People at CTMS

» Search People

Alexander J. Hartemink, Professor of Computer Science and Bass Fellow of Computer Science

 

Alexander J. Hartemink

Computational biology, machine learning, Bayesian statistics, systems biology, transcriptional regulation, genomics and epigenomics, graphical models, Bayesian networks, computational neurobiology, classification, feature selection

Contact Info:
Office Location:  308 Research Drive, LSRC D239, Durham, NC 27708-0129
Office Phone:  (919) 660-6514
Email Address: send me a message
Web Page:  http://www.cs.duke.edu/~amink/

Teaching (Fall 2017):

  • COMPSCI 260.01, INTRO COMPUTATIONAL GENOMICS Synopsis
    Bio Sci 111, TuTh 10:05 AM-11:20 AM
Teaching (Spring 2018):
  • ETHICS 111S.01, THE EXAMINED LIFE Synopsis
    Keohane LEVEL 2, Tu 03:05 PM-05:35 PM

Education:

Ph.D.Massachusetts Institute of Technology2001
S.M. in Electrical Engineering and Computer ScienceMassachusetts Institute of Technology1997
M.Phil. in EconomicsOxford University1996
M.Phil.University of Oxford (UK)1996
A.B. in EconomicsDuke University1994
B.S.Duke University1994
B.S.Duke University1994

Specialties:

Artificial Intelligence

Research Interests: Computational Biology, Computational Genomics, Machine Learning, Bayesian Networks, Classification and Feature Selection

Keywords:

Algorithms • Alternative Splicing • Amino Acid Motifs • Artificial Intelligence • Auditory Cortex • Auditory Pathways • Auditory Perception • Base Sequence • Bayes Theorem • Binding Sites • Binding, Competitive • Biological Clocks • Biological Markers • Brain Mapping • Cell Cycle • Cell Cycle Proteins • Cell Division • Cell Line • Chromatin • Chromatin Immunoprecipitation • Chromosomal Proteins, Non-Histone • Chromosome Mapping • Cluster Analysis • Computational Biology • Computer Simulation • Conserved Sequence • Cooperative Behavior • Cyclin-Dependent Kinases • Cyclins • Data Interpretation, Statistical • Databases, Genetic • Databases, Protein • Deoxyribonucleases • Diagnosis, Computer-Assisted • DNA • DNA, Fungal • DNA-Binding Proteins • Drosophila melanogaster • Drosophila Proteins • Electrophysiology • Evoked Potentials, Auditory • Evolution, Molecular • Exons • Finches • Flow Cytometry • Forkhead Transcription Factors • G1 Phase • Galactose • Gene Expression Profiling • Gene Expression Regulation • Gene Expression Regulation, Developmental • Gene Expression Regulation, Fungal • Gene Library • Gene Targeting • Genes, Fungal • Genetic Engineering • Genetic Linkage • Genetic Variation • Genome • Genome, Fungal • Genome, Human • Genome-Wide Association Study • Genomic Imprinting • Genomics • Helix-Loop-Helix Motifs • High-Throughput Nucleotide Sequencing • Histones • Homeodomain Proteins • Information Storage and Retrieval • Information Theory • Learning • Linear Models • Logistic Models • Markov Chains • Models, Biological • Models, Genetic • Models, Molecular • Models, Neurological • Models, Statistical • Molecular Sequence Data • Motor Activity • Multivariate Analysis • Mutation • Neoplasms • Neural Networks (Computer) • Nucleic Acid Conformation • Nucleosomes • Oligonucleotide Array Sequence Analysis • Origin Recognition Complex • Pattern Recognition, Automated • Periodicity • Plasmids • Probability • Promoter Regions, Genetic • Protein Array Analysis • Protein Binding • Protein Interaction Domains and Motifs • Protein Interaction Mapping • Protein Structure, Tertiary • Proteins • Proteome • Proteomics • Proto-Oncogene Proteins c-myc • Real-Time Polymerase Chain Reaction • Regression Analysis • Regulatory Sequences, Nucleic Acid • Reproducibility of Results • RNA • S Phase • Saccharomyces cerevisiae • Saccharomyces cerevisiae Proteins • Sensitivity and Specificity • Sequence Alignment • Sequence Analysis, DNA • Sequence Homology, Nucleic Acid • Signal Transduction • Software • Songbirds • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization • Support Vector Machines • Synaptic Transmission • Systems Biology • Thermodynamics • Trans-Activators • Transcription Factors • Transcription, Genetic • Transcriptional Activation • Transcriptome • Transfection • Tumor Markers, Biological • Vocalization, Animal • Zinc Fingers

Postdocs Mentored
  • Victoria A. Smith (2001/12-present)  

Recent Publications   (More Publications)

  1. Welch, JD; Hartemink, AJ; Prins, JF, MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics., Genome Biology: biology for the post-genomic era, vol. 18 no. 1 (July, 2017), pp. 138 [doi]  [abs]
  2. Mayhew, MB; Iversen, ES; Hartemink, AJ, Characterization of dependencies between growth and division in budding yeast., Journal of the Royal Society Interface, vol. 14 no. 127 (February, 2017) [doi]  [abs]
  3. Sparks, EE; Drapek, C; Gaudinier, A; Li, S; Ansariola, M; Shen, N; Hennacy, JH; Zhang, J; Turco, G; Petricka, JJ; Foret, J; Hartemink, AJ; Gord├ón, R; Megraw, M; Brady, SM; Benfey, PN, Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors., Developmental Cell, vol. 39 no. 5 (December, 2016), pp. 585-596 [doi]  [abs]
  4. Welch, JD; Hartemink, AJ; Prins, JF, SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data., Genome Biology: biology for the post-genomic era, vol. 17 no. 1 (May, 2016), pp. 106 [doi]  [abs]
  5. Zhong, J; Luo, K; Winter, PS; Crawford, GE; Iversen, ES; Hartemink, AJ, Mapping nucleosome positions using DNase-seq., Genome research, vol. 26 no. 3 (March, 2016), pp. 351-364 [doi]  [abs]