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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
  Wed Sep 021:15 PMOnlineGPCRsG proteins and downstream signalsSmith, Carolyn
  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 \ 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
  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
  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
  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
  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
  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
  
  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
  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 \ Minard, Charles
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 032:30 PMOnlineIntroduction and overviewHilsenbeck, Susan
  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
  Thu Aug 202:30 PMOnlineDifferences between two groupsMinard, Charles
  Mon Aug 242:30 PMOnlineMultiple ComparisonsHilsenbeck, Susan
  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
  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
  Tue Nov 179:00 AMOnline(2C) Case StudiesScientific Misconduct & Research with Animals
  
  
Term 3
  
  Course: GS-GS-5103: Responsible Conduct of Research - Year 3
Course Director(s): Smith, Carolyn
  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
  Tue Jan 1210:00 AMOnlineTools & 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
  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, Lynn
  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).

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