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Course Curriculum Syllabus

2020-2021


  
Term 1
  
  Course: GS-GS-6600: Foundations A: Molecules to Systems
Course Director(s): Sifers, Richard
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 031:15 PMOnlineNucleic AcidsNucleic acid structure, DNA supercoiling, RNA, Aptamers, Nucleic acid-based diseases (chemical biology and drug discovery)Young, Damian
  Mon Aug 035:15 PMOnlineModule 1 - Session A
  Wed Aug 051:15 PMOnlineProteins 1The Amino acids, protein structure (primary, secondary, etc.), Thermodynamics of protein folding, Protein classification into familiesWang, Jin
  Fri Aug 071:15 PMOnlineProteins 2Enzymology (kinetics), Inhibitors (competitive, etc.), Protein-based diseases (chemical biology and drug discovery)Wang, Jin
  Fri Aug 072:30 PMOnlineDiscussion Groups - 1
  Mon Aug 101:15 PMOnlineCarbohydrates 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 105:15 PMOnlineModule 1 - Session B
  Wed Aug 121:15 PMOnlineCellular CompartmentalizationCell organelle evolution and roles, Lipid compositions and exchange among intracellular membranes.Sifers, Richard
  Wed Aug 125:15 PMOnlineModule 2 - Session A
  Fri Aug 141:15 PMOnlineOrganelle BiogenesisProtein trafficking principles, Protein trafficking schemes, Signaling motifs and cognate receptors.Sifers, Richard
  Mon Aug 171:15 PMOnlineProtein topology and metabolismSequence-directed protein topology in cell membranes, Metabolism (mitochondria)Sifers, Richard
  Wed Aug 191:15 PMOnlineVesicular transport of proteinsSecretory pathway and vesicular transport, Vesicle coat proteins, directional protein transport (budding, fusion, lipid recycling), Microtubules and motor proteinsSifers, Richard
  Fri Aug 211:15 PMOnlineLysosomes and related diseasesSpecialized protein sorting beyond the Golgi complex, Lysosomal storage diseasesSifers, Richard
  Fri Aug 212:30 PMOnlineDiscussion Groups - 2
  Fri Aug 215:15 PMOnlineModule 2 - Session B
  Mon Aug 241:15 PMOnlineSignal 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 245:15 PMOnlineModule 3 - Session A
  Wed Aug 261:15 PMOnlineRelevant PTMs in Signal TransductionPhosphorylation, Acetylation, Methylation, Ubiquitination, Lipid additionsYork, Robert
  Fri Aug 281:15 PMOnlineCalcium and Phospholipase signlaingCalcium and its protein complexes, Phosphoinositides, Phospholipase D, Protein kinase C, IP3 receptors, Ca2+-regulated channels, AnnexinsYork, Robert
  Mon Aug 311:15 PMOnlineMembrane-bound receptorsTopics to be covered: Tyrosine kinases and downstream signaling, Serine kinases (i.e., TGF beta) and downstream signalingSmith, Carolyn L.
  Wed Sep 021:15 PMOnlineGPCRsG proteins and downstream signalsSmith, Carolyn L.
  Wed Sep 022:30 PMOnlineDiscussion Groups - 3
  Wed Sep 025:15 PMOnlineModule 3 - Session B
  Fri Sep 041:15 PMOnline
  Wed Sep 091:15 PMOnline
  Fri Sep 111:15 PMOnlineCell division and cell cyclePhases of cell cycle, cyclins and CDKsDang, Weiwei
  Fri Sep 115:15 PMOnline Module 4 - Session A
  Mon Sep 141:15 PMOnlineRegulation of cell cycle and checkpointsFactors regulating cell cycle from yeast to mammals, checkpoint regulatorsDang, Weiwei
  Wed Sep 161:15 PMOnlineDNA replicationDNA replication and its control in cell cycleIra, Grzegorz
  Wed Sep 162:30 PMOnlineDiscussion Groups - 4
  Fri Sep 181:15 PMOnlineDNA damage and repairDNA damage and basic DNA repair pathways (NER,BER, NHEJ, & HR)Ira, Grzegorz
  Fri Sep 185:15 PMOnlineModule 4 - Session B
  Mon Sep 211:15 PMOnlineMendelian GeneticsBasics of Mendel, Punnett Square, tree diagram, altered ratios and epistasisDierick, Herman
  Mon Sep 215:15 PMOnlineModule 5 - Session A
  Wed Sep 231:15 PMOnlineMutations and mutantsRecessive and dominant mutants, types of dominance, penetrance and expressivityDierick, Herman
  Fri Sep 251:15 PMOnlineMeiosis, linkage & mappingMeiosis as the underlying mechanism of Mendelian inheritance, linkage and mapping (2-point, 3-point/deletion mapping)Dierick, Herman
  Mon Sep 281:15 PMOnlineGeneticsDisrupting genes, screening for mutant phenotypes, and identifying genes by complementation analysisBates, David
  Wed Sep 301:15 PMOnlineGene interactionsGenetic suppression and synthetic enhancement, using one gene to find relaBates, David
  Fri Oct 021:15 PMOnlineEpistatis analysisDetermining the order of function of genes in regulatory and metabolic pathwaysBates, David
  
  Course: GS-GS-6206: Orientation to Clinical Translational Research
Course Director(s): Suter, Melissa Anne \ Parihar, Robin
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Aug 041:00 PMOnlineT1 to T4 Translational ResearchCovers the different types of translational research from T1 to T4. Learn how to follow outcomes of translation of basic science to clinics.Suter, Melissa Anne
  Tue Aug 042:00 PMOnlineThe Institutional Review BoardUnderstand IRB rules and regulations; learn composition and role of IRB boards and how they function. Practical aspects of submission and review of an IRB protocolsLuna, Ruth
  Tue Aug 111:00 PMOnlineInformed ConsentRules, regulations and practical aspects surrounding the informed consent process.Berg, Stacey
  Tue Aug 112:00 PMOnlineStudy DesignA basic overview of study designs including cross-sectional, case-control and cohort studiesSuter, Melissa Anne
  Tue Aug 181:00 PMOnlineClinical Trials RecordingLearn about phase I trials, pharmaokinetics; investigational pharmacies; Learn how to conduct a clinical trial including the phases, regulations, compliance, oversight, organization, budget, reporting requirements, adverse events, DSMBs, interim analysis, and endpointsMims, Martha
  Tue Aug 182:00 PMOnlineGood Manufacturing Practice FacilitiesLearn about preparation of materials for human use and quality control used in GMP facilities.Lapteva, Natalia
  Tue Aug 251:00 PMOnlineEpidemiological StudiesA basic overview of epidemiology in translational research including study design and standardized reportingScheurer, Michael
  Tue Aug 252:00 PMOnlineRegulatory AffairsLearn the role of FDA in submitting INDs and IDEs, distinctions between research versus patient care and the distinction between Investigational Drugs, Approved products and over the counter (OTC) productsGrilley, Bambi
  Tue Sep 011:00 PMOnlineEarly-Phase Clinical TrialsHeslop, Helen
  Tue Sep 012:00 PMOnlineTeam Science, Mentorship, and Academic-Industry CollaborationsUnderstand challenges in the process of bench to bedside translation, issues of team science, mentorship and collaboration in translational researchBrenner, Malcolm
  Tue Sep 081:00 PMOnlineRetrospective study design, working with Datasets/DatabasesConsiderations for data abstraction, data management and data analytics
  Tue Sep 082:00 PMOnlinePractical Aspects of BiobankingLearn rules and practical aspects of banking of tissues and other biological specimens. Learn rules and regulations regarding sharing of clinical research resources. Understand MTAs and contracts as they relate to human research samples.Castro, Patricia
  Tue Sep 151:00 PMOnlineClinical Ethics OverviewAn overview of clinical research ethics with focus on the involvement of vulnerable populations.Childress, Andrew
  Tue Sep 152:00 PMOnlineResearch Integrity and MisconductRules and regulations surrounding research integrity and misconduct including reporting and conflicts of interestAnderson, Ronda
  Tue Sep 221:00 PMOnlineCorrelative Science AnalysisBasic principles of correlative science methodologies and their clinical applications Horton, Terzah
  Tue Sep 222:00 PMOnlinePatents/LicensingLearn differences between licensing and patents, basic principles regarding patenting and licensing of discoveries and how they affect clinical translation and use. Learn what types of discoveries can be patentable. Learn how patents and licenses are used and when and why. Learn about using materials obtained from industry in your research. Learn how all this is managed within the context of an academic institutionPitcher, Meagan
  
  Course: GS-GS-5101: Responsible Conduct of Research - Year 1
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Aug 049:00 AMOnline(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 119:00 AMOnline(1L1) Data Acquisition & Record-Keeping ResponsiblitiesResponsibilities for record keeping, challenges in keeping accurate and understandable notebooks, ownership of research materials, reagent/data sharing.Nelson, David
  Tue Aug 189:00 AMOnline(1L3) Resilience Coping with academic challenges Yang, Peggy
  Tue Aug 259:00 AMOnline(1L2) Responsible Authorship and PublicationsGiving 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 Sep 019:00 AMOnline(1C) Case StudiesSmall Group discussions with a faculty discussion leader
  Tue Sep 089:00 AMOnline(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 159:00 AMOnline(1L5) Rigor & ReproducibilityReproducibility, transparency, authentication of key biological and chemical resources, types of replication, blinding and randomizationPautler, Robia
  Tue Sep 229:00 AMOnline(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.
  
  Course: GS-GS-5111: Strategies for Success in Graduate School
Course Director(s): Samuel, Melanie \ Sillitoe, Roy
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 1011:30 AMOnlineHow to Choose a MentorIn 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.Arenkiel, Benjamin Russell
  Mon Aug 1711:30 AMOnlineHow 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 taking ownership over your graduate careerand how to have difficult conversations with your PI. Finally, we will discuss special considerations for rotations given rotation conditionswith CoVID19. Samuel, Melanie
  Mon Aug 3111:30 AMOnlineMastering Time ManagementIn this class, we will discussconcept of a hidden curriculum and the timescale of a PhD. We will alsotalk about time management, provide examplesof ‘getting work done’, and discuss the balance between classwork and rotations.Sillitoe, Roy
  Mon Sep 1411:30 AMOnlineEvidence-Based Decision Making During Challenging MomentsIn this class, we will discuss what how to make decisions when faced with challenges and constraints that can complicate this process.In particular, we will focus on challenges encountered due to the CoVID19 pandemic. Yang, Peggy
  Mon Sep 2811:30 AMOnlineNetworking and Planning your Graduate CareerWe 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). We will also discuss what networking is and provide real life examples of how it impacts science and careersHaseltine, Derek
  
  Course: GS-GS-6400: Foundations B: Biostatistics
Course Director(s): Hilsenbeck, Susan G. \ Minard, Charles
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 032:30 PMOnlineIntroduction and overviewHilsenbeck, Susan G.
  Thu Aug 0612:00 PMOnlineLabs: Install and introduce R, data management
  Mon Aug 102:30 PMOnlineSummarizing numerical dataWang, Tao
  Thu Aug 1312:00 PMOnlineLabs: Summarize data, statistics and graphs
  Mon Aug 172:30 PMOnlineDifferences between groupsHilsenbeck, Susan G.
  Thu Aug 202:30 PMOnlineDifferences between two groupsMinard, Charles
  Mon Aug 242:30 PMOnlineMultiple ComparisonsHilsenbeck, Susan G.
  Thu Aug 2712:00 PMOnlineLabs: ANOVA, t-test, multiple comparisons
  Mon Aug 312:30 PMOnlineRates and ProportionsMinard, Charles
  Thu Sep 0312:00 PMOnlineLabs: Rates and Proportions
  Thu Sep 102:30 PMOnlinePower and sample sizeWang, Tao
  Mon Sep 142:30 PMOnlineConfidence intervalsMinard, Charles
  Thu Sep 1712:00 PMOnlineLabs: Power and sample size, confidence intervals
  Mon Sep 212:30 PMOnlineLinear RegressionWang, Tao
  Thu Sep 242:30 PMOnlineRegression, CorrelationWang, Tao
  Mon Sep 282:30 PMOnline
  Thu Oct 0112:00 PMOnlineLabs: Linear Regression, Correlations
  
  
Term 2
  
  Course: GS-GS-5112: Powerful Presentations
Course Director(s): Samuel, Melanie \ Watkins, Trent
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 131:00 PMOnlineThe 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 201:00 PMOnlineThe 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 271:00 PMOnlineEffective Slide Construction and Zoom DeliveryDesign principles of effective slides; How much evidence to include; Visual reinforcement of verbal message; How to use slides as a presenter; unique considerations for presenting via Zoom. Samuel, Melanie
  Tue Nov 031:00 PMOnlineGroup Work on PresentationsSmall group practice sessions with faculty advisors
  Tue Nov 101:00 PMOnlineGroup Presentations, Part 1
  Tue Nov 171:00 PMOnlineGroup Presentations, Part 2
  Tue Nov 241:00 PMOnlineGroup 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
  
  Course: GS-GS-5102: Responsible Conduct of Research - Year 2
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 139:00 AMOnline(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 Oct 209:00 AMOnline(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 Nov 039:00 AMOnline(2L3) Conflict ResolutionYang, Peggy
  Tue Nov 109:00 AMOnline(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 Nov 179:00 AMOnline(2C) Case StudiesScientific Misconduct & Research with Animals
  
  
Term 3
  
  Course: GS-GS-6101: Neuroscience
Course Director(s): Ray, Russell
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jan 0412:00 PMOnlineDevelopment of the Nervous SystemHow our nervous system arises from a single fertilized egg. Ray, Russell
  Wed Jan 0612:00 PMOnlineSomatic Motor and Sensory SystemsHow the circuits that control our movement and our perception of the world are organizedRay, Russell
  Fri Jan 0812:00 PMOnlineVisceral Motor and Sensory SystemsHow the circuits that drive organ function to keep us alive are organizedRay, Russell
  Mon Jan 1112:00 PMOnlineIon ChannelsHow ionic gradients in neurons are established and used to transmit electrical and chemical information.Ray, Russell
  Wed Jan 1312:00 PMOnlineSynaptic PhysiologyHow neurons transmit information to each otherRay, Russell
  Fri Jan 1512:00 PMOnlineLearning and MemoryMolecular and cellular requirements for storing new information and recalling it later.Ray, Russell
  Wed Jan 2012:00 PMOnlineNeurobiology of DiseaseWhat happens when things go wrong in the brain.Ray, Russell
  Fri Jan 2212:00 PMOnlineNeuroscience in the LabHow we explore the nervous system using genetic, molecular and anatomical techniques.Ray, Russell
  Mon Jan 2512:00 PMOnlineNervous System EvolutionElaboration of the nervous system across species and the relevance to human health and disease. Ray, Russell
  Wed Jan 2712:00 PMOnlineFinal Exam Faculty ReviewRay, Russell
  Fri Jan 2912:00 PMOnlineFinal Exam
  
  Course: GS-GS-5105: Scientific Writing
Course Director(s): Marriott, Susan
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jan 043:00 PMOnlineOverview and WordsMarriott, Susan
  Mon Jan 113:00 PMOnlineSentencesMarriott, Susan
  Mon Jan 253:00 PMOnlineParagraphsMarriott, Susan
  Mon Feb 013:00 PMOnlineThe Process of WritingMarriott, Susan
  
  Course: GS-GS-6203: Data Mining
Course Director(s): Shaulsky, Gad
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Feb 082:00 PMOnlineData 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 Feb 092:00 PMOnlineIntroduction to ClassificationClassification trees. Confusion matrix. Estimation of prediction error. Overfitting. Cross-validation.Zupan, Blaz
  Wed Feb 102:00 PMOnlineClassification ModelsClassification trees, forests, logistic regression, nearest neighbors. Data painting. Area under ROC curve. Analysis of results of classifications. Nomograms.Zupan, Blaz
  Fri Feb 122:00 PMOnlineRegressionLinear regression, polynomial regression and overfitting. Regularization. Effects of regularization on training and test sets. Random forests for regression.Zupan, Blaz
  Tue Feb 162:00 PMOnlineIntroduction 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
  Wed Feb 172:00 PMOnlinePartitional ClusteringIntroduction to k-means clustering. Differences with hierarchical clustering. Silhouette scoring of clustering results. Outlier detection.Zupan, Blaz
  Fri Feb 192:00 PMOnlineData ProjectionsPrincipal component analysis. Multi-dimensional scaling and t-SNE.Zupan, Blaz
  Mon Feb 222:00 PMOnlineGentle 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-6205: Fundamentals of Epidemiology
Course Director(s): Scheurer, Michael \ Brown, Austin
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jan 041:00 PMOnlineOverview of Study DesignsScheurer, Michael
  Mon Jan 042:00 PMOnlineMeasuring DiseaseScheurer, Michael
  Mon Jan 111:00 PMOnlineEcological and Cross-Sectional StudiesMontealegre, Jane
  Mon Jan 112:00 PMOnlineCase-Control StudiesLupo, Philip
  Mon Jan 251:00 PMOnlineCohort StudiesRichard, Melissa
  Mon Jan 252:00 PMOnlineCausation/Assessing the Epidemiological LiteratureBrown, Austin
  Mon Feb 011:00 PMOnlineRates and StandardizationScheurer, Michael
  Mon Feb 012:00 PMOnlineMeasure of EffectScheurer, Michael
  Mon Feb 081:00 PMOnlineScreeningMontealegre, Jane
  Mon Feb 082:00 PMOnlineMolecular EpidemiologyLupo, Philip
  Mon Feb 221:00 PMOnlineJournal Club SessionScheurer, Michael
  Mon Feb 222:00 PMOnlineExam Review
  Mon Mar 011:00 PMOnlineFinal Exam
  
  Course: GS-GS-5108: Pharmacoepidemiology & Pharmacogenetics
Course Director(s): Scheurer, Michael \ Bernhardt, Melanie
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 072:00 PMOnlineIntroductionScheurer, Michael
  Thu Jan 142:00 PMOnlineBasics of Clinical Pharmacokinetics & PharmacodynamicsBernhardt, Melanie
  Thu Jan 212:00 PMOnlineClinical Applications and Case Studies in PharmacogeneticsBernhardt, Melanie
  Thu Jan 282:00 PMOnlineGenomic Techniques, Platforms, TestsFisher, Kevin
  Thu Feb 042:00 PMOnlineClinical and Research Resources in GenomicsScheurer, Michael
  Thu Feb 112:00 PMOnlineBioinformatics in PharmacogenomicsVenner, Eric
  Thu Feb 182:00 PMOnlineMetabolomics & EpigeneticsScheurer, Michael
  Thu Feb 252:00 PMOnlineCase Study & Specific Aims DiscussionScheurer, Michael
  Thu Mar 042:00 PMOnlineFinal Project Due
  
  Course: GS-GS-5107: Leadership Skills
Course Director(s): Fuqua, Suzanne
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 0512:00 PMOnlinePersonality Preference and Leadership StypesFuqua, Suzanne
  Thu Jan 0712:00 PMOnlineLeadership Self-Assessment and Leadership Skills ExercicesFuqua, Suzanne
  Tue Jan 1212:00 PMOnlineEmotional Intelligence, Self and Social AwarenessChang, Eric
  Thu Jan 1412:00 PMOnlineScientific Writing: Words, Sentences and ParagraphsMarriott, Susan
  Tue Jan 1912:00 PMOnlineScientific Writing: Abstract Structure and Manuscript SectionsMarriott, Susan
  Thu Jan 2112:00 PMOnlineTeaching SkillsHilsenbeck, Susan G.
  Tue Jan 2612:00 PMOnlineTeaching Skills ExercisesHilsenbeck, Susan G.
  Thu Jan 2812:00 PMOnlineCommunication and Conflict ResolutionFuqua, Suzanne
  Tue Feb 0212:00 PMOnlineConflict Resolution Skills-Building ExercisesFuqua, Suzanne
  Thu Feb 0412:00 PMOnlineTime ManagementSmith, Carolyn L.
  Tue Feb 0912:00 PMOnlineCreating Mentoring Relationships to Facilitate Career AdvancementRosen, Jeffrey
  Thu Feb 1112:00 PMOnlineNegotiation Skills-Building Exercises & Course Wrap-UpFuqua, Suzanne
  
  Course: GS-GS-6202: Gene Regulation
Course Director(s): Cooper, Thomas
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jan 041:00 PMOnlineIntroduction 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
  Wed Jan 061:00 PMOnlineRNA 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
  Fri Jan 081:00 PMOnlineEukaryotic 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
  Mon Jan 111:00 PMOnlineCoactivaors 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
  Tue Jan 125:15 PMOnlineTA Session #1
  Wed Jan 131:00 PMOnlineRegulation of RNA Polymerase II ElongationTranscriptional elongation. Negative factors that limit elongation (NELF, DSIF); Positive factor that activates elongation (P-TEFb); Foulds, Charles
  Fri Jan 151:00 PMOnlineChromatin - 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
  Wed Jan 201:00 PMOnlineChromatin: Local and GlobalChromatin subdomains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting.Lonard, David
  Fri Jan 221:00 PMOnlineTA Session #2
  Mon Jan 251:00 PMOnlineMidterm ReviewMidterm Exam Faculty Review
  Wed Jan 271:00 PMOnlineMidterm Exam - 1:00-4:00 pmNote special time
  Fri Jan 291:00 PMOnlineRNA 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
  Mon Feb 011:00 PMOnlineAuxiliary 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
  Wed Feb 031:00 PMOnline3' 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
  Fri Feb 051:00 PMOnlineRNA--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
  Mon Feb 081:00 PMOnlinePosttranscriptional 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
  Tue Feb 095:15 PMOnlineTA Session #3
  Wed Feb 101:00 PMOnlineNoncoding 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
  Fri Feb 121:00 PMOnlineTranslational 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 171:00 PMOnlineTranslational 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 191:00 PMOnlineRegulation of Protein Synthesis rates & TurnovermRNA and protein decay. Frameshifts and micropeptides. Ubiquitin-proteosome mediated degradation. Importance of regulation, degron sequences, etc.Catic, Andre
  Mon Feb 221:00 PMOnlineTA Session #4
  Wed Feb 241:00 PMOnlineFinal Exam ReviewFinal Exam Faculty Review
  Mon Mar 011:00 PMOnlineFinal Exam - 1:00-4:00 pmNote special exam place time: 1:00-4:00 pm
  
  Course: GS-GS-5103: Responsible Conduct of Research - Year 3
Course Director(s): Smith, Carolyn L.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 0510:00 AMOnline(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 1210:00 AMOnline(3L3) Navigating the Mid-PointTools & tips for navigating motivation issues typical during the middle years of doctoral study, including unhooking from roadblocks and increasing motivation.Yang, Peggy
  Tue Jan 2610:00 AMOnline(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 Feb 0210:00 AMOnline(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 Feb 0910:00 AMOnline(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 1610:00 AMOnline(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 2810:00 AMOnline(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 Feb 0410:00 AMOnline(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 Feb 1110:00 AMOnline(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 1810:00 AMOnline(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 Feb 2510:00 AMOnline(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.
  
  
Term 4
  
  Course: GP-GP-702: Postdoc-Responsible Conduct of Research - Module 2
Course Director(s): Bertuch, Alison
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Apr 0612:30 PMOnline(2L5) Rigor & Reproducibility AReproducibility, transparency, authentication of key biological and chemical resources, types of replication, blinding and randomization.Bertuch, Alison
  Tue Apr 061:40 PMOnline(2L1) Research Misconduct & Laboratory Safety RefresherDefinitions - 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.Nelson, David
  Tue Apr 062:50 PMOnline(2C) Case StudiesScientific misconduct and experiments with animalsPereira, Frederick
  Tue Apr 064:00 PMOnline(2L2) Ethics of Animal Studies in Biomedical ResearchWhen 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.
  
  Course: GS-GS-5113: Effective Project Design and Management
Course Director(s): Samuel, Buck
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Mar 172:30 PMOnlineOrientation and OverviewGoals of the course, structure of virtual course sessions, and engage with small groupsSamuel, Buck
  Wed Mar 242:30 PMOnlineWhat is a Thesis and How to Get StartedThe concept of a thesis as it relates to project scope and the concept of hypothesis and non-hypothesis driven projects. Samuel, Buck
  Wed Mar 312:30 PMOnlineHow to Generate Ideas and Turn Them into ProjectsThe advantages of being able to develop your own ideas and how mentors can point out the path and you can pave it.Samuel, Buck
  Wed Apr 072:30 PMOnlineHow to Turn a Project into PapersDifferent approaches to paper writing, explain the concept of storyboarding, and discuss different geometric relationships between projects and how they can influence project outcomesSamuel, Buck
  Wed Apr 142:30 PMOnlineIdentifying Publishable Units and Scientific StorytellingSmall group practice sessions focusing on how to identify publishable units, ‘flipping the story’ and moving beyond a timeline of experiments to tell the story that you want.Samuel, Buck
  Wed Apr 212:30 PMOnlineProject ManagementStoryboarding outcomes and participate in small group discussions to provide feedback on what worked wellSamuel, Buck
  Wed Apr 282:30 PMOnlineCase StudiesSamuel, Buck
  Wed May 052:30 PMOnlineCase StudiesSamuel, Buck
  
  Course: GS-GS-6102: Principles of Immunology
Course Director(s): Decker, William K.
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Mar 181:00 PMOnlinePrinciples of ImmunityOverview of the immune system: innate vs. acquired immunity, cells of the immune system, clonal selection principle, strategies for “self-nonself/danger” discrimination.Decker, William K.
  Tue Mar 231:00 PMOnlineInnate ImmunityThe gateway to defense against the world around us: pattern recognition receptors, PAMPs/DAMPs, phagocytes and chemical mediators of immunity.Decker, William K.
  Wed Mar 245:15 PMOnlineTA Session #1TA Session
  Thu Mar 251:00 PMOnlineAntibody 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.
  Tue Mar 301:00 PMOnlineB 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.
  Wed Mar 315:15 PMOnlineTA Session #2TA Session
  Thu Apr 011:00 PMOnlineRole 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.Decker, William K.
  Tue Apr 061:00 PMOnlineT Cell Development and Signaling, Consequences for Transplants and TumorsT cell effector functions, transplantation, autoimmunity, vaccines, tumor immunology.Decker, William K.
  Thu Apr 081:00 PMOnlineFaculty ReviewExam Review
  Tue Apr 131:00 PMOnlineFinal ExamFinal Exam
  
  Course: GP-GP-703: Postdoc-Responsible Conduct of Research - Module 3
Course Director(s): Bertuch, Alison
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Apr 2712:30 PMOnline(3L2) Collaborative RsearchThe values/responsibilities of collaboration, establishing collaborative relationships, grants, contracts, intellectual property considerations, impact of industry collaborations on publication.Zechiedrich, E.
  Tue Apr 272:50 PMOnline(3L1) Authorship/Peer ReviewOrganizing 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 Apr 274:00 PMOnline(3C) Case StudiesPeer review of grants and papers, conflicts of interest, collaboration
  
  Course: GP-GP-701: Postdoc-Responsible Conduct of Research - Module 1
Course Director(s): Bertuch, Alison
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Apr 132:50 PMOnline(1M) The Mentor-Mentee RelationshipDeveloping a group of mentors, what to look for in the mentor/mentee relationship, keeping students on track toward their degree.Smith, Carolyn L.
  Tue Apr 201:40 PMOnline(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 Apr 202:50 PMOnline(1L2) Responsible Authorship and PublicationsGiving 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 Apr 204:00 PMOnline(1C) Case StudiesRecord keeping, ownership of research materials, responsible citation, and plagiarism
  
  Course: GP-GP-704: Postdoc-Responsible Conduct of Research - Module 4
Course Director(s):
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Apr 1312:30 PMOnline(4L1) Research with Human SubjectsDefinition of research with human subjects, experiments with human material, confidentiality of medical data, experiments involving humans, informed consent.Berg, Stacey
  Tue Apr 131:40 PMOnline(4L2) The Scientist as Responsible Member of SocietyContemporary ethical issues in biomedical research and the environmental and societal impacts of scientific researchLazaro-Munoz, Gabriel
  Tue Apr 134:00 PMOnline(4C) Case StudiesResearch with human subjects, societal impact of research (genetics/genomics, stem cells, neuroethics)
  Tue Apr 271:40 PMOnline(4L5) Rigor & Reproducibility BTransparency, passionate disinterest, problems with science lacking rigor and/or reproducibility, outliers and exclusion criteria, detailed protocols, sex as a biological variable, bias.Bertuch, Alison

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