Publications

Ellinor PT, Lunetta KL, Albert CM, Glazer NL, Ritchie MD, Smith AV, Arking DE, Müller M, Krijthe BP, Lubitz SA, Bis JC, Chung MK, Ozaki K, Roberts JD, Smith JG, Pfeufer A, Sinner MF, Lohman K, Ding J, Smith NL, Smith JD, Rienstra M, Rice KM, Van Wagoner DR, Magnani JW, Wakili R, Clauss S, Rotter JI, Steinbeck G Launer LJ, Davies RW, Borkovich M, Harris TB, Lin HH, Völker U, Völzke H, Milan DJ, Hofman A, Boerwinkle E, Chen LY, Soliman EZ, Voight BF, Li G, Chakravarti A, Kubo M, Tedrow U, Rose LM,Ridker PM, Conen D, Tsunoda T, Furukawa T, Sotoodehnia N, Xu S, Kamatani N, Levy D, Nakamura Y, Parvez B, Mahida S, Furie KL, Rosand J, Muhammad R, Psaty BM, Meitinger T, Perz S, Wichmann H-E, Witteman JCM, Kao WHL, Kathiresan S, Roden DM, Uitterlinden AG, Rivadeneira F, McKnight B, Sjögren M, Newman AB, Liu Y, Gollob MH, Melander O, Tanaka T, Stricker BHCh, Felix SB, Alonso A, Darbar D, Barnard J, Chasman DI, Heckbert SR, Benjamin EJ, Gudnason V, Kääb S. Meta-analysis identifies six new susceptibility loci for atrial fibrillation. Nat Genet, 2012, 44: 670–675.
Medina-Medina N, Broka A, Lacey S, Lin HH, Klings ES, Baldwin CT, Steinberg MH, and Sebastiani P. Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment. Advances in Intelligent and Soft Computing, 2012, 154:197-207
Cheng XY, Huang WJ, Hu SC, Zhang HL, Wang H, Zhang JX, Lin HH, Chen YZ, Zou Q, Ji ZL. A Global Characterization and Identification of Multifunctional Enzymes. PLoS One, 2012, 7(6): e38979
Schnabel R, Baccarelli A, Lin HH, Ellinor PT, and Benjamin EJ. Next Steps in Cardiovascular Disease Genomic Research - Sequencing, Epigenetics, and Transcriptomics. Clinical Chemistry, 2012, 58(1):113-26
Zhang GL*, Lin HH*, Keskina DB, Reinherza EL, Brusic V. Dana-Farber Repository for Machine Learning in Immunology. Journal of Immunological Methods , 2011, 374(1-2): 18-25. *Equal contribution
Zhang ZP, Lin HH. Genomic profiling by machine learning. Workshop on Informatics Applications in Therapeutics, International Conference in Bioinformatics & Biomedicine, 2011, 12-15: 662-668
Magnani JW, Rienstra M, Lin HH, Sinner MF, Lubitz SA, McManus DD, Dupuis J, Ellinor PT, Benjamin EJ. Atrial fibrillation: Current knowledge and future directions in epidemiology and genomics. Circulation , 2011, 124: 1982-1993
Lin HH. Microarray Data Analysis of Gene Expression Evolution. Gene Regulation and Systems Biology, 2009, 3:211–214
Zhang HL, Lin HH, Tao L, Ma XH, Dai JL, Jia J and Cao ZW. Prediction of Antibiotic Resistance Proteins from Sequence Derived Properties Irrespective of Sequence Similarity. International Journal of Antimicrobial Agents, 2008, 32: 221-226
Lin HH, Zhang GL, Tongchusak S, Reinherz EL and Brusic V. Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics, 2008, 9(Suppl 12):S22
Han LY, Ma XH, Lin HH, Jia J, Zhu F, Xue Y, Li ZR, Cao ZW, Ji ZL, Chen YZ. A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. J Mol Graph Model, 2008, 26(8):1276-86
Sangket U, Phongdara A, Chotigeat W, Nathan D, Kim WY, Bhak J, Ngamphiw C, Tongsima S, Khan AM, Lin HH, Tan TW. Automatic Synchronization and Distribution of Biological Databases and Software over Low-Bandwidth Networks among Developing Countries. Bioinformatics, 2008, 24(2): 299-301
Zhu F, Han LY, Chen X, Lin HH, Ong S, Xie B, Zhang HL and Chen YZ. Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines. Y.Z. Chen. Current Protein and Peptide Science, 2008, 9:70-95
Lin HH, Ray S, Tongchusak S, Reinherz EL and Brusic V. Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunology, 2008, 9:8
Tang ZQ, Lin HH, Zhang HL, Han LY, Chen X, Chen YZ. Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines. Bioinformatics and Biology Insights, 2007, 1: 19-47
Ong AK, Lin HH, Chen YZ, Li ZR, Cao ZW. Efficacy of different protein descriptors in predicting protein functional families. BMC Bioinformatics, 2007, 8 (1) 300
Tang ZQ, Han LY, Lin HH, Cui J, Jia J, Low BC, Li BW, Chen YZ. Derivation of Stable Microarray Cancer-differentiating Signatures by a Feature-selection Method Incorporating Consensus Scoring of Multiple Random Sampling and Gene-Ranking Consistency Evaluation. Cancer Research, 2007, 67(20):9996-10003
Lin HH, Han LY, Yap CW, Xue Y, Liu XH, Zhu F, and Chen YZ. Prediction of Factor Xa Inhibitors by Machine Learning Methods. Journal of Molecular Graphics and Modelling, 2007, 26 (2): 505-518
Cui J, Han LY, Lin HH, Tang ZQ, Ji ZL, Cao ZW, Li YX, and Y.Z. Chen. Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology. Current Bioinformatics, 2007 2(2): 95-112
Li H, Yap CW, Ung CY, Xue Y, Li ZR, Han LY, Lin HH and Chen YZ. Machine Learning Approaches for Predicting Compounds That Interact with Therapeutic and ADMET Related Proteins. J. Pharm. Sci. 2007, 96(11): 2838-2860
Han LY, Zheng CJ, Xie B, Jia J, Ma XH, Zhu F, Lin HH, Chen X, and Chen YZ. Support vector machine approach for predicting druggable proteins. Drug Discovery Today, 2007, 12, 304-313
Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, and Chen YZ. Prediction of the Functional Class of Metal-Binding Proteins from Sequence Derived Physicochemical Properties by Support Vector Machine Approach. BMC Bioinformatics, 2006, 7(S5), S13
Zheng CJ, Han LY, Chen X, Cao ZW, Cui J, Lin HH, Zhang HL, Li H and Chen YZ. Information of ADME-associated proteins and potential application for pharmacogenetic prediction of drug responses. Curr. Pharmacogenomics, 2006, 4(2): 87-103
Cui J, Han LY, Lin HH, Zhang HL, Tang ZQ, Zheng CJ, Cao ZW, and Chen YZ. Prediction of MHC-Binding Peptides of Flexible Lengths from Sequence-Derived Structural and Physicochemical Properties. Mol. Immunol., 2006, 44(5):866-77
Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, and Chen YZ. Prediction of the Functional Class of Lipid-Binding Proteins from Sequence Derived Properties Irrespective of Sequence Similarity. J. Lipid Res., 2006, 47(4):824-31
Li ZR, Lin HH, Han LY, Jiang L, Chen X, and Chen YZ. PROFEAT: A Web Server for Computing Structural and Physicochemical Features of Proteins and Peptides from Amino Acid Sequence. Nucl. Acids. Res., 2006, 34:W32-7
Han LY, Cui J, Lin HH, Ji ZL, Cao ZW, Li YX, and Chen YZ. Recent progresses in the application of machine learning approach for predicting protein functional independent of sequence similarity. Proteomics, 2006, 6: 4023:4037
Cui J, Han LY, Lin HH, Tang ZQ, Zheng CJ, Cao ZW, and Chen YZ. MHC-BPS: MHC-Binder Prediction Server for Identifying Peptides of Flexible Lengths from Sequence-Derived Physicochemical Properties. Immunogenetics, 2006, 58(8):607-13.
Han LY, Lin HH, Chen X, Zheng CJ, Ji ZL, Cao ZW, Xie B, and Chen YZ. PEARLS: Program for Energetic Analysis of Receptor-Ligand System. J. Chem. Inf. Model, 2006, 23(1):445-450
Lin HH, Han LY, Cai CZ, Ji ZL, and Chen YZ. Classification of Transporter Families from Primary Sequence by Support Vector Machine Approach. Proteins, 2006, 62 (1): 218-31
Cao ZW, Han LY, Zheng CJ, Ji ZL, Chen X, Lin HH and Chen YZ. Computer Prediction of Drug Resistance Mutations in Proteins. Drug Discovery Today, 2005, 10 (7), 521-529
Han LY, Zheng CJ, Lin HH, Cui J, Li H, Zhang HL, Tang ZQ, and Chen YZ. Prediction of Functional Class of Novel Plant Proteins by a Statistical Learning Method. New Phytologist, 2005, 168:109-121
Cao ZW, Xue Y, Han LY, Xie B, Zhou H, Zheng CJ, Lin HH, and Chen YZ. MoViES: Molecular Vibrations Evaluation Server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucl. Acids. Res. 2004 32: W679-W685