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Course Curriculum Syllabus

2019-2020


  
Term 1
  
  Course: GS-GS-5101: Responsible Conduct of Research - Year 1
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jul 309:00 AMN315(1L6) Setting Goals for Your Scientific Development & Success in Graduate SchoolCareer 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, where to get help and information, thinking now about the next step.Smith, Carolyn L.
  Tue Aug 069:00 AMN315(1L1) Data Acquisition and Record Keeping ResponsibilitiesResponsibilities for record keeping, challenges in keeping accurate and understandable notebooks, ownership of research materials, reagent/data sharing.Nelson, David
  Tue Aug 139:00 AMN315(1L2) Responsible Authorship and PublicationGiving credit when credit is due, when to cite or not, how to use direct quotes, paraphrasing, plagiarism, copyright and copyright permission.Smith, Carolyn L.
  Tue Aug 209:00 AMN315(1C) Case StudiesRecord keeping, ownership of research materials, responsible citation, and plagiarism
  Tue Aug 279:00 AMN315(1L7) The Funding Structure of Science & Public PolicyGovernment organizations, private funding sources, applying for fellowships, structure of a grant, grant review system, consequences of fraud in grant applications, science advocacyLee, Brendan
  Tue Sep 039:00 AMN315(1M) The Mentor/Mentee RelationshipSelecting a lab and developing a group of mentors, what to look for in the mentor/mentee relationship, keeping on track toward your degree.Smith, Carolyn L.
  Tue Sep 109:00 AMN315(1L3) ResilienceCoping with academic challengesYang, Peggy
  Tue Sep 179:00 AMN315(1L5) Rigor and ReproducibilityReproducibility, transparency, authentication of key biological and chemical resources, types of replication, blinding and randomizationPautler, Robia
  
  Course: GS-GS-6400: Foundations B: Biostatistics
Course Director(s): Hilsenbeck, Susan G. \ Minard, Charles
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jul 292:30 PMN315Introduction and overviewHilsenbeck, Susan G.
  Thu Aug 0112:00 PMMultipleLab: Install and introduce R, data management
  Mon Aug 052:30 PMN315Summarizing numerical dataWang, Tao
  Thu Aug 0812:00 PMMultipleLab: Summarize data, statistics and graphs
  Mon Aug 122:30 PMN315Differences between groupsHilsenbeck, Susan G.
  Thu Aug 152:30 PMN315Differences between two groupsMinard, Charles
  Mon Aug 192:30 PMN315Multiple ComparisonsHilsenbeck, Susan G.
  Thu Aug 2212:00 PMMultipleLab: ANOVA, t-test, multiple comparisons
  Mon Aug 262:30 PMN315Rates and ProportionsMinard, Charles
  Thu Aug 2912:00 PMMultipleLab: Rates and Proportions
  Thu Sep 052:30 PMN315Power and sample sizeWang, Tao
  Mon Sep 092:30 PMN315Confidence intervalsMinard, Charles
  Thu Sep 1212:00 PMMultipleLab: Power and sample size, confidence intervals
  Mon Sep 162:30 PMN315Linear RegressionWang, Tao
  Thu Sep 192:30 PMN315Regression, CorrelationWang, Tao
  Thu Sep 193:30 PMN311Midterm Review
  Fri Sep 202:30 PMN315Midterm Review
  Mon Sep 232:30 PMKleberg
  Thu Sep 2612:00 PMMultipleLab: Linear Regression, Correlations
  
  Course: GS-GS-6203: Data Mining
Course Director(s): Shaulsky, Gad
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Sep 0910:00 AMN315Data ExplorationData preparation for machine learning, introduction to data analysis workflows, visual programming as a means of design of data analysis workflows, basic data exploration and visualization, rigor and reproducibility in data mining.Zupan, Blaz
  Tue Sep 1010:00 AMN315Introduction to ClassificationClassification trees. Confusion matrix. Estimation of prediction error. Overfitting. Cross-validation.Zupan, Blaz
  Wed Sep 1110:00 AMN315Classification ModelsClassification trees, forests, logistic regression, nearest neighbors. Data painting. Area under ROC curve. Analysis of results of classifications. Nomograms.Zupan, Blaz
  Fri Sep 1310:00 AMN315RegressionLinear regression, polynomial regression and overfitting. Regularization. Effects of regularization on training and test sets. Random forests for regression.Zupan, Blaz
  Mon Sep 1610:00 AMN315Introduction to ClusteringEstimating similarities between data instances. Distances between clusters. Hierarchical clustering. Explorative analysis of clustering results. Hierarchical clustering of attribute-value data and text documents.Zupan, Blaz
  Tue Sep 1710:00 AMN315Partitional ClusteringIntroduction to k-means clustering. Differences with hierarchical clustering. Silhouette scoring of clustering results. Outlier detection.Zupan, Blaz
  Wed Sep 1810:00 AMN315Data ProjectionsPrincipal component analysis. Multi-dimensional scaling and t-SNE.Zupan, Blaz
  Fri Sep 2010:00 AMN315Gentle Introduction to Deep LearningImage embedding. Image data analysis – examples with clustering, classification and outlier detection with images. Course wrap-up.Zupan, Blaz
  
  Course: GS-GS-6600: Foundations A: Molecules to Systems
Course Director(s): Sifers, Richard
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jul 291:15 PMN315Nucleic AcidsNucleic acid structure, DNA supercoiling, RNA, Aptamers, Nucleic acid-based diseases (chemical biology and drug discovery)Young, Damian
  Mon Jul 295:15 PMN315Module 1 - Session A
  Wed Jul 311:15 PMN315Proteins 1The Amino acids, protein structure (primary, secondary, etc.), Thermodynamics of protein folding, Protein classification into familiesWang, Jin
  Fri Aug 021:15 PMN315Proteins 2Enzymology (kinetics), Inhibitors (competitive, etc.), Protein-based diseases (chemical biology and drug discovery)Wang, Jin
  Mon Aug 051:15 PMN315Carbohydrates and LipidsMonosaccharides, Polysaccharides, Glycoproteins, Carbohydrate-based diseases, (chemical biology and drug discovery), Lipid classification, Properties of lipids and aggregates, Lipid-based diseases (chemical biology)Young, Damian
  Mon Aug 055:15 PMN315Module 1 - Session B
  Wed Aug 071:15 PMN315Cellular CompartmentalizationCell organelle evolution and roles, Lipid compositions and exchange among intracellular membranes.Sifers, Richard
  Wed Aug 072:30 PMMultipleDiscussion Groups - 1
  Wed Aug 075:15 PMN315Module 2 - Session A
  Fri Aug 091:15 PMN315Organelle BiogenesisProtein trafficking principles, Protein trafficking schemes, Signaling motifs and cognate receptors.Sifers, Richard
  Mon Aug 121:15 PMN315Protein topology and metabolismSequence-directed protein topology in cell membranes, Metabolism (mitochondria)Sifers, Richard
  Wed Aug 141:15 PMN315Vesicular transport of proteinsSecretory pathway and vesicular transport, Vesicle coat proteins, directional protein transport (budding, fusion, lipid recycling), Microtubules and motor proteinsSifers, Richard
  Fri Aug 161:15 PMN315Lysosomes and related diseasesSpecialized protein sorting beyond the Golgi complex, Lysosomal storage diseasesSardiello, Marco
  Fri Aug 162:30 PMMultipleDiscussion Groups - 2
  Fri Aug 165:15 PMN315Module 2 - Session B
  Mon Aug 191:15 PMN315Signal transduction and ion transport overviewLevels and mechanisms, General properties of membrane and nuclear receptors, Mechanisms to transmit signals throughout cells, Crosstalk, ExosomesYork, Robert
  Mon Aug 195:15 PMN315Module 3 - Session A
  Wed Aug 211:15 PMN315Relevant PTMs in Signal TransductionPhosphorylation, Acetylation, Methylation, Ubiquitination, Lipid additionsYork, Robert
  Fri Aug 231:15 PMN315Calcium and Phospholipase signlaingCalcium and its protein complexes, Phosphoinositides, Phospholipase D, Protein kinase C, IP3 receptors, Ca2+-regulated channels, AnnexinsYork, Robert
  Fri Aug 232:30 PMMultipleDiscussion Groups - 3
  Mon Aug 261:15 PMN315GPCRsG proteins and downstream signalsSmith, Carolyn L.
  Wed Aug 281:15 PMN315Membrane-bound receptorsTopics to be covered: Tyrosine kinases and downstream signaling, Serine kinases (i.e., TGF beta) and downstream signalingSmith, Carolyn L.
  Wed Aug 282:30 PMN315
  Wed Aug 285:15 PMN315Module 3 - Session B
  Fri Aug 301:00 PMN315
  Wed Sep 041:15 PMN315Cell division and cell cyclePhases of cell cycle, cyclins and CDKsDang, Weiwei
  Wed Sep 045:15 PMN315 Module 4 - Session A
  Fri Sep 061:15 PMN315Regulation of cell cycle and checkpointsFactors regulating cell cycle from yeast to mammals, checkpoint regulatorsDang, Weiwei
  Mon Sep 091:15 PMN315DNA replicationDNA replication and its control in cell cycleIra, Grzegorz
  Wed Sep 111:15 PMN315DNA damage and repairDNA damage and basic DNA repair pathways (NER,BER, NHEJ, & HR)Ira, Grzegorz
  Wed Sep 112:30 PMMultipleDiscussion Groups - 4
  Wed Sep 115:15 PMN315Module 4 - Session B
  Fri Sep 131:15 PMN315Mendelian GeneticsBasics of Mendel, Punnett Square, tree diagram, altered ratios and epistasisDierick, Herman
  Fri Sep 135:15 PMN315Module 5 - Session A
  Mon Sep 161:15 PMN315Mutations and mutantsRecessive and dominant mutants, types of dominance, penetrance and expressivityDierick, Herman
  Wed Sep 181:15 PMN315Meiosis, linkage & mappingMeiosis as the underlying mechanism of Mendelian inheritance, linkage and mapping (2-point, 3-point/deletion mapping)Dierick, Herman
  Fri Sep 201:15 PMN315GeneticsDisrupting genes, screening for mutant phenotypes, and identifying genes by complementation analysisBates, David
  Mon Sep 231:15 PMN315Gene interactionsGenetic suppression and synthetic enhancement, using one gene to find relaBates, David
  Wed Sep 251:15 PMN315Epistatis analysisDetermining the order of function of genes in regulatory and metabolic pathwaysBates, David
  Fri Sep 271:15 PMN315Human pedigree analysis and genomicsPedigree analysis using Bayesian analysis. Going from sequence to disease causing mutationDierick, Herman
  Fri Sep 272:30 PMMultipleDiscussion Groups - 5
  Fri Sep 275:15 PMN315Module 5 - Session B
  
  Course: GS-GS-5111: Strategies for Success in Graduate School
Course Director(s): Samuel, Melanie \ Sillitoe, Roy
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jul 301:00 PMN315Introduction and the Lifecycle of a Graduate CareerIn this class, we will introduce the course content, set expectations, and discuss the trajectory for each year of graduate school. In addition, we will provide a roadmap and suggested milestones, outline the concept of hidden curriculum, and discuss frequent pitfalls that will motivate the rest of the classes in this course. Samuel, Melanie
  Tue Aug 061:00 PMN315Mastering Time ManagementIn this class, we will discuss the timescale of a PhD, talk about time management and provide examples, and discuss the balance between classwork and rotations.Sillitoe, Roy
  Thu Aug 221:00 PMN315How to be an Effective MenteeWe will discuss how to set yourself up for success in navigating and fostering your relationship with your mentor and understanding your role in a lab. We will also discuss concepts that include imposter syndrome and taking ownership over your graduate career.Finally, we will introduce the concept of a Profile of Self. Arenkiel, Benjamin Russell
  Tue Aug 271:00 PMN315Profiles of Self and Finding a Mentor MatchIn this class, we will discuss the characteristics of good mentors and how to choose and evaluate a lab. We will also discuss your profile in small groups to gain insight on how your profile plays into your mentor decision.Samuel, Melanie
  Tue Sep 031:00 PMN315Planning Your FutureWe will discuss the principles of inside out versus outside in motivation,the choices and day to day realities of different career paths, resources for career planning, and what goes in the Individual Development Plan (IDP).Sillitoe, Roy
  Tue Sep 101:00 PMN315Burnout and Mental HealthIn this class, we will review the local resources for maintaining wellness throughout your training. We will also discuss appropriate workplace behavior and how to be a productive learner and scientist in topics ranging from email and social media to workplace culture and interactions with colleagues in the lab.Yang, Peggy
  Tue Sep 171:00 PMN315Tips and Tricks from the TrenchesIn this class, we will host a panel of successful students at different stages of their graduate career; each will give a brief presentation on the challenges and successes they’ve encountered, followed by a class discussion. Samuel, Melanie
  Tue Sep 241:00 PMN315NetworkingIn this class, we will discuss what networking is, provide real life examples of how it impacts science and careers, discuss the impact of social media, and provide recommendations on how to network locally, nationally, and internationally. Haseltine, Derek
  
  
Term 2
  
  Course: GS-GS-5102: Responsible Conduct of Research - Year 2
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 159:00 AMN315(2M) Mentorship Year TwoMeeting with 2nd year students and their mentors, matching expectations between mentor & student, developing communications channels, picking an appropriate thesis topic, the thesis committee as a resourceSmith, Carolyn L.
  Tue Oct 229:00 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 LaboratoryNelson, David
  Tue Oct 299:00 AMN315(2L2) Ethics of Biomedical Studies 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.Pereira, Frederick
  Tue Nov 059:00 AMN315(2C) Case StudiesScientific Misconduct & Research with Animals
  Tue Nov 129:00 AMN315(2L3) Conflict ResolutionYang, Peggy
  
  Course: GS-GS-5112: Powerful Presentations
Course Director(s): Samuel, Melanie
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 081:00 PMN315The Presentation LandscapeWhy presentations are important; the diverse purposes and formats that talks can have; and distinct venues and audiences for talks.Samuel, Melanie
  Tue Oct 151:00 PMN315The Art of Outstanding PresentationsDefining you audience and your message; Compelling introductions; Effective body; Stellar conclusions; How to deliver a talk; How to answer questionsSamuel, Melanie
  Tue Oct 221:00 PMN315Effective Slide ConstructionDesign principles of effective slides; How much evidence to include; Visual reinforcement of verbal message; How to use slides as a presenterSamuel, Melanie
  Tue Oct 291:00 PMN315Group Work on PresentationsSmall group practice sessions with faculty advisors
  Tue Nov 051:00 PMN315Group Presentations, Part 1
  Tue Nov 121:00 PMN315Group Presentations, Part 2
  Tue Nov 191:00 PMN315Group Feedback and Award PresentationsSummarize and discuss class and advisor feedback. Award first and second place to the highest rated talks in each group.Samuel, Melanie
  
  
Term 3
  
  Course: GS-GS-5103: Responsible Conduct of Research - Year 3
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 0710:00 AMN315(3M) MentorshipMeeting with 3rd year students and their mentors, matching expectations between mentor student, developing communication channels, assessing your progress, risky experiments and backup projects, the thesis committee as a resource.Smith, Carolyn L.
  Tue Jan 1410:00 AMN315(3L5) Rigor and Reproducibility - Part BContinuation of discussions on reproducibility, transparency, authentication of key biological and chemical resources, types of replication, blinding and randomization.Bertuch, Alison
  Tue Jan 2110:00 AMN315(3L1) Authorship/Peer Review & Other Conflicts of InterestOrganizing your paper, preparing manuscripts, who should be an author, responsibilities of an author, manuscript review systems, responsibilities of a reviewer, dealing with criticism - (NIH a) Other Conflicts of Interest - conflicts of interest in the peer review process, financial and professional conflicts and their management.Smith, Carolyn L.
  Tue Jan 2810:00 AMN315(3L2) Collaborative Research including Collaborations with IndustryThe values/responsibilities of collaboration, establishing collaborative relationships, grants, contracts, intellectual property considerations, impact of industry collaborations on publication, thesis submission.Zechiedrich, E.
  Tue Feb 0410:00 AMN315(3C) Case Studies: Peer Review & CollaborationPeer review of grants and papers, conflicts of interest, collaboration (small group discussion format with faculty facilitator).
  
  Course: GS-GS-5104: Responsible Conduct of Research - Year 4
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 0910:00 AMN315(4L1) Ethics of Research with Human SubjectsDefinition of research with human subjects, experiments with human material, confidentiality of medical data, experiments involving humans, informed consent.Berg, Stacey
  Thu Jan 1610:00 AMN315(4L2) The Scientist as a Responsible Member of SocietyContemporary ethical issues in biomedical research and the environmental and societal impacts of scientific researchLazaro-Munoz, Gabriel
  Thu Jan 2310:00 AMN315(4C) Case Studies: Human Research and Science & SocietyResearch with human subjects, societal impact of research (genetics/genomics, stem cells, neuroethics) (small group discussion format with faculty facilitator.
  Thu Jan 3010:00 AMN315(4M) MentorshipMeeting with 4nd year students and their mentors, matching expectations between mentor student, maintaining communication channels, timeline for graduation, backup projects, the thesis committee as a resource, career decisions, the next steps.Smith, Carolyn L.
  Thu Feb 0610:00 AMN315(4L3) Steps to GraduationExplanation of the benchmarks and deadlines for the completion of academic study beyond the 4th year, including dissertation prep, binding, and other required steps to graduate.Smith, Carolyn L.
  
  Course: GS-GS-5105: Scientific Writing
Course Director(s): Marriott, Susan
  DateStart TimeRoomLectureDescriptionLecturer
  Fri Jan 248:30 AMN315Overview and WordsMarriott, Susan
  Fri Jan 318:30 AMN315SentencesMarriott, Susan
  Fri Feb 078:30 AMN315ParagraphsMarriott, Susan
  Fri Feb 148:30 AMN315The Process of WritingMarriott, Susan
  
  Course: GS-GS-5107: Leadership Skills
Course Director(s): Fuqua, Suzanne
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jan 0612:00 PMN317Personality Preference and Leadership StypesFuqua, Suzanne
  Wed Jan 0812:00 PMN317Leadership Self-Assessment and Leadership Skills-Building ExercisesFuqua, Suzanne
  Mon Jan 1312:00 PMN317Emotional Intelligence, Self and Social AwarenessChang, Eric
  Wed Jan 1512:00 PMN317Scientific Writing: Words, Sentences and ParagraphsMarriott, Susan
  Wed Jan 2212:00 PMN317Scientific Writing: Abstract Structure and Manuscript SectionsMarriott, Susan
  Mon Jan 2712:00 PMN317Communication and Conflict ResolutionFuqua, Suzanne
  Wed Jan 2912:00 PMN317Conflict Resolution Skills-Building ExercisesFuqua, Suzanne
  Mon Feb 0312:00 PMN317Teaching SkillsHilsenbeck, Susan G.
  Wed Feb 0512:00 PMN317Teaching Skills ExercisesHilsenbeck, Susan G.
  Mon Feb 1012:00 PMN317Time ManagementSmith, Carolyn L.
  Wed Feb 1212:00 PMN317Creating Mentoring Relationships to Facilitate Career AdvancementRosen, Jeffrey
  Wed Feb 1912:00 PMN317Negotiation Skills-Building Exercises & Course Wrap-UpFuqua, Suzanne
  
  Course: GS-GS-6101: Neuroscience
Course Director(s): Ray, Russell
  DateStart TimeRoomLectureDescriptionLecturer
  Fri Jan 0312:00 PMN311Development of the Nervous SystemHow our nervous system arises from a single fertilized egg. Ray, Russell
  Mon Jan 0612:00 PMN311Somatic Motor and Sensory SystemsHow the circuits that control our movement and our perception of the world are organizedRay, Russell
  Wed Jan 0812:00 PMN311Visceral Motor and Sensory SystemsHow the circuits that drive organ function to keep us alive are organizedRay, Russell
  Fri Jan 1012:00 PMN311Synaptic PhysiologyHow ionic gradients in neurons are established and used to transmit electrical and chemical information.Ray, Russell
  Mon Jan 1312:00 PMN311Learning and MemoryMolecular and cellular requirements for storing new information and recalling it later.Ray, Russell
  Wed Jan 1512:00 PMN311Neurobiology of DiseaseWhat happens when things go wrong in the brain.Ray, Russell
  Fri Jan 1712:00 PMN311Neuroscience in the LabHow we explore the nervous system using genetic, molecular and anatomical techniques.Ray, Russell
  Wed Jan 2212:00 PMN311Nervous System EvolutionElaboration of the nervous system across species and the relevance to human health and disease. Ray, Russell
  Fri Jan 2412:00 PMN311Final Exam Faculty Review
  Mon Jan 2712:00 PMN311Final Exam
  
  Course: GS-GS-6202: Gene Regulation
Course Director(s): Cooper, Thomas
  DateStart TimeRoomLectureDescriptionLecturer
  Fri Jan 031:15 PMN315Introduction to Gene RegulationOverview of gene expression regulation: transcription initiation, termination, alternative RNA splicing, 3' end processing, nuclear export, cytoplasmic mRNA stability, translational, protein degradation and quantitative approaches.Cooper, Thomas
  Mon Jan 061:15 PMN315RNA Polymerase and Control of Transcription in BacteriaThe bacterial enzyme summarizing the kinetics and thermodynamics and interactions with DNA. Subunit function of the bacterial enzyme compared with the subunit structure of the eukaryotic enzyme. Noise in transcription and logic of transcriptional circuits.Herman, Christophe
  Wed Jan 081:15 PMN315Eukaryotic RNA Polymerase and Transcriptional InitiationStructures and activities of the three eukaryotic RNA polymerases. Modes of DNA Binding and Basic Transcription Factors Pathways for transcription initiation by RNA pol II holoenzyme plus general transcription factors. Structures 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.Foulds, Charles
  Fri Jan 101:15 PMN315Coactivaors and CorepressorsIdentification of transcriptional coregulators and evolution of understanding of transcriptional activation. Enzymatic activities of coactivators and corepressors. Post-transcriptional modulation of coregulatory function. Why are there so many coregulators?Foulds, Charles
  Fri Jan 105:15 PMN315TA Session #1
  Mon Jan 131:15 PMN315Regulation of RNA Polymerase II ElongationTranscriptional elongation. Negative factors that limit elongation (NELF, DSIF); Positive factor that activates elongation (P-TEFb); Foulds, Charles
  Wed Jan 151:15 PMN315Chromatin - Relationship Between DNA Sequence Genes, Transcription and ChromatinRelationship between primary DNA sequence, chromatin and transcription. Histones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regionsLonard, David
  Fri Jan 171:15 PMN315Chromatin: Local and GlobalChromatin subdomains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting.Lonard, David
  Tue Jan 215:15 PMN315TA Session #2
  Wed Jan 221:15 PMN315Midterm ReviewMidterm Exam Faculty Review
  Thu Jan 231:15 PMN315Midterm Exam - 1:00-4:00 pmNote special day and time: Thursday 1:00-4:00 pm
  Mon Jan 271:15 PMN315RNA Chemistry, RNA Binding Proteins and Splicing of Pre-mRNAThe spliceosome. Domain structure of RNA binding proteins. How the spliceosome finds vertebrate exons, intron definition vs exon definition.Cooper, Thomas
  Wed Jan 291:15 PMN315Auxiliary Splicing Elements; Alternative SplicingSplicing enhancers and silencers and cognate binding regulatory proteins, effects of alternative splicing on coding potential; regulatory factors and mechanisms of regulation; splicing and human disease (direct cause and as genetic modifier).Cooper, Thomas
  Fri Jan 311:15 PMN3153' End Formation / Polyadenylation; Nuclear-cytoplasmic Transport3' end formation of pol II genes, transcription termination; cotranscriptional regulation of splicing and 3’ end formation; nuclear-cytoplasmic transport.Cooper, Thomas
  Mon Feb 031:15 PMN315RNA--and DNA--EditingRNA editing, insertional/deletion editing (mitochondrial mRNA editing, contrast with trans-esterification, editsome complex, spliceosome), ADAR activity and function, interplay with the microRNA pathway, AMPA receptor, cytosine deaminases.Neilson, Joel
  Wed Feb 051:15 PMN315Posttranscriptional mRNA RegulationThe impact of turnover on steady state RNA levels e.g. NMD, histone gene expression during the cell cycle. Modes and mechanisms of RNA decay. Poly A shortening and 5' -> 3' degradation, P-bodies and mRNA decay. Non-polyA shortening mechanisms. Translation coupled mRNA degradation. Role of 3'UTR sequences in mRNA localization.Neilson, Joel
  Thu Feb 065:15 PMN315TA Session #3
  Fri Feb 071:15 PMN315Noncoding RNA FunctionBiogenesis and function of microRNAs. MicroRNA target prediction. RNAi. Modes of effecting RNAi in eukaryotic systems and forward genetic screens with shRNA libraries. LincRNAs and chromatin.Neilson, Joel
  Mon Feb 101:15 PMN315Translational RegulationReview of protein synthesis and initiation steps, Cap - dependent and cap independent translation. 5'-3' interactions and recycling. Global regulation mechanisms; eIF2 kinase mechanisms, eIF4E inhibitors, viral mechanisms, mTOR, TOP mRNAs.Catic, Andre
  Wed Feb 121:15 PMN315Translational Regulation II MechanismsMRNA-specific regulation; scanning blockers, (uORFs, IRE, auto regulatory systems), cellular IRESs, shunt mechanisms, 3' UTR-based regulation (CPEB in oocytes and neurons) - stress mechanisms (stress granules and P bodies), Frameshifting.Catic, Andre
  Fri Feb 141:15 PMN315Regulation of Protein TurnoverUbiquitin-proteosome mediated degradation. Importance of regulation, protein motifs, PEST sequences, etc.Catic, Andre
  Tue Feb 185:15 PMN315TA Session #4
  Wed Feb 191:15 PMN315Final Exam ReviewFinal Exam Faculty Review
  Mon Feb 241:15 PMN315Final Exam - 1:00-4:00 pmNote special exam place time: 1:00-4:00 pm - Kleberg Auditorium
  
  Course: GS-GS-6201: Cell Division and Cancer
Course Director(s): Chang, Eric \ Ira, Grzegorz
  DateStart TimeRoomLectureDescriptionLecturer
  Fri Jan 032:30 PMN315Review of Principles of Cell Cycle RegulationCDKs, cyclins, CKIs, and proteolysis.
  Mon Jan 062:30 PMN315Cell Cycle CheckpointsInteractive paper discussion
  Wed Jan 082:30 PMN315S phase Entry as Mediated by Cyclin-D and CDK4/6How CDK4/6 regulates G1 to S-phase progression and how this was discovered as a key drug target for cancer
  Fri Jan 102:30 PMN315Genome Instability in Cancer ISpontaneous DNA damage and genome instability in cancer. DNA damage and cancer therapy.
  Mon Jan 132:30 PMN315Genome Instability in Cancer IIInteractive discussion.
  Wed Jan 152:30 PMN315p53 and DNA Damage CheckpointsHow p53 controls the DNA damage checkpoint and the impact on cancer when p53 is lost.
  Fri Jan 172:30 PMN315TA Session
  Wed Jan 222:30 PMN315Midterm Exam Review
  Fri Jan 242:30 PMN315Midterm - 2:30-4:30 pmNote: Extended time: 2:30-4:30 pm
  Mon Jan 272:30 PMN315TelomeresNucleoprotein structure, telomere replication, and telomere repeat RNA.
  Wed Jan 292:30 PMN315Telomere Dysfunction and Telomere Maintenance in CancerTelomere-mediated senescence and crisis, mechanisms telomere maintenance in cancer
  Fri Jan 312:30 PMN315The Study of Telomeres in CancerInteractive paper discussion
  Mon Feb 032:30 PMN315Chromosome Nuclear Organization3D chromosome organization and folding.
  Wed Feb 052:30 PMN315Chromosome DuplicationChromatin duplication and M phase chromosomes organization.
  Fri Feb 072:30 PMN315How Chromatin Deregulation Impacts Tumor ProgressionHow deregulation in chromatin structure impact transcription and tumor formation
  Mon Feb 102:30 PMN315M-phase/Spindle CheckpointMechanisms of spindle formation and function, kinetochore/spindle attachment, and its relevance to cancer
  Wed Feb 122:30 PMN315Cell Cycle and Gene ExpressionRNA regulation of the cell cycle.
  Fri Feb 142:30 PMN315TA Session
  Wed Feb 192:30 PMN315Final Exam Review
  Mon Feb 242:30 PMN315Final Exam: 2:30-4:30 pmNote: Extended time: 2:30-4:30 pm
  
  
Term 4
  
  Course: GS-GS-5106: Intellectual Property
Course Director(s): Turley, C.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Mar 109:00 AMN311Introduction and OverviewBrief introduction to law, including discussion of statutes, regulations, guidelines, and judicial interpretation (case law). Also included will be a brief discussion of the US Courts and how case law is made.Turley, C.
  Thu Mar 129:00 AMN311Patents OverviewWhat patents are and how to obtain a patent.Turley, C.
  Tue Mar 179:00 AMN311Patents in DepthWhat can be patented, how to read and understand a patent. Discussion of cases involving patentability of life forms and genes.Turley, C.
  Thu Mar 199:00 AMN311Patent Infringement and International PatentingWhat constitutes infringement. How to obtain patents outside of the USA.Turley, C.
  Tue Mar 249:00 AMN311Trademarks, Trade Secrets, and AgreementsOverview of trademarks and trade secrets and how these differ from patents. Overview of the different types of intellectual property agreements you may encounter as an inventor.Turley, C.
  Thu Mar 269:00 AMN311CopyrightsCopyright law, particularly with regard to course content and articles and other faculty publications.Turley, C.
  Tue Mar 319:00 AMN311ReviewReview of key concepts learned in class as applied to real-world situations.Turley, C.
  Thu Apr 029:00 AMN311"Now What?"Now that you have learned about intellectual property, what can you do with this information?Turley, C.
  
  Course: GS-GS-6102: Principles of Immunology
Course Director(s): Spencer, David
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Mar 101:30 PMN311Principles of ImmunityOverview of the immune system: innate vs. acquired immunity, cells of the immune system, clonal selection principle, strategies for “self-nonself/danger” discrimination.Levitt, Jonathan
  Thu Mar 121:30 PMN311Innate ImmunityThe gateway to defense against the world around us: pattern recognition receptors, PAMPs/DAMPs, phagocytes and chemical mediators of immunity.Levitt, Jonathan
  Thu Mar 125:15 PMN311TA Session #1TA Session
  Tue Mar 171:30 PMN311Antibody Structure, Antigen Receptor Diversity and B Cell DevelopmentAntigens for B cells, Antibody receptor structure and genetics, generation of diversity, gene rearrangements and class switching.Decker, William K.
  Thu Mar 191:30 PMN311B Cell Activation, MHC, and Antigen PresentationB cell development and selection. Self-nonself recognition, tolerance, T cell antigen recognition, MHC structure and function. MHC antigen presentation and processing.Decker, William K.
  Thu Mar 195:15 PMN311TA Session #2TA Session
  Tue Mar 241:30 PMN311Role and Development of T LymphocytesTypes of T cells, T cell selection and central tolerance, education at thymic university, T cell activation and peripheral tolerance, signaling in T cells, anergy in T cells, apoptosis.Levitt, Jonathan
  Thu Mar 261:30 PMN311T Cell Development and Signaling, Consequences for Transplants and TumorsT cell effector functions, transplantation, autoimmunity, vaccines, tumor immunology.Levitt, Jonathan
  Tue Mar 311:30 PMN311Faculty ReviewExam Review
  Thu Apr 021:00 PMN311Final Exam (1-4 pm)Final Exam (1:00-4:00 pm)

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