed A Fuhrman, Fengzhu Sun

January 2017 Bioinformatics

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang

January 2017 Bioinformatics

2016

Whole genome sequencing and its applications in medical genetics

Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang

January 2016 Quantitative Biology

WALT: fast and accurate read mapping for bisulfite sequencing

Haifeng Chen, Andrew D Smith, Ting Chen

January 2016 Bioinformatics

Tongue coating and the salivary microbial communities vary in children with halitosis

Wen Ren, Zhe Xun, Zicheng Wang, Qun Zhang, Xuenan Liu, Hui Zheng, Qian Zhang, Yifei Zhang, Linshuang Zhang, Chunyan Wu, others

January 2016 Scientific reports

Reading the underlying information from massive metagenomic sequencing data

Xuegong Zhang, Shansong Liu, Hongfei Cui, Ting Chen

January 2016 Proceedings of the IEEE

mLDM: a new hierarchical Bayesian statistical model for sparse microbioal association discovery

Yuqing Yang, Ning Chen, Ting Chen

January 2016 bioRxiv

Global inference of disease-causing single nucleotide variants from exome sequencing data

Mengmeng Wu, Ting Chen, Rui Jiang

January 2016 BMC bioinformatics

Effect of k-tuple length on sample-comparison with high-throughput sequencing data

Ying Wang, Xiaoye Lei, Shun Wang, Zicheng Wang, Nianfeng Song, Feng Zeng, Ting Chen

January 2016 Biochemical and biophysical research communications

DeepEnhancer: predicting enhancers by convolutional neural networks

Xu Min, Ning Chen, Ting Chen, Rui Jiang

January 2016 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

2015

Subgingival microbiome in patients with healthy and ailing dental implants

Hui Zheng, Lixin Xu, Zicheng Wang, Lianshuo Li, Jieni Zhang, Qian Zhang, Ting Chen, Jiuxiang Lin, Feng Chen

January 2015 Scientific reports

Prioritization of nonsynonymous single nucleotide variants for exome sequencing studies via integrative learning on multiple genomic data

Mengmeng Wu, Jiaxin Wu, Ting Chen, Rui Jiang

January 2015 Scientific reports

Network-based method to infer the contributions of proteins to the etiology of drug side effects

Rui Li, Ting Chen, Shao Li

January 2015 Quantitative Biology

Global optimization-based inference of chemogenomic features from drug--target interactions

Songpeng Zu, Ting Chen, Shao Li

January 2015 Bioinformatics

2014

Integrative data analysis of multi-platform cancer data with a multimodal deep learning approach

Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng

January 2014 IEEE/ACM transactions on computational biology and bioinformatics

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks

Xiaotu Ma, Ting Chen, Fengzhu Sun

January 2014 Briefings in Bioinformatics

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs

Congmin Zhu, Rui Jiang, Ting Chen

January 2014 Quantitative Biology

Comparison of metatranscriptomic samples based on k-tuple frequencies

Ying Wang, Lin Liu, Lina Chen, Ting Chen, Fengzhu Sun

January 2014 PLoS One

2013

PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data

Feng Zeng, Rui Jiang, Ting Chen

January 2013 Bioinformatics

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data

Feng Zeng, Rui Jiang, Ting Chen

January 2013 Nucleic acids research

FadE: whole genome methylation analysis for multiple sequencing platforms

Tade Souaiaia, Zheng Zhang, Ting Chen

January 2013 Nucleic Acids Research

Exploring functional variant discovery in non-coding regions with SInBaD

Kjong-Van Lehmann, Ting Chen

January 2013 Nucleic acids research

2012

OTU analysis using metagenomic shotgun sequencing data

Xiaolin Hao, Ting Chen

January 2012 PloS one

Modeling RNA degradation for RNA-Seq with applications

Lin Wan, Xiting Yan, Ting Chen, Fengzhu Sun

January 2012 Biostatistics

Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome

Bai Jiang, Xujun Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang, Shao Li

January 2012 Scientific reports

Enabling data and compute intensive workflows in bioinformatics

Gaurang Mehta, Ewa Deelman, James A Knowles, Ting Chen, Ying Wang, Jens Vöckler, Steven Buyske, Tara Matise

January 2012 Euro-Par 2011: Parallel Processing Workshops: CCPI, CGWS, HeteroPar, HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC, Bordeaux, France, August 29–September 2, 2011, Revised Selected Papers, Part II 17

Computational methods for the analysis of tag sequences in metagenomics studies

Qin Chang, Yihui Luan, Ting Chen, Jed A Fuhrman, Fengzhu Sun

January 2012 Frontiers in Bioscience-Scholar

2011

RseqFlow: workflows for RNA-Seq data analysis

Ying Wang, Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew Clark, Hee Jae Yoon, Lin Wan, Oleg V Evgrafov, others

January 2011 Bioinformatics

ComB: SNP calling and mapping analysis for color and nucleotide space platforms

Tade Souaiaia, Zach Frazier, Ting Chen

January 2011 Journal of Computational Biology

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

Xiaolin Hao, Rui Jiang, Ting Chen

January 2011 Bioinformatics

Accurate genome relative abundance estimation based on shotgun metagenomic reads

Li C Xia, Jacob A Cram, Ting Chen, Jed A Fuhrman, Fengzhu Sun

January 2011 PloS one

2010

MSPEP: A spectral alignment algorithm for the detection of post translational modifications

Lijuan Mo, Yunhu Wan, Austin Yang, Ting Chen

March 2010

2009

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

Yangho Chen, Tade Souaiaia, Ting Chen

January 2009 Bioinformatics

Bayesian models and Gibbs sampling strategies for local graph alignment and motif identification in stochastic biological networks

Rui Jiang, Ting Chen, Fengzhu Sun

January 2009

An Integer programming approach for the selection of tag SNPs using multi-allelic LD

Ting Chen, Yang-Ho Chen

January 2009 Communications in Information and Systems

2008

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

Li Wang, Fengzhu Sun, Ting Chen

January 2008 Genome Biology

PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information

Yunhu Wan, Diane Cripps, Stefani Thomas, Patricia Campbell, Nicholas Ambulos, Ting Chen, Austin Yang

January 2008 Journal of proteome research

Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity

LI Jia, Benjamin P Berman, Unnati Jariwala, Xiting Yan, Jon P Cogan, Allison Walters, Ting Chen, Grant Buchanan, Baruch Frenkel, Gerhard A Coetzee

January 2008 PloS one

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, others

January 2008 Genome biology

2007

Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search

Debojyoti Dutta, Ting Chen

January 2007 Bioinformatics

Single nucleotide polymorphism data analysis-state-of-the-art review on this emerging field from a signal processing viewpoint

Shih-Chieh Su, C-C Jay Kuo, Ting Chen

January 2007 IEEE Signal Processing Magazine

Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations

Rui Jiang, Hua Yang, Linqi Zhou, C-C Jay Kuo, Fengzhu Sun, Ting Chen

January 2007 The American Journal of Human Genetics

MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry

Lijuan Mo, Debojyoti Dutta, Yunhu Wan, Ting Chen

January 2007 Analytical chemistry

Ensemble feature selection: consistent descriptor subsets for multiple QSAR models

Debojyoti Dutta, Rajarshi Guha, David Wild, Ting Chen

January 2007 Journal of Chemical Information and Modeling

Counting clusters using R-NN curves

Rajarshi Guha, Debojyoti Dutta, David J Wild, Ting Chen

January 2007 Journal of chemical information and modeling

2006

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy

Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen

January 2006 BMC bioinformatics

Scalable partitioning and exploration of chemical spaces using geometric hashing

Debojyoti Dutta, Rajarshi Guha, Peter C Jurs, Ting Chen

January 2006 Journal of chemical information and modeling

R-NN curves: an intuitive approach to outlier detection using a distance based method

Rajarshi Guha, Debojyoti Dutta, Peter C Jurs, Ting Chen

January 2006 Journal of chemical information and modeling

PepHMM: a hidden Markov model based scoring function for mass spectrometry database search

Yunhu Wan, Austin Yang, Ting Chen

January 2006 Analytical Chemistry

Network motif identification in stochastic networks

Rui Jiang, Zhidong Tu, Ting Chen, Fengzhu Sun

January 2006 Proceedings of the National Academy of Sciences

Local lazy regression: making use of the neighborhood to improve QSAR predictions

Rajarshi Guha, Debojyoti Dutta, Peter C Jurs, Ting Chen

January 2006 Journal of chemical information and modeling

Further understanding human disease genes by comparing with housekeeping genes and other genes

Zhidong Tu, Li Wang, Min Xu, Xianghong Zhou, Ting Chen, Fengzhu Sun

January 2006 BMC genomics

DYNAMIC PROGRAMMING ALGORITHMS FOR PARTITIONING SEQUENCE VARIATION IN HUMAN CHROMOSOMES

K Zhang, F Sun, MS Waterman, T Chen

January 2006 Advances and Developments, 1994-2005

Diffusion kernel-based logistic regression models for protein function prediction

Hyunju Lee, Zhidong Tu, Minghua Deng, Fengzhu Sun, Ting Chen

January 2006 Omics: a journal of integrative biology

An integrative approach for causal gene identification and gene regulatory pathway inference

Zhidong Tu, Li Wang, Michelle N Arbeitman, Ting Chen, Fengzhu Sun

January 2006 Bioinformatics

An integrated approach to the prediction of domain-domain interactions

Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen

January 2006 BMC bioinformatics

2005

Leaky ribosomal scanning in mammalian genomes: significance of histone H4 alternative translation in vivo

Elisheva Smith, Todd E Meyerrose, Thomas Kohler, Malka Namdar-Attar, Natti Bab, Olga Lahat, Tommy Noh, Jingjing Li, Mazen W Karaman, Joseph G Hacia, others

January 2005 Nucleic acids research

Inference of missing SNPs and information quantity measurements for haplotype blocks

Shih-Chieh Su, C-C Jay Kuo, Ting Chen

January 2005 Bioinformatics

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms

Kui Zhang, Zhaohui Qin, Ting Chen, Jun S Liu, Michael S Waterman, Fengzhu Sun

January 2005 Bioinformatics

Data integration for the study of protein interactions

FZ Sun, Ting Chen, MH Deng, Hyunju Lee, Zhidong Tu

January 2005 Meta-analysis and Combining Information in Genetics and Genomics. Chapman and Hall

CH 12 Application of Proteomics in Basic Biological Sciences and Cancer

Christoph Borchers, Ting Chen, Nouri Neamati

January 2005 Molecular Carcinogenesis and the Molecular Biology of Human Cancer

Assessment of the reliability of protein-protein interactions using protein localization and gene expression data

Hyun-Ju Lee, Minghua Deng, Fengzhu Sun, Ting Chen

January 2005 Proceedings of the Korean Society for Bioinformatics Conference

An approximation algorithm for haplotype inference by maximum parsimony

Yao-Ting Huang, Kun-Mao Chao, Ting Chen

January 2005 Proceedings of the 2005 ACM symposium on Applied computing

2004

Mapping gene ontology to proteins based on protein--protein interaction data

Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen

January 2004 Bioinformatics

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies

Kui Zhang, Zhaohui S Qin, Jun S Liu, Ting Chen, Michael S Waterman, Fengzhu Sun

January 2004 Genome research

Approximation algorithms for the selection of robust tag SNPs

Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao

January 2004 Algorithms in Bioinformatics: 4th International Workshop, WABI 2004, Bergen, Norway, September 17-21, 2004. Proceedings 4

Algorithms for de novo peptide sequencing using tandem mass spectrometry

Bingwen Lu, Ting Chen

January 2004 Drug Discovery Today: BioSilico

2003

Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data

Kui Zhang, Fengzhu Sun, Michael S Waterman, Ting Chen

January 2003 The American Journal of Human Genetics

An integrative analysis of protein function prediction

M Deng, T Chen, F Sun

January 2003 7th Annual International Conference on Computational Molecular Biology (RECOMB03)

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications

Bingwen Lu, Ting Chen

January 2003 Bioinformatics

A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry

Bingwen Lu, Ting Chen

January 2003 Journal of Computational Biology

2002

Prediction of protein function using protein-protein interaction data

Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun

January 2002 Proceedings. IEEE Computer Society Bioinformatics Conference

Inferring domain-domain interactions from protein-protein interactions

Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen

January 2002 Proceedings of the sixth annual international conference on Computational biology

A dynamic programming algorithm for haplotype block partitioning

Kui Zhang, Minghua Deng, Ting Chen, Michael S Waterman, Fengzhu Sun

January 2002 Proceedings of the National Academy of Sciences

2001

Genome-wide location analysis of ORC and MCM proteins: high-resolution mapping of replication origins in S. cerevisiae

JJ Wyrick, JG Aparicio, T Chen, JD Barnett, EG Jennings, RA Young, SP Bell, OM Aparicio

January 2001 Science

Gene-finding via tandem mass spectrometry

Ting Chen

January 2001 Proceedings of the fifth annual international conference on Computational biology

Algorithms for identifying protein cross-links via tandem mass spectrometry

Ting Chen, Jacob D Jaffe, George M Church

January 2001 Proceedings of the fifth annual international conference on Computational biology

A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry

Ting Chen, Ming-Yang Kao, Matthew Tepel, John Rush, George M Church

January 2001 Journal of Computational Biology

2000

A case study in genome-level fragment assembly

Ting Chen, Steven S Skiena

January 2000 Bioinformatics

1999

On the informational asymmetry between upper and lower bounds for ultrametric evolutionary trees

Ting Chen, Ming-Yang Kao

January 1999 Algorithms-ESA’99: 7th Annual European Symposium Prague, Czech Republic, July 16–18, 1999 Proceedings 7

Modeling gene expression with differential equations

Ting Chen, Hongyu L He, George M Church

January 1999 Biocomputing'99

Identifying gene regulatory networks from experimental data

Ting Chen, Vladimir Filkov, Steven S Skiena

January 1999 Proceedings of the third annual international conference on Computational molecular biology

1998

Pombe: a fission yeast gene-finding and exon--intron structure prediction system

T Chen, MQ Zhang

January 1998 Yeast

1997

Trie-based data structures for fragment assembly

Ting Chen, Steven Skiena

March 1997 The Eighth Symposium on Combinatorial Pattern Matching, Aarhus, Denmark, June

Trie-based data structures for sequence assembly

Ting Chen, Steven S Skiena

January 1997 Combinatorial Pattern Matching: 8th Annual Symposium, CPM 97 Aarhus, Denmark, June 30–July 2, 1997 Proceedings 8

1996

Sorting with fixed-length reversals

Ting Chen, Steven S Skiena

January 1996 Discrete Applied Mathematics

(150 papers)

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