Fengfeng Zhou

Fengfeng Zhou

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Detecting Methylomic Biomarkers of Pediatric Autism in the Peripheral Blood Leukocytes.

Interdiscip Sci 2019 Jun 16;11(2):237-246. Epub 2019 Apr 16.

BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, Jilin, China.

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http://dx.doi.org/10.1007/s12539-019-00328-9DOI Listing
June 2019

sefOri: selecting the best-engineered squence features to predict DNA replication origins.

Bioinformatics 2019 Jun 20. Epub 2019 Jun 20.

BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education,Jilin University, Changchun, Jilin, China.

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http://dx.doi.org/10.1093/bioinformatics/btz506DOI Listing
June 2019

Diagnosis of Breast Hyperplasia and Evaluation of RuXian-I Based on Metabolomics Deep Belief Networks.

Int J Mol Sci 2019 May 28;20(11). Epub 2019 May 28.

Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China.

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http://dx.doi.org/10.3390/ijms20112620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600413PMC
May 2019

Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model.

Sci Rep 2019 Mar 12;9(1):4192. Epub 2019 Mar 12.

Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture, and Plant Science, Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, 57006, USA.

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http://www.nature.com/articles/s41598-019-40780-7
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http://dx.doi.org/10.1038/s41598-019-40780-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414665PMC
March 2019

Age Is Important for the Early-Stage Detection of Breast Cancer on Both Transcriptomic and Methylomic Biomarkers.

Front Genet 2019 26;10:212. Epub 2019 Mar 26.

BioKnow Health Informatics Lab, College of Computer Science and Technology, Jilin University, Changchun, China.

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https://www.frontiersin.org/article/10.3389/fgene.2019.00212
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http://dx.doi.org/10.3389/fgene.2019.00212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448048PMC
March 2019

An accurate regression of developmental stages for breast cancer based on transcriptomic biomarkers.

Biomark Med 2019 01 28;13(1):5-15. Epub 2018 Nov 28.

BioKnow Health Informatics Lab, College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China.

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https://www.futuremedicine.com/doi/10.2217/bmm-2018-0305
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http://dx.doi.org/10.2217/bmm-2018-0305DOI Listing
January 2019

pyHIVE, a health-related image visualization and engineering system using Python.

BMC Bioinformatics 2018 Nov 26;19(1):452. Epub 2018 Nov 26.

BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, Jilin, China.

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http://dx.doi.org/10.1186/s12859-018-2477-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258460PMC
November 2018

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances.

J Vis Exp 2018 10 11(140). Epub 2018 Oct 11.

College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University;

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https://www.jove.com/video/57738/selecting-multiple-biomarke
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http://dx.doi.org/10.3791/57738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235481PMC
October 2018

TriZ-a rotation-tolerant image feature and its application in endoscope-based disease diagnosis.

Comput Biol Med 2018 08 15;99:182-190. Epub 2018 Jun 15.

College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2018.06.006DOI Listing
August 2018

Gender specificity improves the early-stage detection of clear cell renal cell carcinoma based on methylomic biomarkers.

Biomark Med 2018 06 30;12(6):607-618. Epub 2018 Apr 30.

College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.

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http://dx.doi.org/10.2217/bmm-2018-0084DOI Listing
June 2018

Author Correction: Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways.

Sci Rep 2018 Jun 7;8(1):8995. Epub 2018 Jun 7.

Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry, College of Computer Science and Technology, Jilin University, Changchun, 130012, China.

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http://dx.doi.org/10.1038/s41598-018-27349-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990538PMC
June 2018

Cortical and Subcortical Brain Morphometry Differences Between Patients With Autism Spectrum Disorder and Healthy Individuals Across the Lifespan: Results From the ENIGMA ASD Working Group.

Am J Psychiatry 2018 04 17;175(4):359-369. Epub 2017 Nov 17.

From the Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Donders Center for Cognitive Neuroimaging, Radboud University Medical Center, Nijmegen, the Netherlands; the Karakter Child and Adolescent Psychiatry University Center, Nijmegen; the Bloorview Research Institute, University of Toronto, Toronto; the Child and Adolescent Psychiatry Department, Gregorio Marañón General University Hospital, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid; Institut de Neurosciences de la Timone, Aix Marseille Université, CNRS, Marseille, France; the Department of Psychology, Carnegie Mellon University, Pittsburgh; the IRCCS Stella Maris Foundation, Pisa, Italy; the Department of Forensic and Neurodevelopmental Sciences and the Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology, and Neuroscience, King's College London; the Institute for Pediatric Neuroscience, Child Study Center, NYU Langone Health, New York; the Department of Psychology and Department of Brain and Cognitive Sciences, Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, Israel; Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, the Netherlands; the Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany; the Department of Behavioral Neuroscience, Oregon Health and Science University, Portland; the Department of Psychiatry, University of Pittsburgh, Pittsburgh; the Department of Psychiatry, School of Medicine, and the Trinity College Institute of Neuroscience, Trinity College, Dublin; the National Institute for Nuclear Physics, Pisa Division, Pisa, Italy; the Mouse Imaging Centre and the Department of Diagnostic Imaging, Hospital for Sick Children, University of Toronto, Toronto; the Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy; the Behavioural Genetics Clinic, Adult Autism Service, Behavioural and Developmental Psychiatry Clinical Academic Group, South London and Maudsley Foundation NHS Trust, London; the Laboratory of Neuroimaging, University of São Paulo Medical School, São Paulo, Brazil; the Imaging Genetics Center, Mark and Mary Stevens Institution for Neuroimaging and Informatics, University of Southern California, Marina del Rey; the Department of Speech, Language, and Hearing Sciences, George Washington University, Washington, D.C.; the College of Computer Science and Technology and the Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China.

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http://dx.doi.org/10.1176/appi.ajp.2017.17010100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546164PMC
April 2018

An OMIC biomarker detection algorithm TriVote and its application in methylomic biomarker detection.

Epigenomics 2018 04 19;10(4):335-347. Epub 2018 Jan 19.

College of Software, Jilin University, Changchun, Jilin 130012, PR China.

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http://dx.doi.org/10.2217/epi-2017-0097DOI Listing
April 2018

Integration of 24 Feature Types to Accurately Detect and Predict Seizures Using Scalp EEG Signals.

Sensors (Basel) 2018 Apr 28;18(5). Epub 2018 Apr 28.

College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.

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http://dx.doi.org/10.3390/s18051372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5982573PMC
April 2018

hMuLab: A Biomedical Hybrid MUlti-LABel Classifier Based on Multiple Linear Regression.

IEEE/ACM Trans Comput Biol Bioinform 2017 Sep-Oct;14(5):1173-1180. Epub 2016 Aug 31.

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http://dx.doi.org/10.1109/TCBB.2016.2603507DOI Listing
March 2018

Proteomic biomarkers for lung cancer progression.

Biomark Med 2018 03 9;12(3):205-215. Epub 2018 Feb 9.

College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China.

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http://dx.doi.org/10.2217/bmm-2018-0015DOI Listing
March 2018

Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways.

Sci Rep 2018 01 10;8(1):267. Epub 2018 Jan 10.

Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry, College of Computer Science and Technology, Jilin University, Changchun, 130012, China.

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http://dx.doi.org/10.1038/s41598-017-17842-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762767PMC
January 2018

Multiple similarly effective solutions exist for biomedical feature selection and classification problems.

Sci Rep 2017 10 9;7(1):12830. Epub 2017 Oct 9.

College of Software, Jilin University, Changchun, Jilin, 130012, China.

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http://dx.doi.org/10.1038/s41598-017-13184-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634418PMC
October 2017

RIFS: a randomly restarted incremental feature selection algorithm.

Sci Rep 2017 10 12;7(1):13013. Epub 2017 Oct 12.

College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.

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http://dx.doi.org/10.1038/s41598-017-13259-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638869PMC
October 2017

Rectified-Linear-Unit-Based Deep Learning for Biomedical Multi-label Data.

Interdiscip Sci 2017 Sep 11;9(3):419-422. Epub 2016 Nov 11.

College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, People's Republic of China.

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http://dx.doi.org/10.1007/s12539-016-0196-1DOI Listing
September 2017

A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs.

Biomed Res Int 2016 18;2016:7237053. Epub 2016 Apr 18.

College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.

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http://dx.doi.org/10.1155/2016/7237053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852346PMC
February 2017

Gly-PseAAC: Identifying protein lysine glycation through sequences.

Gene 2017 Feb 11;602:1-7. Epub 2016 Nov 11.

College of Computer Science and Technology, Jilin University, Changchun 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2016.11.021DOI Listing
February 2017

Machine learning based detection of age-related macular degeneration (AMD) and diabetic macular edema (DME) from optical coherence tomography (OCT) images.

Biomed Opt Express 2016 Dec 3;7(12):4928-4940. Epub 2016 Nov 3.

College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China; http://www.healthinformaticslab.org/ffzhou/.

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http://dx.doi.org/10.1364/BOE.7.004928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175542PMC
December 2016

CD3D and PRKCQ work together to discriminate between B-cell and T-cell acute lymphoblastic leukemia.

Comput Biol Med 2016 10 11;77:16-22. Epub 2016 Jul 11.

College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2016.07.004DOI Listing
October 2016

CRISPRdigger: detecting CRISPRs with better direct repeat annotations.

Sci Rep 2016 09 6;6:32942. Epub 2016 Sep 6.

College of Computer Science and Technology, Changchun, Jilin, 130012, China.

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http://dx.doi.org/10.1038/srep32942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011713PMC
September 2016

Constraint programming based biomarker optimization.

Biomed Res Int 2015 5;2015:910515. Epub 2015 May 5.

Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.

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http://dx.doi.org/10.1155/2015/910515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437250PMC
March 2016

McTwo: a two-step feature selection algorithm based on maximal information coefficient.

BMC Bioinformatics 2016 Mar 23;17:142. Epub 2016 Mar 23.

Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China.

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http://dx.doi.org/10.1186/s12859-016-0990-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804474PMC
March 2016

A novel electrocardiogram parameterization algorithm and its application in myocardial infarction detection.

Comput Biol Med 2015 Jun 20;61:178-84. Epub 2014 Aug 20.

Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, PR China. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2014.08.010DOI Listing
June 2015

Personalized clinical data screening: Special issue on health informatics.

Comput Biol Med 2015 Jun 11;61:161-2. Epub 2015 Apr 11.

Wanqian Technology, Co. Ltd, Shenzhen, Guangdong 518055, China.

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http://dx.doi.org/10.1016/j.compbiomed.2015.04.005DOI Listing
June 2015

jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.

Interdiscip Sci 2015 Jun 6;7(2):194-9. Epub 2015 Aug 6.

Shenzhen Institutes of Advanced Technology, Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, 518055, China.

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http://dx.doi.org/10.1007/s12539-015-0260-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551539PMC
June 2015

jEcho: an evolved weight vector to characterize the protein's post-translational modification motifs.

Interdiscip Sci 2015 Apr 11. Epub 2015 Apr 11.

Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, 518055, China.

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http://dx.doi.org/10.1007/s12539-014-0253-6DOI Listing
April 2015

Evolutionary optimization of transcription factor binding motif detection.

Adv Exp Med Biol 2015 ;827:261-74

School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin, China.

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http://dx.doi.org/10.1007/978-94-017-9245-5_15DOI Listing
March 2015

Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization.

Mol Biol Rep 2014 Sep 10;41(9):5883-9. Epub 2014 Aug 10.

Norman Bethune Medical College of Jilin University, Changchun, 130021, Jilin, China.

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http://dx.doi.org/10.1007/s11033-014-3463-4DOI Listing
September 2014

WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.

BMC Bioinformatics 2014 May 30;15:164. Epub 2014 May 30.

School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P,R, China.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-15-164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4094983PMC
May 2014

Normalizing electrocardiograms of both healthy persons and cardiovascular disease patients for biometric authentication.

PLoS One 2013 20;8(8):e71523. Epub 2013 Aug 20.

Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong, P.R. China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071523PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748040PMC
April 2014

A novel molecular typing method of Mycobacteria based on DNA barcoding visualization.

J Clin Bioinforma 2014 Feb 20;4(1). Epub 2014 Feb 20.

Department of Pathogenobiology, Basic Medical College of Jilin University, Changchun, Jilin, China.

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http://dx.doi.org/10.1186/2043-9113-4-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931916PMC
February 2014

Gene expression profile based classification models of psoriasis.

Genomics 2014 Jan 13;103(1):48-55. Epub 2013 Nov 13.

Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2013.11.001DOI Listing
January 2014

Clinical effects of Xinmailong therapy in patients with chronic heart failure.

Int J Med Sci 2013 23;10(5):624-33. Epub 2013 Mar 23.

Cardiovascular Internal Department, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China, 410008.

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http://dx.doi.org/10.7150/ijms.5779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619101PMC
September 2013

Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom.

Genomics 2013 May 6;101(5):290-5. Epub 2013 Mar 6.

Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E Mach 1, 38010 S. Michele all'Adige (TN), Italy.

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https://linkinghub.elsevier.com/retrieve/pii/S08887543130003
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http://dx.doi.org/10.1016/j.ygeno.2013.02.008DOI Listing
May 2013

WinHAP: an efficient haplotype phasing algorithm based on scalable sliding windows.

PLoS One 2012 14;7(8):e43163. Epub 2012 Aug 14.

Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043163PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419172PMC
February 2013

Screening features to improve the class prediction of acute myeloid leukemia and myelodysplastic syndrome.

Gene 2013 Jan 7;512(2):348-54. Epub 2012 Oct 7.

Shenzhen Institutes of Advanced Technology, and Health Informatics Key Laboratory, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China.

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https://linkinghub.elsevier.com/retrieve/pii/S03781119120123
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http://dx.doi.org/10.1016/j.gene.2012.09.123DOI Listing
January 2013

QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.

PLoS One 2012 5;7(3):e32660. Epub 2012 Mar 5.

Research Center for Biomedical Information Technology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032660PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293860PMC
July 2012

Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation.

IEEE Int Conf Bioinform Biomed Workshops 2011 Nov;2011:50-57

The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University.

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http://dx.doi.org/10.1109/BIBMW.2011.6112354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983420PMC
November 2011

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.

Bioinformatics 2010 Aug 10;26(16):2051-2. Epub 2010 Jun 10.

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916713PMC
August 2010

GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems.

BMC Microbiol 2010 Mar 4;10:69. Epub 2010 Mar 4.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-
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http://dx.doi.org/10.1186/1471-2180-10-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838879PMC
March 2010

Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes.

FEBS Lett 2010 Jan;584(1):194-8

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 7229, USA.

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http://doi.wiley.com/10.1016/j.febslet.2009.11.067
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http://dx.doi.org/10.1016/j.febslet.2009.11.067DOI Listing
January 2010

Large-scale analyses of glycosylation in cellulases.

Genomics Proteomics Bioinformatics 2009 Dec;7(4):194-9

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology/Institute of Bioinformatics, University of Georgia, Athens, GA 30602-7229, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S167202290860049
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http://dx.doi.org/10.1016/S1672-0229(08)60049-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054413PMC
December 2009

De novo computational prediction of non-coding RNA genes in prokaryotic genomes.

Bioinformatics 2009 Nov 10;25(22):2897-905. Epub 2009 Sep 10.

School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773258PMC
November 2009

MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.

Gene 2009 May 10;436(1-2):1-7. Epub 2009 Feb 10.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, 120 Green Street Athens, GA 30602, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S037811190900051
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http://dx.doi.org/10.1016/j.gene.2009.01.019DOI Listing
May 2009

Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice.

Genomics 2009 Apr 9;93(4):383-91. Epub 2009 Jan 9.

James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430800307
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http://dx.doi.org/10.1016/j.ygeno.2008.11.012DOI Listing
April 2009

Genomic and proteomic characterization of a thermophilic Geobacillus bacteriophage GBSV1.

Res Microbiol 2009 Mar 3;160(2):166-71. Epub 2009 Jan 3.

Institute of Plant Virology and College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, PR China.

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http://linkinghub.elsevier.com/retrieve/pii/S092325080800225
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http://dx.doi.org/10.1016/j.resmic.2008.12.005DOI Listing
March 2009

RepPop: a database for repetitive elements in Populus trichocarpa.

BMC Genomics 2009 Jan 9;10:14. Epub 2009 Jan 9.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645430PMC
January 2009

Barcodes for genomes and applications.

BMC Bioinformatics 2008 Dec 17;9:546. Epub 2008 Dec 17.

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621371PMC
December 2008

A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4.

Genetics 2008 Aug 27;179(4):2291-7. Epub 2008 Jul 27.

Computational Systems Biology Laborator, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.108.089995
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http://dx.doi.org/10.1534/genetics.108.089995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516098PMC
August 2008

Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria.

Biochem Biophys Res Commun 2008 Jan 21;365(4):790-4. Epub 2007 Nov 21.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1016/j.bbrc.2007.11.038DOI Listing
January 2008

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

BMC Genomics 2008 Jan 24;9:36. Epub 2008 Jan 24.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246112PMC
January 2008

A general user interface for prediction servers of proteins' post-translational modification sites.

Nat Protoc 2006 ;1(3):1318-21

Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1038/nprot.2006.209DOI Listing
June 2007

SUMOsp: a web server for sumoylation site prediction.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W254-7

Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of China, Hefei, China 230027.

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http://dx.doi.org/10.1093/nar/gkl207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538802PMC
July 2006

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).

Bioinformatics 2006 Apr 24;22(7):894-6. Epub 2006 Jan 24.

Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl013DOI Listing
April 2006

GPS: a comprehensive www server for phosphorylation sites prediction.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W184-7

School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China.

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http://dx.doi.org/10.1093/nar/gki393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160154PMC
July 2005

A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus.

FEBS Lett 2005 Jun;579(16):3369-75

National High-Performance Computing Center at Hefei, University of Science and Technology of China, Hefei 230027, China.

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http://doi.wiley.com/10.1016/j.febslet.2005.04.076
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June 2005