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Course Curriculum Syllabus

2016-2017


  
Term 1
  
  Course: GS-GS-501: Organization of the Cell
Course Director(s): Pedersen, Steen E \ Sifers, Richard N
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Mon Aug 012:30 PMN315Overview and the Secretory PathwayCourse organization, outline etc. General protein expression and maturation. The secretory pathway and nature of various organelles.Sifers, Richard N
  2Wed Aug 032:30 PMN315Nuclear TransportOverall structure of the nucleus and nuclear pore complexes. Transport of proteins and RNAs into and out of the nucleus. Nuclear transport and the control of gene expressionSifers, Richard N
  1Thu Aug 045:15 PMN315TA #1Review of general cell structures, their function and generation. Concepts of vesicular transport and protein import and export for the organelles
  3Fri Aug 052:30 PMN315Mitochondria and PeroxisomesStructure and biogenesis of mitochondria and peroxisomes. Protein import into these organellesSifers, Richard N
  4Mon Aug 082:30 PMN315The Endoplasmic ReticulumQuality control checkpoint and mother of the endomembrane systemSifers, Richard N
  5Wed Aug 102:30 PMN315The Golgi ComplexRegulated vesicular trafficking in the endomembrane systemSifers, Richard N
  2Thu Aug 115:15 PMN315TA #2Review of additional protein trafficking schemes
  6Fri Aug 122:30 PMN315Cytoskeleton IActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  7Mon Aug 152:30 PMN315Cytoskeleton IIActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  1Wed Aug 172:30 PMN315Midterm Review
  3Thu Aug 185:15 PMN315TA #3Review of cytoskeleton
  1Fri Aug 191:15 PMN315OC Midterm Exam
  8Mon Aug 222:30 PMN315Vesicular Transport in ReverseThe plasma membrane-endosome-lysosome connectionSifers, Richard N
  9Wed Aug 242:30 PMN315ApoptosisApoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis.Sifers, Richard N
  4Thu Aug 255:15 PMN315TA #4Review of endocytosis, lysosomes, and apoptosis.
  10Fri Aug 262:30 PMN315G ProteinsSignaling mechanisms, ligand recognition and conformation changes by receptors, GDP release kinetics, G protein structure and function, effectors, signal processing, inactivation and desensitization, receptor kinases and arrestins, putative roles for PKC.Wensel, Theodore G
  11Tue Aug 302:30 PMN315Growth Factors/Tyrosine Kinase SignalingLigands and signals, structure of families of membrane receptors with intrinsic tyrosine kinase activity and introduction to cascades activated by binding to phosphotyrosines, SH2 and SH3 domains, tyrosine kinases associated with membrane bound receptorsWensel, Theodore G
  5Thu Sep 015:15 PMN315TA #5Review of G-protein signaling and tyrosine kinase signaling
  12Fri Sep 022:30 PMN315Calcium and phospholipase signalingCalcium and its protein complexes. Phosphoinositides, phospholipase C, protein kinase C, IP3 receptors, proteins regulated by Ca, calmodulin, Ca-regulated channels, annexins, overview of methods for monitoring intracellular Ca and phosphoplipase activityWensel, Theodore G
  13Wed Sep 072:30 PMN315Energy Transduction and BioenergeticsMembrane permeability, mechanisms of transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosisPedersen, Steen E
  6Thu Sep 085:15 PMN315TA #6Review of calcium signaling and bio-energetics.
  14Fri Sep 092:30 PMN315Transport MechanismsActive and passive transport, symporters, antiporters, ATPasesPedersen, Steen E
  15Mon Sep 122:30 PMN315Ion channelsNernst potential, electrical properties of excitable membranes, action potential and energy transductionPedersen, Steen E
  1Wed Sep 142:30 PMN315Faculty Review
  7Thu Sep 155:15 PMN315TA #7Review of transporters and ion channels
  1Fri Sep 161:15 PMN315OC Final Exam1:00-4:00
  
  Course: GS-GS-502: Molecular Methods
Course Director(s): Weigel, Nancy L
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Mon Aug 011:15 PMN315IntroductionOverview of course contents and scheduleWeigel, Nancy L
  2Wed Aug 031:15 PMN315DNA Manipulation, Amplification and DetectionEnzymes to modify, label amplify or quantify nucleic acids; Polymerase chain reaction (PCR) and derivatives such as hybrid PCR, quantitative PCR, real time PCR, droplet PCRVenken, Koen J. T.
  3Fri Aug 051:15 PMN315DNA Cloning IApplications of cloning, vectors, transformation methods, plasmid purification systems, traditional cloning methods, cloning diagnosis.Venken, Koen J. T.
  4Mon Aug 081:15 PMN315DNA Cloning IIApplications of advanced cloning and mutagenesis; Gateway, sequence and ligation independent cloning, Gibson cloning, Type II's cloning; mutagenesisVenken, Koen J. T.
  1Tue Aug 095:15 PMN315TA #1Lectures 1-4
  5Wed Aug 101:15 PMN315Flow CytometryIntroduction to the technique of flow cytometry and cell sorting, detecting fluorescent cells through expressed antigens and endogenous fluorescent moleculesSederstrom, Joel
  6Fri Aug 121:15 PMN315cDNA and Genomic LibrariesConstruction and handling of cDNA libraries; whole genome libraries, targeted strategies such as exome and regional capture, circulating cell-free genomic librariesMetzker, Michael Lee
  7Mon Aug 151:15 PMN315First-Generation Sequencing and GenotypingIntroduction to Maxam-Gilbert, Sanger and automated Sanger sequencing; microarrays, high-throughput genotyping assaysMetzker, Michael Lee
  8Wed Aug 171:15 PMN315Next Generation SequencingTechnology approaches and advances of current NGS platforms focusing on both clonally-amplified and single molecule strategies, alignment for variant detection; haplotype phasing and structural variant detection.Metzker, Michael Lee
  2Wed Aug 175:15 PMN315TA #2Lectures 5-7
  9Mon Aug 221:15 PMN315Genomic ProfilingFunctional assays using NGS: RNA sequencing (RNA-Seq) and data analysis, single cell analyses, other functional sequencing assaysZong, Chenghang
  10Wed Aug 241:15 PMN315Antibody Production, Characterization and Research ApplicationsMonoclonal antibodies(mAbs) - mouse and rabbit hybridomas, B cell IgG cloning and recombinant single domain mAbs; polyclonal antibodies; antibodies to protein post-translational modifications and peptides, characterization and validation of Abs.Edwards, Dean
  3Wed Aug 245:15 PMN315TA #3Lectures 8-9
  1Fri Aug 261:15 PMN315Midterm Review
  1Wed Aug 311:15 PMN315MM Midterm Exam
  11Fri Sep 021:15 PMN315CRISPR/Cas9Purification of epitope tagged proteins; inclusion bodies; protein refolding strategies; disulfide formation and artificial chaperones.Heaney, Jason D
  12Tue Sep 062:30 PMN315Detection of Protein-Protein InteractionsPrinciples of: Western immunoblotting, Westerns coupled to co-immunoprecipitation; in vitro (GST) pull-down assays; yeast two-hybrid system; bimolecular fluorescence complementation(BiFC) and phage displayLydon, John P
  13Wed Sep 071:15 PMN315Visualizing ProteinsImmunohistochemical detection methods; lacZ reporters; green fluorescence protein (GFP) reporters; luciferase reporters; fluorescence resonance energy transfer (FRET); bimolecular fluorescence complementation (BiFC); fluorescence recovery after photobleachingLydon, John P
  4Wed Sep 075:15 PMN315TA #4Lectures 10-13
  14Fri Sep 091:15 PMN315High Throughput MethodsChromatin immunoprecipitation (ChIP) on ChIP (ChIP-Chip); ChIP and high throughput DNA sequencing (ChIP-Seq); protein microarrays (i.e.reverse and forward phase protein microarrays); tissue microarrays.Lydon, John P
  15Mon Sep 121:15 PMN315Protein ExpressionExpression systems (E.coli, yeast, insect and mammalian cells), fusion tags (6x His, GST, MBP, intein); co-expression for protein complexes and in vitro translationYork, Robert Brian
  16Wed Sep 141:15 PMN315Protein PurificationCell disruption methods; centrifugation, ammonium sulfate precipitation, liquid chromatography (affinity, ion exchange, hydrophobic, size exclusion); SDS-PAGE; evaluating protein concentration (Bradford and extinction coefficients) and biological assays.York, Robert Brian
  17Mon Sep 191:15 PMN315Proteomics Mass Spectrometry - Basic PrinciplesMass spectometer instruments and analytical methods; principles of identification for peptides and post-translational modifications (PTMs); data processingMalovannaya, Anna
  5Tue Sep 205:15 PMN315TA #5Lectures 14-16
  18Wed Sep 211:15 PMN315Proteomics Mass Spectrometry - Applications in BiologyMS-based quantification, global proteome profiling, PTM profiling, protein-protein interaction networks from IP/MSMalovannaya, Anna
  19Fri Sep 231:15 PMN315RNA Interference and genetic screensRNA interference(RNAi) mechanisms, RNAi tools, genetic screening methods, technical considerations in using RNAiWestbrook, Thomas
  6Fri Sep 235:15 PMN315TA #6Lectures 17-19
  1Wed Sep 281:15 PMN315Faculty Review
  1Fri Sep 301:15 PMN315MM Final Exam1:00-4:00
  
  Course: GS-GS-503: Genetics A
Course Director(s): Herman, Christophe \ Dierick, Herman A.
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Tue Aug 021:15 PMN315Mendelian GeneticsGene nomenclature: gene/allele/genotype/phenotype. Dominant v. recessive mutations. Mendel's laws. Penetrance v. expressivity.Dierick, Herman A.
  2Thu Aug 041:15 PMN315Cellular Mechanisms of Mendelian Genetics and LinkageMeiosis v. mitosis. Linkage. Two-point and three-point mapping. Complementation.Dierick, Herman A.
  3Tue Aug 091:15 PMN315Statistical Methods in Genetics.Basics of pedigrees. Binomial statistics: identifying probabilities of alternative choices. Bayesian statistics: altering a priori probability. X square tests: testing data against a model.Dierick, Herman A.
  4Thu Aug 111:15 PMN315Population GeneticsMultifactorial traits: continuous, dichotomous and meristic traits. Polygeneticity and heritability. Allele frequencies, genotype frequencies and Hardy Weinberg. Inbreeding and inbreeding coefficients. Selection and balanced polymorphisms.Dierick, Herman A.
  1Mon Aug 155:15 PMN315TA #1General Genetic Principles
  5Tue Aug 161:15 PMN315Genetic ScreensMutant building: discovering genes involved in a biological process through screens. Mutagens and screen saturation. Yeast genetics and tetrad analysis.Bates, David B.
  6Thu Aug 181:15 PMN315Selecting and Identifying MutantsIdentifying mutated genes. Selection and screening strategies, reporter genes and secondary screens.Bates, David B.
  7Tue Aug 231:15 PMN315Genetic SuppressionGenetics as a study of how proteins interact, fold and function. Mechanisms of genetic suppression. Genetic enhancement and synthetic lethality.Bates, David B.
  8Thu Aug 251:15 PMN315Epistasis and Pathway AnalysisDetermining the order of action of proteins in a pathway by epistasis analysis. Ordering genes in metabolic and regulatory pathways.Bates, David B.
  1Thu Aug 252:30 PMN315Faculty Review
  2Fri Aug 265:15 PMN315TA #2Phenotype, pathway analysis and genetics screens
  1Mon Aug 291:15 PMN315GA Mid-term Exam1:00-4:00
  9Thu Sep 011:15 PMN315Viral/Phage Genetics.Virus cycle, complementation group.Herman, Christophe
  10Tue Sep 061:15 PMN315Bacterial Genetics IGenetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation.Rosenberg, Susan M
  11Thu Sep 081:15 PMN315Bacterial Genetics IIRecombination.Rosenberg, Susan M
  12Tue Sep 131:15 PMN315Bacterial Genetics IIISOS response, transpositionRosenberg, Susan M
  13Thu Sep 151:15 PMN315Genetic Engineering IArtificial chromosomes, recombineering in bacteria, homing endonucleases (I-SceI), seamless versus remnant engineeringVenken, Koen J. T.
  3Mon Sep 195:15 PMN315TA #3Bacterial Genetics
  14Tue Sep 201:15 PMN315Genetic Engineering IIIntegrases, Zn finger technology, TALE technology, Crispr/Cas technologyVenken, Koen J. T.
  1Thu Sep 221:15 PMN315Faculty Review
  4Thu Sep 225:15 PMN315TA #4Genetic Engineering
  1Mon Sep 261:15 PMN315GA Final Exam1:00-4:00
  
  Course: GS-GS-528: Responsible Conduct of Research - Year 1
Course Director(s): Bertuch, Alison Ann
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Thu Aug 042:30 PMN315Accessing the Scientific Literature and Other Resources Accessing the scientific literature (e.g., Pubmed, Scopus, Google Scholar). Navigating the plethora of journals and papers. Resources in the TMC Library.
  2Thu Aug 112:30 PMN315Rigor and Reproducibility The scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparencyBertuch, Alison Ann
  3Thu Aug 182:30 PMN315Professionalism in Science Government organizations, private funding sources, applying for fellowships, structure of a grant, grant review system, consequences of fraud in grant applications, science advocacy. Kuspa, Adam
  4Tue Aug 232:30 PMN315Setting Goals for Your Scientific Development and Coping with Challenges Career paths for the professional scientist, career decisions (how and when to make them), what to do in your first year to ensure your success, developing curiosity, coursework (what to expect in grad school), lifelong learning, selecting rotations, where to get help and information, thinking now about the next stepSmith, Carolyn L
  5Thu Sep 012:30 PMN315Data Acquisition and Record Keeping Responsibilities Responsibilities for record keeping, challenges in keeping accurate and understandable notebooks, ownership of research materials, reagent/data sharingNelson, David L
  6Thu Sep 082:30 PMN315Responsible Authorship and Publication Giving credit when credit is due, when to cite or not, how to use direct quotes, paraphrasing, plagiarism, copyright and copyright permission Smith, Carolyn L
  7Thu Sep 152:30 PMN315Case Studies Data Management/PlagiarismRecord keeping, ownership of research materials, responsible citation, and plagiarism
  8Thu Sep 222:30 PMN315Progress to Degree – Year 1 Selecting a lab and developing a group of mentors, what to look for in the mentor/mentee relationship, keeping on track toward your degree. Building resilienceBertuch, Alison Ann
  
  
Term 2
  
  Course: GS-GS-527: ABC-Applications to Biology of Computation
Course Director(s): Lichtarge, Olivier \ Milosavljevic, Aleksandar
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Tue Oct 119:00 AMN315Big Data GeneticsThis lecture will introduce genome interpretation and will cover(1) opportunities for genetics-driven biology that will be opened by the sequencing of millions of genomes during this decade; (2) efforts by the Clinical Genome Resource project to developMilosavljevic, Aleksandar
  1Wed Oct 125:15 PMN315TA #1Hardware and Contemporary Computing Infrastructure.This TA session will be held in 301A.
  2Thu Oct 139:00 AMN315Network BiologyInference and knowledge representation.This lecture will focus on (1) inference of pathways, networks, and network modules; (2) Interpretation of Big Data experiments using networks, pathways, and modules as background knowledge; (3) Computational represMilosavljevic, Aleksandar
  2Fri Oct 145:15 PMN315TA #2A Beginner’s guide to UNIX / Linux and qsub commands.This TA session will be held in 301A.
  3Tue Oct 189:00 AMN315A Primer in Network Biology IElements in transcription networks, network motif and graph theory.Liu, Zhandong
  4Fri Oct 219:00 AMN315A Primer in Network Biology IINetwork inference from genomics data. This class will be held in 201ALiu, Zhandong
  5Tue Oct 259:00 AMN315Computational Analysis of Networks and Pathways IIntroduction to computational methods to analyze biological information from networks.Liu, Zhandong
  6Thu Oct 279:00 AMN315Computational Analysis of Networks and Pathways IIComputational methods to decode and to analyze biological information from networks - advanced topics.Liu, Zhandong
  7Tue Nov 019:00 AMN315Genome StructureVariation, evolution and cancerMilosavljevic, Aleksandar
  8Thu Nov 039:00 AMN315Cancer GenomicsApplication of NGS variation analysis onto tumor samples.How do tumor genomes differentiate from normal genomes? What have we learned from large- scale cancer genome sequencing such as TCGA, etc.?Chen, Ken
  9Tue Nov 089:00 AMN315Recent Developments in Gene MappingFocused on gene mapping approach and current approach and challenges in functional annotation, interpretation and prioritization.It will review the basic disease models (common vs rare) and gene mapping frameworks(GWAS, Exome, CVAS vs RVAS). It will alsYu, Fuli
  10Thu Nov 109:00 AMN315Cancer Genomic MedicinePractical challenges on implementing NGS-based tests in a cancer clinics.Why is it important(some case examples)? Progresses made so far.What are the missing pieces? Opportunities for biomedical computational science.Chen, Edward S
  11Tue Nov 159:00 AMN315NGS Variation AnalysisFocused on the SNP calling algorithms in NGS datasets, for both personal genome(when N = 1) and population genomic studies(when N = many). It will serve as an introduction lecture and review the most popular SNP callers applied the NGS data analysis, incluYu, Fuli
  12Thu Nov 179:00 AMN315From Sequence to StructureA brief overview of the sequence-based tools and algorithms used to interpret protein structure and function.This lecture will also highlight current approaches in homology and template-free modeling.Baker, Matthew L
  13Mon Nov 219:00 AMN315Macromolecular StructureThis lecture focuses on methods for interpreting and modeling macromolecular structure and function, as well as validation methods commonly used with these techniques.A particular emphasis will be on integrative or hybrid methods that combine multiple tyBaker, Matthew L
  14Tue Nov 229:00 AMN315Sequence-Structure-Function IThis lecture will be an overview of common tools utilized in evolutionary analysis: BLAST, alignments, substitution matrices, and phylogenetic trees.Wilkins, Angela Dawn
  15Tue Nov 299:00 AMN315Sequence-Structure-Function IIThis lecture will focus on tools that take advantage of evolutionary information in order identify function and functional sites.Wilkins, Angela Dawn
  16Thu Dec 019:00 AMN315Evolutionary AnalysisA formal approach to the genotype-phenotype relationship with molecular, clinical and population genetics applications.This class will be held in N315Lichtarge, Olivier
  1Thu Dec 089:00 AMN315ABC - Final ExamFinal Exam will be held in N315.
  
  Course: GS-GS-504: Genetics B
Course Director(s): Zhou, Zheng
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Tue Oct 111:15 PMN315IntroductionForward and reverse genetics.Strengths of model systems.Nomenclature.The concept of maternal effect.Zhou, Zheng
  2Thu Oct 131:15 PMN315Yeast IBasic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffleIra, Grzegorz
  3Tue Oct 181:15 PMN315Yeast IIGenome analysis and functional genomics.The impact of the yeast genome project.Systematic manipulation of entire gene sets to monitor mRNA expression and protein localization in vivo.Ira, Grzegorz
  1Wed Oct 195:15 PMN315GB-TA1Held in N315
  4Tue Oct 251:15 PMN315C.elegans IAdvantages and special considerations of hermaphrodite genetics.How to construct strains, strategies of genetic screens, cloning genes, balancers.Zhou, Zheng
  5Thu Oct 271:15 PMN315C.elegans IIC.elegans transformation.Impact of the C.elegans genome project.Reverse genetics using RNA interference and gene deletions.Studies of gene interaction.Zhou, Zheng
  2Thu Oct 275:15 PMN315GB-TA2Held in N315
  6Tue Nov 011:15 PMN315Drosophila IIntroduction.Nomenclature and markers; chromosome cytology(polytene chromosomes) and chromosome rearrangements; using balancer chromosomes to follow segregation and to isolate mutations; P-elements and transformation; site-specific integration using thMardon, Graeme
  7Thu Nov 031:15 PMN315Drosophila IIGenetic screens.Mutagens: ems, x-rays and P-elements; classic genetic screens to identify mutations in Drosophila: F1, F2, F3 screens; modifier(suppressor and enhancer) screens; isolating mutations, mapping lethal mutations; deficiency mapping; high-thMardon, Graeme
  3Fri Nov 045:15 PMN315GB-TA3Held in 201A
  8Tue Nov 081:15 PMN315Drosophila IIIGene function.Mosaic analysis; autonomy versus non-autonomy; mitotic recombination using the FLP/FRT system, methods of marking clones; ectopic expression using heat shock, GAL4-UAS, and flp-out; MARCM analysis.Mardon, Graeme
  1Tue Nov 082:30 PMN315Faculty Review
  1Thu Nov 101:15 PMN315GB Midterm Exam1:00-4:00
  9Tue Nov 151:15 PMN315Mouse Genetics IInbred mice. Microsatellite markers. Mapping genes in mice using crosses.Matzuk, Martin Matthew
  10Thu Nov 171:15 PMN315Mouse Genetics IIInsertion of DNA and retrotransposons.Knock-outs and ins.Conditional knock-outs.Matzuk, Martin Matthew
  4Fri Nov 185:15 PMN315GB-TA4Held in 201A
  11Mon Nov 211:15 PMN315Human Genetics IDisease loci and pedigrees.Lupski, James R
  12Tue Nov 291:15 PMN315Human Genetics IIMapping with DNA markers.Sources of polymorphisms. Simple vs. complex traits. Genome scans for quantitative trait loci.Lupski, James R
  13Thu Dec 011:15 PMN315Human Genetics IIIEffect of imprinting on pedigrees.Models for specific mechanisms of imprinting.Model for evolutionary significance.Lupski, James R
  5Fri Dec 025:15 PMN315GB-TA5Held in 201A
  1Wed Dec 071:15 PMN315Faculty Review
  1Fri Dec 091:15 PMN315GB Final Exam1:00-4:00
  
  Course: GS-GS-505: Cell Division
Course Director(s): Ira, Grzegorz \ Chang, Eric C
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Mon Oct 101:15 PMN315Course Introduction/Cell Cycle OverviewDiscovery of cell cycle regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF
  2Wed Oct 121:15 PMN315S phaseInitiation and control of DNA replication at origins of replicationsIra, Grzegorz
  3Fri Oct 141:15 PMN315Principles of cell cycle regulation ICDKs, cyclins, CKIs, and proteolysis
  4Mon Oct 171:15 PMN315Principles of cell cycle regulation IICell cycle transitions, G1/S and G2M
  1Tue Oct 185:15 PMN315TA #1Review of cell cycle basics, S phase
  5Wed Oct 191:15 PMN315Cell Cycle CheckpointsIntroduction to cell cycle checkpoints, the DNA damage checkpoint
  6Fri Oct 211:15 PMN315DNA DamageDNA damage and repairIra, Grzegorz
  7Mon Oct 241:15 PMN315DNA RepairRepair of double strand breaks by homologous and non-homologous recombinationIra, Grzegorz
  1Mon Oct 242:30 PMN315Faculty Review MidtermLectures 1-7
  2Tue Oct 255:15 PMN315TA #2Review of DNA recombination and repair
  1Wed Oct 261:15 PMN315CD Midterm ExamLectures 1-7
  8Fri Oct 281:15 PMN315ChromosomesChromatin duplication and M phase chromosomes organizationDang, Weiwei
  9Mon Oct 311:15 PMN315TelomeresStructure and synthesis.Telomere dysfunction-induced DNA damage checkpoint response.Crisis and survival in the absence of telomerase.Bertuch, Alison Ann
  10Fri Nov 041:15 PMN315M phase spindleMechanisms of spindle formation and function, kinetochore/spindle attachmentChang, Eric C
  11Mon Nov 071:15 PMN315CytokinesisCytokinesis mechanismsSokac, Anna Marie
  3Tue Nov 085:15 PMN315TA #3Review of chromosome/chromatin/telomeres
  12Wed Nov 091:15 PMN315Growth regulationThe cell cycle in growth regulation, development and cancerWestbrook, Thomas
  13Fri Nov 111:15 PMN315CD13
  1Tue Nov 152:30 PMN315Faculty ReviewLecture 8-12
  4Tue Nov 155:15 PMN315TA #4Review of cytokinesis, spindle & kinetochore assembly and growth regulation
  1Wed Nov 161:15 PMN315CD Final ExamLectures 8-12. (1:00-4:00 PM)
  
  Course: GS-GS-506: Development
Course Director(s): Groves, Andrew Kelton
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Wed Oct 122:30 PMN315DE Seminar
  2Fri Oct 142:30 PMN315Core Concepts in Developmental BiologyGroves, Andrew Kelton
  3Mon Oct 172:30 PMN315Setting up the vertebrate body plan IAxis determination and gastrulationGroves, Andrew Kelton
  4Wed Oct 192:30 PMN315Setting up the vertebrate body plan IIMammalian development and embryonic stem cellsGroves, Andrew Kelton
  5Fri Oct 212:30 PMN315Patterning the embryo from head to tailGroves, Andrew Kelton
  1Fri Oct 215:15 PMN315TA #1
  2Fri Oct 285:15 PMN315TA #2
  1Mon Oct 312:30 PMN315Mid-Term Faculty Review
  1Wed Nov 021:15 PMN315DE Midterm Exam1:00-4:00
  6Fri Nov 042:30 PMN315ES cells, pluripotency and reprogramming / iPSGroves, Andrew Kelton
  7Mon Nov 072:30 PMN315Stem cells in the adultNguyen, Hoang
  8Wed Nov 092:30 PMN315Introduction to Drosophila embryogenesisOverview of Drosophila oogenesis and embryogenesisJafar-Nejad, Hamed
  3Thu Nov 105:15 PMN315TA #3
  9Fri Nov 112:30 PMN315Embryonic patterning in Drosophila - IMaternal-effect genes and the establishment of the anteroposterior axesJafar-Nejad, Hamed
  10Mon Nov 142:30 PMN315Embryonic patterning in Drosophila IIMaternal-effect genes and the establishment of the dorsoventral axesJafar-Nejad, Hamed
  11Thu Nov 172:30 PMN315Limb DevelopmentA model system to illustrate developmental conceptsGroves, Andrew Kelton
  4Thu Nov 175:15 PMN315
  1Fri Nov 182:30 PMN315Faculty Review
  1Tue Nov 221:15 PMN315DE Final Exam1:00-4:00
  
  Course: GS-GS-508: Cancer
Course Director(s): Pangas, Stephanie A
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Mon Nov 141:15 PMN315Introduction to Cancer CourseMouse models of cancer using lung cancer as an examplePangas, Stephanie A
  2Fri Nov 181:15 PMN315OncogenesPangas, Stephanie A
  3Mon Nov 212:30 PMN315Cancer as a Multi-Step ProcessPangas, Stephanie A
  4Mon Nov 282:30 PMN315Tumor Cell - Stromal InteractionsChen, Xi
  5Wed Nov 302:30 PMN315MetastasisZhang, Xiang
  6Fri Dec 022:30 PMN315Cancer Stem CellsChan, Keith
  1Mon Dec 051:15 PMN315Faculty Review
  1Tue Dec 061:15 PMN315CA Final Exam1:00-4:00
  
  Course: GS-GS-515: Ethics - Year 2
Course Director(s): Bertuch, Alison Ann
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Mon Oct 1010:00 AMN315(2L1) Research misconduct - (NIH b3) Safe Practices in the LaboratoryDefinitions - Falsification, fabrication, plagiarism – whistleblowers, allegations, investigations, penalties. College policy and mechanisms for handling misconduct allegations, federal policies and procedures. (NIH b3) Safe Practices in the Laboratory
  2Mon Oct 1710:00 AMN315(2M) MentorshipMeeting with 2nd year students and their mentors, matching expectations between mentor student, developing communication channels, picking an appropriate thesis topic, the thesis committee as a resource
  3Mon Oct 2410:00 AMN315(2L2) Ethics of Experiments with Animalswhen can animals be used ethically in research, avoiding unnecessary pain/suffering and euthanasia, appropriate selection of numbers/types of animals in research, animal use approval
  4Mon Oct 3110:00 AMN315(2C) Case Studies - Scientific Misconduct/Animalsscientific misconduct and experiments with animals (small group discussion format with faculty facilitator)
  5Mon Nov 0710:00 AMN315Rigor and ReproducibiltyCell culture
  
  Course: GS-GS-523: Method and Logic in Molecular Biology
Course Director(s): Mardon, Graeme
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Thu Oct 1311:00 AMN315Method and Logic MeetingAttendance at this class (to be held in N315) is mandatory for all students who intend to take this course.This organizational meeting begins at 10:15 and runs until 11:45 AM.
  2Tue Oct 1811:00 AMN315Method and Logic MeetingClasses will be held in N302, N304, N310, N317 and M303 from this class onwards. Classes begin at 10 AM and end at noon.
  3Fri Oct 2111:00 AMN315Method and Logic Meeting
  4Tue Oct 2511:00 AMN315Method and Logic Meeting
  5Thu Oct 2711:00 AMN315Method and Logic Meeting
  6Tue Nov 0111:00 AMN315Method and Logic Meeting
  7Thu Nov 0311:00 AMN315Method and Logic Meeting
  8Tue Nov 0811:00 AMN315Method and Logic Meeting
  9Thu Nov 1011:00 AMN315Method and Logic Meeting
  10Tue Nov 1511:00 AMN315Method and Logic Meeting
  11Thu Nov 1711:00 AMN315Method and Logic Meeting
  12Tue Nov 2911:00 AMN315Method and Logic Meeting
  13Thu Dec 0111:00 AMN315Method and Logic Meeting
  
  Course: GS-GS-527: ABC-Applications to Biology of Computation
Course Director(s): Lichtarge, Olivier \ Milosavljevic, Aleksandar
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Tue Oct 119:00 AMN315Big Data GeneticsThis lecture will introduce genome interpretation and will cover(1) opportunities for genetics-driven biology that will be opened by the sequencing of millions of genomes during this decade; (2) efforts by the Clinical Genome Resource project to developMilosavljevic, Aleksandar
  1Wed Oct 125:15 PMN315TA #1Hardware and Contemporary Computing Infrastructure.This TA session will be held in 301A.
  2Thu Oct 139:00 AMN315Network BiologyInference and knowledge representation.This lecture will focus on (1) inference of pathways, networks, and network modules; (2) Interpretation of Big Data experiments using networks, pathways, and modules as background knowledge; (3) Computational represMilosavljevic, Aleksandar
  2Fri Oct 145:15 PMN315TA #2A Beginner’s guide to UNIX / Linux and qsub commands.This TA session will be held in 301A.
  3Tue Oct 189:00 AMN315A Primer in Network Biology IElements in transcription networks, network motif and graph theory.Liu, Zhandong
  4Fri Oct 219:00 AMN315A Primer in Network Biology IINetwork inference from genomics data. This class will be held in 201ALiu, Zhandong
  5Tue Oct 259:00 AMN315Computational Analysis of Networks and Pathways IIntroduction to computational methods to analyze biological information from networks.Liu, Zhandong
  6Thu Oct 279:00 AMN315Computational Analysis of Networks and Pathways IIComputational methods to decode and to analyze biological information from networks - advanced topics.Liu, Zhandong
  7Tue Nov 019:00 AMN315Genome StructureVariation, evolution and cancerMilosavljevic, Aleksandar
  8Thu Nov 039:00 AMN315Cancer GenomicsApplication of NGS variation analysis onto tumor samples.How do tumor genomes differentiate from normal genomes? What have we learned from large- scale cancer genome sequencing such as TCGA, etc.?Chen, Ken
  9Tue Nov 089:00 AMN315Recent Developments in Gene MappingFocused on gene mapping approach and current approach and challenges in functional annotation, interpretation and prioritization.It will review the basic disease models (common vs rare) and gene mapping frameworks(GWAS, Exome, CVAS vs RVAS). It will alsYu, Fuli
  10Thu Nov 109:00 AMN315Cancer Genomic MedicinePractical challenges on implementing NGS-based tests in a cancer clinics.Why is it important(some case examples)? Progresses made so far.What are the missing pieces? Opportunities for biomedical computational science.Chen, Edward S
  11Tue Nov 159:00 AMN315NGS Variation AnalysisFocused on the SNP calling algorithms in NGS datasets, for both personal genome(when N = 1) and population genomic studies(when N = many). It will serve as an introduction lecture and review the most popular SNP callers applied the NGS data analysis, incluYu, Fuli
  12Thu Nov 179:00 AMN315From Sequence to StructureA brief overview of the sequence-based tools and algorithms used to interpret protein structure and function.This lecture will also highlight current approaches in homology and template-free modeling.Baker, Matthew L
  13Mon Nov 219:00 AMN315Macromolecular StructureThis lecture focuses on methods for interpreting and modeling macromolecular structure and function, as well as validation methods commonly used with these techniques.A particular emphasis will be on integrative or hybrid methods that combine multiple tyBaker, Matthew L
  14Tue Nov 229:00 AMN315Sequence-Structure-Function IThis lecture will be an overview of common tools utilized in evolutionary analysis: BLAST, alignments, substitution matrices, and phylogenetic trees.Wilkins, Angela Dawn
  15Tue Nov 299:00 AMN315Sequence-Structure-Function IIThis lecture will focus on tools that take advantage of evolutionary information in order identify function and functional sites.Wilkins, Angela Dawn
  16Thu Dec 019:00 AMN315Evolutionary AnalysisA formal approach to the genotype-phenotype relationship with molecular, clinical and population genetics applications.This class will be held in N315Lichtarge, Olivier
  1Thu Dec 089:00 AMN315ABC - Final ExamFinal Exam will be held in N315.
  
  
Term 3
  
  Course: GS-GS-509: Gene Regulation
Course Director(s): Cooper, Thomas
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Wed Jan 041:15 PMN315Introduction to Gene RegulationSites of Gene Regulation: transcription initiation, termination, alternative RNA splicing, 3' end processing, nuclear export, cytoplasmic mRNA stability, translational regulation, protein degradation. Analysis of gene expression.
  2Fri Jan 061:15 PMN315RNA Polymerasethe bacterial enzyme summarizing the kinetics and thermodynamics of the protein and its interactions with DNA, subunit function of the bacterial enzyme compared with the subunit structure of the eukaryotic enzyme.Regulatory functions of the polymerase.
  3Mon Jan 091:15 PMN315Control of transcription in bacteriadegradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits.
  4Wed Jan 111:15 PMN315Eukaryotic RNA polymerase and transcriptional initiationStructures and activities of the 3 eukaryotic RNA polymerases.Pathways for transcription initiation by RNA pol II holoenzyme plus general transcription factors.
  5Fri Jan 131:15 PMN315Modes of DNA binding and basic transcription factorsStructures of DNA binding domains and the molecular basis for DNA sequence recognition.How do transcription factors find their sites? Genome wide networks of transcriptional regulation.
  6Wed Jan 181:15 PMN315Coactivators and corepressorsIdentification of transcriptional coregulators and evolution of understanding of transcriptional activation.Enymatic activities of coactivators and corepressors.Post-transcriptional modulation of coregulator function.Why are there so many coregulato
  7Fri Jan 201:15 PMN315Chromatin 1 - LocalHistones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regions, polytene/lapbrush chromosomes.
  
  Course: GS-GS-511: Neuroscience
Course Director(s): Jankowsky, Joanna Louisa
  No.DateStart TimeRoomLectureDescriptionLecturer
  1Tue Jan 032:30 PMN315Cellular and Structural NeuroanatomyMajor subdivions of the mammalian brain, their general organization and the specialized cells required for function.Al-Ramahi, Ismael
  2Thu Jan 052:30 PMN315Neuronal BiophysicsStructure and function of the major membrane proteins responsible for establishing ionic gradients in neurons and how they are used to transmit electrical information.Al-Ramahi, Ismael
  3Tue Jan 102:30 PMN315Synaptic PhysiologySpecialized structures and proteins that allow electrical signals to be converted to chemical messengers and then back again to facilitate cell-cell communication
  4Thu Jan 122:30 PMN315Learning and MemoryMolecular and cellular requirements for storing new information and reacalling it later.
  5Tue Jan 172:30 PMN315Neurobiology of DiseaseWhat happens when things go wrong in the brain.
  1Wed Jan 182:30 PMN315Faculty Review
  1Thu Jan 191:15 PMN315NE Final Exam1:00-4:00

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