Course Guide 2021 - medicine.yale.edu

BBSCOURSEGUIDEYaleUniversity

AcomprehensivelistingofgraduatelevelcoursesaffiliatedwiththeYaleCombinedProgramintheBiological&BiomedicalSciences

LastupdatedAugust19,2021

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Thisguidecontainsallcoursesofferedbythe11Ph.D.programsaffiliatedwiththeYaleBBSProgram.Courses

withan“a”inthecoursenumberareofferedinthefallsemester.Courseswitha“b”inthecoursenumberareofferedinthespringsemester.Somecoursesareofferedonlyeveryotheryearandarenotedassuch.Somecoursesarelimitedtostudentsinspecialprogramsandarenotedassuch

VisittheOnlineCourseInformationsystemathttps://courses.yale.edu/tofindcoursetimes,dates,andlocations.CELLBIOLOGYCBIO501a/502b,MoleculestoSystemsThiscourseisdesignedtoprovidemedicalstudentswithacurrentandcomprehensivereviewofbiologicstructureandfunctionatthecellular,tissue,andorgansystemlevels.Areascoveredincludestructureandorganizationofcells;regulation of the cell cycle and mitosis; protein biosynthesis and membrane targeting; cell motility and thecytoskeleton; signal transduction; cell adhesion; cell and tissue organizationof organ systems. Clinical correlationsessions,whichillustratethecontributionsofcellbiologytospecificmedicalproblems,areinterspersedinthelectureschedule.Histophysiologylaboratoriesprovidepracticalexperiencewithanunderstandingofexploringcellandtissuestructure. The course is offered only toM.D. andM.D./Ph.D. students. It runs for three terms from September toDecemberofthenextacademicyeartocoincidewiththeSchoolofMedicinecurriculum.Registrationandthereleaseofgradestakesplaceinthethirdterm.Thecourseisequivalenttotwograduatecredits.CBIO600a/601b,FrontiersinMedicine“FrontiersinMedicine,”agraduatecreditcourseforfirst-yearMD-PhDstudentsandanelectivecourseformedicalstudents,emphasizestheconnectionsbetweenbasicandclinicalscience,humanphysiologyanddisease.ItparallelsthecontentofYaleMedicalSchool’sfirst-yearcoursesandisdesignedforstudentswhoareconsideringacareerinmedicalresearchorwhochoosetoexplorescientifictopicsindepth,learnaboutcutting-edgeresearchandimprovetheir presentation skills. Discussions cover the challenges faced in research, selecting your topic and pursuing anacademiccareer.EnrollmentislimitedtothosewhohavetakenoraretakingtheMastersCourses.Selecttopicsarepresentedbyeminent facultywhoserveasexcellentrolemodels foryouracademiccareers. Inmostsessions, twostudentsreviewrelevantmanuscriptsundertheguidanceofafacultymentorandpresentthematerialtothegroup.Priortothestartofclass,studentsarerequiredtosubmitquestionsconcerningtechniquesandconceptsthatmaynotbeclearfromtheassignedpapers.Thesequestionswillthenbeaddressedduringthepresentation.Studentevaluationsare graded on attendance, participation in group discussions and formal presentations. The course runs fromSeptembertomid-Mayandprovidesgraduatecreditifneeded.Itisequivalenttotwograduatecredits.CBIO602a/MB&B602a/MCDB602a,MolecularCellBiologyAcomprehensive introduction to themolecularandmechanistic aspectsof cellbiology forgraduate students inallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.CBIO603a/MCDB603a,SeminarinMolecularCellBiologyAgraduate-levelseminarcourseinmoderncellbiology.Theclassisdevotedtothereadingandcriticalevaluationofclassical and current papers. The topics are coordinated with the CBIO 602a lecture schedule. Thus, concurrentenrollmentinCBIO602aisrequired.CBIO604b,SystemsCellBiologyIntroductiontotheorganizationandfunctionofcellswithincomplexmulticellularsystemsasencounteredinthehumanbody. Covers major tissues and organs as well as the cardiovascular, immune, and nervous systems, with specialemphasisonthemolecularandcellularbasesofdevelopmentalprocessesandhumandiseases.Lecturessupplementedbyelectronic-basedtutorialsonthehistologyoftissuesandorgans.

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CBIO606b,AdvancedTopicsinCellBiologyThisseminarcourse,whichmeetsonceweekly,coversadvancedtopicsincellbiology.Eachtopicisspreadovertwoorthreesessions,whichstartwithan introductoryoverviewandare followedbyadiscussionofkeypapers ledbyanexpertinthefield.CBIO630b/MCDB630bBiochemicalandBiophysicalApproachesinMolecularandCellularBiologyThecourseoffersan introduction into thebiochemicalandbiophysical techniquesused inmoderncellbiologyresearch,includingspectroscopy,lightmicroscopy,kinetics,mathematicalmodeling,structuralbiologytechniques(x-ray,electronmicroscopy,NMR),massspectrometry.CBIO655a/GENE655a,StemCells:BiologyandApplicationThiscourseisdesignedforfirst-yearorsecond-yearstudentstolearnthefundamentalsofstemcellbiologyandtogainfamiliaritywith current research in the field. The course is presented in a lecture anddiscussion format based onprimaryliterature.Topicsincludestemcellconcepts,methodologiesforstemcellresearch,embryonicstemcells,adultstem cells, cloning and stem cell reprogramming, and clinical applications of stem cell research. Prerequisites:undergraduate-levelcellbiology,molecularbiology,andgenetics.CBIO701b,IlluminatingCellularFunctionIntroductiontotheprinciplesandpracticalmethodsoflivecellimaging.Coversprinciplesoffluorescentmicroscopy(including genetically encoded probes and physiological indicators), image formation, image detection, and imageanalysis.Includeshands-ondemonstrationsofstate-of-the-artinstrumentation,suchasvideo-rateconfocalandsuper-resolution"nanoscopes." Thecourseisequivalentto½graduatecredit.CBIO900a/GENE900a/MCDB900a,ResearchSkillsandEthicsIThiscourseconsistsofseminarsthatcoversethics,grantwriting,andtrainingforscientificspeakingforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO901b/GENE901b/MCDB901b,ResearchSkillsandEthicsIIThiscourseconsistsofseminarsthatcoversethics,grantwriting,andtrainingforscientificspeakingforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO903aorb,ReadingCourseinCellBiologyIndependentstudyofspecifictopicsincellbiologythroughdirectedreadingoftheliteratureunderfacultysupervision.StudentmaychooseanytopicandanyYalefacultysubjecttoapprovalbytheCellBiologyDGS.OpentoCellBiologystudents,andtostudentsinotherdepartmentswithapprovalfromtheirrespectiveDGS.Termpaperrequired.CBIO911a/GENE911a/MCDB911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO912a/GENE912a/MCDB912ab,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO913b/GENE913b/MCDB913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO914b/GENE914b/MCDB914b,FourthLaboratoryRotation(optional)FourthlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.

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CELLULARANDMOLECULARPHYSIOLOGYhttp://physiology.yale.edu/education/courses.aspxC&MP550a/ENAS550a/MCDB550a/PHAR550a,PhysiologicalSystemsThecoursedevelopsafoundationinhumanphysiologybyexaminingthehomeostasisofvitalparameterswithinthebody,andthebiophysicalpropertiesofcells,tissues,andorgans.Basicconceptsincellandmembranephysiologyaresynthesizedthroughexploringthefunctionofskeletal,smooth,andcardiacmuscle.Thephysicalbasisofbloodflow,mechanismsofvascularexchange,cardiacperformance,andregulationofoverallcirculatoryfunctionarediscussed.Respiratoryphysiologyexploresthemechanicsofventilation,gasdiffusion,andacid-basebalance.Renalphysiologyexaminestheformationandcompositionofurineandtheregulationofelectrolyte,fluid,andacid-basebalance.Organsof thedigestive systemarediscussed from theperspectiveof substratemetabolismand energybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.C&MP560b/ENAS570b/MCDB560b/PHAR560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical, andphysiological levels.Students learnabout thedifferentclassesofmolecularmachines thatmediatemembrane transport, generate electrical currents, or performmechanical displacement. Emphasis is placed on therelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocell functionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.C&MP570b,MitochondrialBioenergeticsandIntermediaryMetabolism.The course will present a comprehensive introduction to the fundamentals of mitochondrial physiology andpathophysiology, with topics including glucose, lipid, amino acid, and cholesterol metabolism; mitochondrialbioenergetics;fluxmodeling;inheritedandacquiredmetabolicdisorders;andcommonmethodsusedtocharacterizemetabolism.Inadditiontothesekeytopics,studentswillgainexperienceinreviewingpapersandcriticallyevaluatingexperimentaldesignandimplementation.Thematerialwillbepresentedinamixed lecture/discussionformat.TheclasswillbeofferedWednesdaysandFridaysfrom10:30-11:45thissemester.Pleasecontacteitheroftheinstructors([email protected],[email protected])ifyouhaveanyquestions.C&MP570b,SensoryPhysiologyThecourseprovidesanoverviewofthemammalianspecialsensorysystems,includingmolecularandcellularbasesofvision, audition, taste, olfaction, and somatosensation. Faculty with focus in those areas lead presentations anddiscussionsonperipheralandcentralmechanisms.Psychophysicalaspectsofsensationareintroduced.C&MP600,MedicalPhysiologyCaseConferences(openonlytoMD/PhD&MRSPstudents)Two-termcoursetaughtingroupsoftentotwelvestudentsbythesamegroupleader(s)throughouttheyear.Workshopformatpermitsstudentstoapplybasicconceptsofphysiologytoclinicalsyndromesanddiseaseprocesses.Studentsare expected to participate actively in a weekly discussion of a clinical case that illustrates principles of humanphysiologyandpathophysiologyatthewhole-body,system,organ,cellular,ormolecularlevel.Prerequisites:C&MP550aandpermissionoftheinstructor.Creditforfullyearonly.C&MP610,MedicalResearchScholarsProgram:MentoredClinicalExperience(openonlytoMRSPstudents)Thegoalsof thecourseareto introduceMRSPstudentstoaspectsofclinically importanthumandiseases.Studentsexplore eachdisease over three one-and-one-half-hour sessions ledby a clinician-scientistwho is an expert in therelevantorgansystem.Studentsexploretwodiseaseprocessesperterm.Thefirstofthethreesessionsisdevotedtoa

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discussionoftheclinicalpresentation,naturalhistory,pathology,epidemiology,treatment,andprognosisofthediseaseprocess.DuringthissessionstudentshavetheopportunitytoviewgrossormicroscopicspecimensofdiseasedtissueinassociationwithmembersofthePathologyfaculty.Studentsareassignedreadingsinpathology,pathophysiology,andclinicaltextstoprepareforthefirstclasssession.Thesecondsessionfocusesontranslationalaspectsofthediseaseprocess.Studentsreadandpresentpapersrelevanttothemolecularbasisofthediseaseandcutting-edgeapproachesto its therapy. In the third session studentsmeetwithpatientswhohaveexperienced thediseaseand/orvisit andexplorefacilitiesassociatedwithdiagnosisandtreatmentof thediseaseprocess.Priortothethirdsessionstudentsreceiveguidanceastowhattheywillobserveandhowtoapproachtheexperience;andattheendofthesession,thegroupdiscussesitsthoughtsandimpressions.Studentsareexpectedtoprepareforsessions,toparticipateactively,andtobescrupulouslyrespectfulofpatientsandpatientfacilities.C&MP620b,FundamentalsinNeurophysiologyThecourseisdesignedforstudentswhowishtogainatheoreticalandpracticalknowledgeofmodernneurophysiology.Graduatestudentsspecializinginneurophysiologyandnon-neurophysiologyareencouragedtoattend,asthecoursebeginsataverybasiclevelandprogressestomorecomplicatedtopics.Topicsincludepropertiesofionchannels,firingpropertiesofneurons,synaptictransmission,andneurophysiologymethodology.C&MP630a/PATH680a/PHAR502a,SeminarinMolecularMedicine,Pharmacology,andPhysiologyReadingsanddiscussiononadiverserangeofcurrenttopicsinmolecularmedicine,pharmacology,andphysiology.Theclass emphasizes analysis of primary research literature and development of presentation and writing skills.Contemporaryarticlesareassignedonarelated topiceveryweek,andastudent leadsdiscussionswith input fromfacultywhoareexpertsinthetopicarea.Theoverallgoalistocoveraspecifictopicofmedicalrelevance(e.g.,cancer,neurodegeneration) from theperspectiveof threeprimarydisciplines (i.e., physiology: normal function; pathology:abnormalfunction;andpharmacology:intervention).C&MP650/PATH660/PHAR580,EthicsOrganized to foster discussion, the course is taught by faculty in the Pharmacology, Pathology, and Physiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.C&MP710b/MB&B710b4,ElectronCryo-MicroscopyforProteinStructureDeterminationUnderstandingcellularfunctionrequiresstructuralandbiochemicalstudiesatanever-increasinglevelofcomplexity.Thecourseisanintroductiontotheconceptsandapplicationsofhigh-resolutionelectroncryo-microscopy.Thisrapidlyemerging new technique is the only method that allows biological macromolecules to be studied at all levels ofresolutionfromcellularorganizationtonearatomicdetail.Countsas0.5credit.

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COMPUTATIONALBIOLOGYANDBIOINFORMATICShttps://cbb.yale.edu/graduate-program/example-courses-three-course-areasCB&B523b/MB&B523b/PHYS523b/ENAS541b,BiologicalPhysics(Courseofferedeveryotheryear).Thecoursehastwoaims:1)tointroducestudentstothephysicsofbiologicalsystemsand2)tointroducestudentstothebasicsofscientificcomputing.Thecoursewillfocusonstudiesofabroad-rangeofbiophysicalphenomenaincludingdiffusion, polymer statistics, protein folding,macromolecular crowding, cellmotion, and tissue development usingcomputational toolsandmethods.Wewillprovide intensivetutorials forMatlab includingbasicsyntax,arrays, for-loops,conditionalstatements,functions,plotting,andimportingandexportingdata.CB&B555a/CPSC453a/GENE555a/CPSC553a,UnsupervisedLearningBigDataThiscourse introducesbiologyasasystemsanddatascience tocomputerscienceandbiomedicalsciencestudentsthroughopencomputationalproblemsinbiology,thetypesofhigh-throughputdatathatarebeingproducedbymodernbiological technologies, and computational approaches that may be used to tacle such problems. We will coverapplicationsofmachine learningmethods in theanalysisofhigh-throughputbiologicaldata, especially focusingongenomicandproteomicdata.Thiswill includemethods fordenoisingdata,non-lineardimensionalityreduction forvisualizationandprogressionanalysis,unsupervisedclustering,andinformationtheoreticanalysisofgeneregulatoryandsignalingnetworks.Students’gradeswillbebasedonprogrammingassignments,amid-term,paperpresentationandafinalproject.CB&B562b/AMTH562b/MB&B562b/MCDB562b/PHYS562b,ModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topics includetime-dependentdynamics inregulatory,signal-transduction,andneuronalnetworks; fluctuations,growth,and form;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalf itstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.CB&B567b/S&DS567/MB&B567,TopicsinDeepLearning:MethodsandBiomedicalApplicationsThis course provides an introduction to recent developments in deep learning, covering topics ranging frombasicbackpropagation, to optimization, to the latest developments in deep generativemodels and network robustness.Applicationsinnaturallanguageprocessingandcomputervisionareusedasrunningexamples.Severalcasestudiesinbiomedical applications are covered in detail. Prerequisite:S&DS 565or permission of the instructor. Enrollmentlimited.CB&B601b/IBIO601b,FundamentalsofResearch:ResponsibleConductofResearch Aweeklyseminarpresentedbyfacultytrainersontopicsrelatingtoproperconductofresearch.Requiredforfirst-yearCB&Bstudents,firstyearImmunobiologystudents,andtraininggrant-fundedpostdocs.Pass/Fail.CB&B634a,CompMethodsforInformaticsThiscourseintroducesthekeycomputationalmethodsandconceptsnecessaryfortakinganinformaticsprojectfromstarttofinishusingAPIstoqueryonlineresources,readingandwritingcommonbiomedicaldataformats,choosingappropriate data structures for storing and manipulating data, implementing computationally efficient andparallelizable algorithms for analyzing data, and developing appropriate visualizations for communicating healthinformation.TheFAIRdata-sharingguidelinesarediscussed.Currentissuesinbighealthdataarediscussed,includingsuccessfulapplicationsaswellasprivacyandbiasconcerns.Thiscoursehasasignificantprogrammingcomponent,andfamiliaritywithprogrammingisassumed.CB&B645b/BIS692b/STAT645b,StatisticalMethodsinGeneticsandBioinformatics(Courseofferedeveryotheryear)Introduction to problems, algorithms, and data analysis approaches in computational biology and bioinformatics;stochasticmodelingandstatisticalmethodsappliedtoproblemssuchasmappingdisease-associatedgenes,analyzinggene expression microarray data, sequence alignment, and SNP analysis. Statistical methods include maximum

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likelihood, EM, Bayesian inference,Markov chainMonte Carlo, and somemethods of classification and clustering;modelsincludehiddenMarkovmodels,Bayesiannetworks,andthecoalescent.Thelimitationsofcurrentmodels,andthe futureopportunities formodelbuilding,arecriticallyaddressed.Prerequisite:STAT538a,542b,or661a.Priorknowledgeofbiologyisnotrequired,butsomeinterestinthesubjectandawillingnesstocarryoutcalculationsusingRisassumed.CB&B647b/GENE645b/BIS645b,StatisticalMethodsinHumanGenetics(Courseofferedeveryotheryear)Probabilitymodelingandstatisticalmethodologyfortheanalysisofhumangeneticsdataarepresented.Topicsincludepopulation genetics, single locus andpolygenic inheritance, linkage analysis, quantitative trait analysis, associationanalysis, haplotype analysis, population structure, whole genome genotyping platforms, copy number variation,pathwayanalysis,andgeneticriskpredictionmodels.CB&B663b,DeepLearningTheoryandApplicationsDeepneuralnetworkshavegainedimmensepopularitywithinthepastdecadeduetotheirsuccessinmanyimportantmachine-learningtaskssuchasimagerecognition,speechrecognition,andnaturallanguageprocessing.Thiscourseprovidesaprincipledandhands-onapproachtodeeplearningwithneuralnetworks.Studentsmastertheprinciplesand practices underlying neural networks, including modern methods of deep learning, and apply deep learningmethodstoreal-worldproblemsincludingimagerecognition,naturallanguageprocessing,andbiomedicalapplications.Course work includes homework, a final exam, and a final project—either group or individual, depending onenrollment—withbothawrittenandoral(i.e.,presentation)component.Thecourseassumesbasicpriorknowledgeinlinearalgebraandprobability.Prerequisites:CPSC202andknowledgeofPythonprogramming.CB&B711a,712b,713b,LabRotations Three2.5–3-monthresearchrotationsinfacultylaboratoriesarerequiredduringthefirstyearofgraduatestudy.Theserotationsarearrangedbyeachstudentwithindividualfacultymembers.CB&B740a/BIS560a,IntrotoHealthInformaticsThecourseprovidesanintroductiontoclinicalandtranslationalinformatics.Topicsinclude(1)overviewofbiomedicalinformatics, (2) design, function, and evaluation of clinical information systems, (3) clinical decision making andpracticeguidelines,(4)clinicaldecisionsupportsystems,(5)informaticssupportofclinicalresearch,(6)privacyandconfidentialityofclinicaldata,(7)standards,and(8)topicsintranslationalbioinformatics.Permissionoftheinstructorrequired.CB&B745b/AMTH745b/CPSC745b,AdvancedTopicsinMachineLearningandDataMining(Courseofferedeveryotheryear)Anoverviewofadvancesinthepastdecadeinmachinelearningandautomaticdataminingapproachesfordealingwiththebroadscopeofmoderndata-analysischallenges,includingdeeplearning,kernelmethods,dictionarylearning,andbagofwords/features.Thisyear,thefocusisonabroadscopeofbiomedicaldata-analysistasks,suchassinglecellRNAsequencing,single-cellsignalingandproteomicanalysis,healthcareassessment,andmedicaldiagnosisandtreatmentrecommendations.Theseminarisbasedonstudentpresentationsanddiscussionsofrecentprominentpublicationsfromleadingjournalsandconferences in the field. Prerequisite: basic concepts in data analysis (e.g., CPSC 545 or 563) or permission of theinstructor.CB&B750b/BIS550b,CoreTopicsinBiomedicalInformaticsThecoursefocusesonprovidinganintroductiontocommonunifyingthemesthatserveasthefoundationfordifferentareasofbiomedicalinformatics,includingclinical,neuro-,andgenomeinformatics.Thecourseisdesignedforstudentswithsignificantcomputerexperienceandcourseworkwhoplantobuilddatabasesandcomputationaltoolsforuseinbiomedical research. Emphasis is on understanding basic principles underlying informatics approaches tointeroperationamongbiomedicaldatabasesandsoftwaretools,standardizedbiomedicalvocabulariesandontologies,biomedicalnaturallanguageprocessing,modelingofbiologicalsystems,highperformancecomputationinbiomedicine,andotherrelatedtopics.

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CB&B752b/MB&B752b,BiologicalDataScience:Mining&ModelingBiomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generationsequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of proteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffun

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EXPERIMENTALPATHOLOGYhttp://catalog.yale.edu/gsas/degree-granting-departments-programs/experimental-pathology/#coursestextPATH620,622,LaboratoryRotationsinExperimentalPathologyLaboratoryrotationsforfirst-yeargraduatestudents.PATH625a,PathobiologyofNeurodegenerationAgingindividualsthroughouttheworldsufferfromneurodegenerativediseasesthatresisttreatmentandpreventionand are among the costliest chronic diseases in the United States. In this course, we will cover their causes,complications,andtherationalebehindthetreatmentsthatarenowavailable.WewillbeginbyreviewingnormalbrainfunctionsandhowtheyareimpairedandthenevaluatetheevidencelinkingtoxicproteindepositsofamyloidandtautoAlzheimer’sdementia.Ourinabilitytodesigneffectiveanti-amyloidtreatmentshasturnedourattentiontomanyother pathogenic factors, which we will also cover. These include toxic mutations, blood vessel damage, myelindysfunction,Inflammation,autophagyandneuronalcelldeath.Wewillalsoexploreimmunetherapy,braintraining,protective lifestyles, false alarms and uncertain claims, and the economics of dementia. This coursewill require aworkingknowledgeofmolecularandcellbiologyandproteinbiochemistry.Itwillbegearedtotheinterestsofstudentsplanningacareerinneurobiology/brain-relatedresearcheitherinacademicsorindustry.Applicantsinterestedinthiscourse should send me a brief description of their background and future goals ([email protected]).Enrollmentwillbelimited.PATH630b/ENAS535b,Biomaterial-TissueInteractionsThe course addresses the interactions between tissues and biomaterials, with an emphasis on the importance ofmolecular-andcellular-leveleventsindictatingtheperformanceandlongevityofclinicallyrelevantdevices.Inaddition,specificareassuchasbiomaterialsfortissueengineeringandtheimportanceofstem/progenitorcells,andbiomaterial-mediatedgeneanddrugdeliveryareaddressed.PATH640a/BBS640a,DevelopingandWritingaScientificResearchProposalThecoursewillcovertheintricaciesofscientificwritingandguidestudentsinthedevelopmentofascientificresearchproposal on the topic of their research.All elements of anNIH fellowship applicationwill be covered, and eligiblestudentswillsubmittheirapplicationsforfunding.PATH650b,CellularandMolecularBiologyofCancerAcomprehensivesurveyofcancerresearchfromthecellulartotheclinicallevel.Therelationofcancertointracellularandintercellularregulationofcellproliferationisemphasized,asareanimalmodelsforcancerresearch.Backgroundinmoleculargeneticsandcellbiologyisassumed.Opentoadvancedundergraduateswithpermissionoftheorganizers.PATH660a/C&MP650a/PHAR580a,TheResponsibleConductofResearchOrganized to foster discussion, the course is taught by faculty in the Pharmacology, Pathology, and Physiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.PATH670b,BiologicalMechanismsofReactiontoInjuryAnintroductiontohumanbiologyanddiseaseasamanifestationofreactiontoinjury.Topicsincludeorganstructureandfunction,cellinjury,circulatoryandinflammatoryresponses,disorderedphysiology,andneoplasia.PATH679a/680ab/C&MP630a/PHAR502a,SeminarinMolecularMedicine,Pharmacology,andPhysiologyReadingsanddiscussiononadiverserangeofcurrenttopicsinmolecularmedicine,pharmacology,andphysiology.Theclass emphasizes analysis of primary research literature and development of presentation and writing skills.Contemporaryarticlesareassignedonarelatedtopiceveryweek,andastudentleaddiscussionwithinputfromfacultywho are experts in the topic area. The overall goal is to cover a specific topic of medical relevance (e.g., cancer,neurodegeneration) from theperspectiveof threeprimarydisciplines (i.e., physiology: normal function; pathology:abnormalfunction;andpharmacology:intervention).

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PATH681a/BBS681a,AdvancedTopicsinCancerBiologyThisadvancedgraduatelevelcoursefocusesonreadingsanddiscussiononthreetofourmajortopicsincancerbiology,suchastargetedtherapy,tumorimmunology,tumormetabolism,andgenomicevolutionofcancer.Foreachtopic,theclassstartswithan interactive lecture, followedbycriticalanalysisofprimaryresearch literature.Recentresearcharticlesareassignedonthesetopics,andastudentleaddiscussionwithinputfromfacultywhoareexpertsinthetopicarea.Pre-requisites:PATH650boratthediscretionoftheinstructor.PATH682b,CancerClinicalTranslationThiscoursebuildsuponbasiccancerbiologyknowledgetoseetheimpactofscientificknowledgeonreal-worldclinicaloncologyissuesthroughdidacticsessions,workingtumorboardattendance,andworkshopdiscussions.Thefirsthalfofthecourseemphasizespracticalissuesinmovingresearchideasintotheclinic,designandexecutionofstandardandnovel formsofclinical trials,andstatisticalanalysisofclinical trialdata.Thesecondhalfcoverstheperspectivesofcliniciansonthemostimportantoutstandingbiologicalquestionsthatshouldbeaddressedbycancerinvestigators.Classsizeislimited,withpriorityforCancerBiologyTrainingProgramtrainees.Advancedundergraduatesorgraduatestudentsmaybeadmittedwithpermissionoftheorganizers.PATH690a,MolecularMechanismsofDiseaseThiscoursecoversaspectsofthefundamentalmolecularandcellularmechanismsunderlyingvarioushumandiseases.Many of the disorders discussed represent major forms of infectious, degenerative, vascular, neoplastic, andinflammatory disease. Additionally, certain rarer diseases that illustrate good models for investigation and/orapplicationofbasicbiologicprinciplesarecoveredinthecourse.Theobjectiveistohighlightadvancesinexperimentalandmolecularmedicineastheyrelatetounderstandingthepathogenesisofdiseaseandtheformulationoftherapies.


GENETICShttp://catalog.yale.edu/gsas/degree-granting-departments-programs/genetics/#coursestextGENE555a/CB&B555a/CPSC453a/553a,ComputationalMethodsforAnalysisandModelingofBiologicalData.Thiscourse introducesbiologyasasystemsanddatascience tocomputerscienceandbiomedicalsciencestudentsthroughopencomputationalproblemsinbiology,thetypesofhigh-throughputdatathatarebeingproducedbymodernbiological technologies, and computational approaches that may be used to tackle such problems.We will coverapplicationsofmachine learningmethods in theanalysisofhigh-throughputbiologicaldata, especially focusingongenomicandproteomicdata.Thiswill includemethods fordenoisingdata,non-lineardimensionalityreduction forvisualizationandprogressionanalysis,unsupervisedclustering,andinformationtheoreticanalysisofgeneregulatoryandsignalingnetworks.Students’gradeswillbebasedonprogrammingassignments,amid-term,paperpresentationandafinalproject.Prerequisite:GENE760orpermissionoftheinstructorGENE625a/MB&B625a/MCDB625a,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapers illustratingtheverybestofgeneticanalysisanddissectthemindetail inthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.GENE655a/CBIO655a,StemCells:BiologyandApplicationThiscourseisdesignedforfirst-yearorsecond-yearstudentstolearnthefundamentalsofstemcellbiologyandtogainfamiliaritywith current research in the field. The course is presented in a lecture anddiscussion format based onprimaryliterature.Topicsincludestemcellconcepts,methodologiesforstemcellresearch,embryonicstemcells,adultstem cells, cloning and stem cell reprogramming, and clinical applications of stem cell research. Prerequisites:undergraduate-levelcellbiology,molecularbiology,andgenetics.GENE675and676,GraduateStudentSeminar:CriticalAnalysisandPresentationofScientificLiteratureStudentsgainexperienceinpreparinganddeliveringseminarsandindiscussingpresentationsbyotherstudents.Avarietyoftopicsinmolecular,cellular,developmental,andpopulationgeneticsarecovered.Requiredforallsecond-yearstudentsinGenetics.GradedSatisfactory/Unsatisfactory.GENE734b/MBIO734b,MolecularBiologyofAnimalVirusesLecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cellinteractions.GENE743b/MB&B743b/MCDB743b,AdvancedEukaryoticMolecularBiologySelectedtopics in transcriptionalcontrol, regulationofchromatinstructure,mRNAprocessing,mRNAstability,RNAinterference,translation,proteindegradation,DNAreplication,DNArepair,site-specificDNArecombination,somatichypermutation.Prerequisite:biochemistryorpermissionoftheinstructor.GENE760b,GenomicMethodsforGeneticAnalysisIntroductiontotheanalysisandinterpretationofgenomicdatasets.Thefocusisonnext-generationsequencing(NGS)applicationsincludingRNA-seq,ChIP-seq,andexomeandwholegenomesequencing.Bytheendofthecourse,eachstudentwillbeabletoprocessandanalyzelarge-scaleNGSdatasetsandinterprettheresults.Thiscourseisintendedonly for graduate studentswho are interested in genomic approaches butwho have had little prior experience ingenomicsorbioinformatics.Enrollmentlimitedtotwenty.Prerequisite:permissionoftheinstructor.GENE777b/MCDB677b,MechanismsofDevelopmentAn advanced course onmechanisms of animal and plant development focusing on the genetic specification of cellorganization and identity during embryogenesis and somatic differentiation. The use of evolutionarily conservedsignalingpathwaystocarryoutdevelopmentaldecisions inarangeofanimals ishighlighted.Coursework includes


studentparticipationincriticalanalysisofprimaryliteratureandaresearchproposaltermpaper.GENE900a/CBIO900a/MCDB900a,ResearchSkillsandEthicsIThis course consists of seminars that covers ethics, grant writing, and training for scientific speaking forMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE901b/CBIO901b/MCDB901b,ResearchSkillsandEthicsIIThis course consists of seminars that covers ethics, grant writing, and training for scientific speaking forMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE911a/CBIO911a/MCDB911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE912a/CBIO912a/MCDB912a,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE913b/CBIO913b/MCDB913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE914b/CBIO914b/MCDB914b,FourthLaboratoryRotation(optional)FourthlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE921aandb,ReadingCourseinGeneticsandMolecularBiologyDirectedreadingwithfaculty.Termpaperrequired.Prerequisite:permissionofGeneticsDGS.


IMMUNOBIOLOGYIBIO503,ResponsibleConductinResearch,RefresherCourseNIH requirement, 4th year students to receive training in the responsible conduct of research every 4 years, andImmunobiology503bmeetsthisrequirement.Thecoursehastwocomponents:

1. Onelarge-groupsessionwillbeheldforall4thyearstudentsthroughtheBBS.ThemaintopicswillbeScientificMisconductandAuthorship.

2. TwoImmunobiologyfacultyfacilitatediscussionsbasedonRCRtopicswhicharegatheredinadvancefromthestudents. These anonymous-hypothetical stories are selected by the faculty and discussed. A workshopenvironmentwherestudentsarethenaskedtoanalyzeeachcaseandsuggestcoursesofactions.

IBIO530/MCDB530,BiologyoftheImmuneSystem,The development of the immune system. Cellular and molecular mechanisms of immune recognition. Effectorresponsesagainstpathogens;autoimmunity.Also,MCDB430a–RequiredforallFirstYearImmunology/BBSstudentsIBIO531,AdvancedImmunologyThehistoricaldevelopmentandcentralparadigmsofkeyareasinimmunology.Thecourseattemptstodevelopaclear understanding of how these paradigmswere established experimentally. Landmark studies are discussed todeterminehowtheconclusionswereobtainedandwhytheywereimportantatthetimetheyweredone.Lectureanddiscussion format; readingsof primary researchpapers and reviewarticles. Prerequisite: IBIO530aor equivalent.Enrollmentlimitedtofifteen.RequiredforallfirstyearBBS/ImmunologyStudents.IBIO532,ImmunobiologySeminar:Inflammation Thecoursewillfocusonfundamentalprinciplesandbiologicalbasisofinflammationandinflammatorydiseases.Thegoalofthecourseistodevelopaframeworkforunderstandinginflammationandinflammatorydiseasesfromthefirstprinciples.Thecourseisdividedintothreeparts.Part1will focusonconceptualfoundations. Thestudentswillbeintroducedtothefundamentalconceptsofhomeostasisandadaptation.Buildingontheseconcepts,wewilldevelopamodern perspective on inflammation and its relation to diseases. Part 2 will cover all the traditional topics ofinflammation biology, including inflammatory inducers, sensors, molecular mediators and effector responses.Regulation and resolution of inflammation will be introduced from a systems perspective. Part 3 will focus oninflammatorydiseases,theiroriginandchangingspectruminmodernworld.Thecoursewillendwithdiscussionofevolutionaryperspectivesonhealthanddiseases.Thecourseisdesignedtobeinteractiveandstudentsareexpectedtoactivelyparticipateinthediscussions.Evaluationwillbebasedonstudents’participationinclassesaswellasonwrittenessay.Prerequisites:Basiccellandmolecularbiologyandintroductoryimmunologycourses.Thecourseisbestsuitedformedicalstudentsandgraduatestudents.Seniorundergraduatesmajoringinbiologicalscienceswouldalsobenefitfromthecourse.MSTPandPhDstudentscantakeitforcredit.Everyoneelseiswelcomedtoaudit.IBIO537,ImmunobiologySeminar:InflammatoryDiseasesThiscourseisconductedasanadvancedseminarconsideringbothreviewarticlesandprimaryliteraturedescribingcurrentinvestigationsintotheimmunologicalmechanismsunderlyingaspectrumofhumandiseases,includingthoseknown tobeinflammatory, allergic,orautoimmunedisorders (systemic lupuserythematosus, rheumatoidarthritis,inflammatoryboweldisease,asthma)aswellasprevalentclinicalpathologieswithimmuneandinflammatorydrivers(metabolicsyndrome,stroke,cancermetastasis).Prerequisites: IBIO530and IBIO531.Enrollment limited to fifteen,withpreferencegiven tostudentswhorequireparticipationinIBIOseminarstocompletetheircourserequirements.IBIO601,FundamentalsofResearch:ResponsibleConductofResearch Faculty ledpresentationson topics relating toproper conductof research. Required for firstyear Immunobiologystudents.Pass/Fail.


IBIO611:Researchrotation1Intensiveexperienceinthedesignandexecutionofexperimentsinimmunologyorotherareasofbiology.Studentsdesignafocused research project in consultation with a faculty mentor and execute the designed experiments in the mentor'slaboratory.Studentsareexpectedtoreadrelevantbackgroundpapersfromtheliterature,designandperformexperiments,interprettheresultingdata,andproposefollowupexperiments.Studentsarealsoexpectedtoattendthementor'sweeklylabmeeting(s)aswellasweeklyImmunobiologydepartmentalseminarsandResearchinProgressseminars.ThecourseconcludeswiththestudentgivingabriefpresentationoftheworkperformedatRotationTalks,attendedbyotherfirstyear Immunology Track graduate students. Evaluation is by thementor and trainee. Pass/Fail. (1 course credit;minimumof20hours/week).RequiredforallfirstyearImmunology/BBSstudents.IBIO612,ResearchRotation2SeedescriptionunderIBIO611a.IBIO613,ResearchRotation3SeedescriptionunderIBIO611a.


INTERDEPARTMENTALNEUROSCIENCEPROGRAMhttps://medicine.yale.edu/inp/academics/courses.aspxINP507,CellularandMolecularMechanismsofNeurologicalDiseasesThiscoursefocusesondiseasessuchasAlzheimer’s,Parkinson’s,Schizophrenia,MultipleSclerosis,andEpilepsy, inwhichmodernneurosciencehasadvancedmechanisticexplanationsforclinicalconditions.Thecoursewillhighlightrecentgenetic,molecular,electrophysiological,andimagingexperimentsinparsingdiseasemechanisms.INP510,StructuralandFunctionalOrganizationoftheHumanNervousSystemAn integrative overview of the structure and function of the human brain pertaining to major neurological andpsychiatricdisorders.Neuroanatomy,neurophysiology,andclinicalcorrelationsareinterrelatedtoprovideessentialbackgroundintheneurosciences.Lecturesinneurocytologyandneuroanatomysurveyneuronalorganizationinthehumanbrain,withemphasisonlongfibertractsrelatedtoclinicalneurology.Weeklythree-hourlaboratorysectionsinclosecollaborationwithfacultymembers.Lecturesinneurophysiologycovervariousaspectsofneuralfunctionatthe cellular level,with a strong emphasis on themammalian nervous system. Clinical correlations consist of fivesessionsgivenbyoneor two facultymembers representingbothbasicandclinical sciences. Thesesessions relateneurologicalsymptomstocellularprocessesinvariousdiseasesofthebrain.Variableclassschedule;contactcourseinstructor.Registrationforthiscourseisbypermissionoftheinstructor.INP511/INP512,LabRotationforFirst-YearStudentsRequiredforallfirst-yearNeurosciencegraduatestudents.Rotationperiodisoneterm.GradingisSat/UnsatbasedonPI’srotationevaluation.INP513/INP514,SecondYearThesisResearchRequired for all second-year INP graduate students. Both terms required. Grading is Sat/Unsat based on PI’scertification.INP519,TutorialByarrangementwithfacultyandapprovalofDGS.INP530/PSYC530,FoundationsofNeuroscience:BiologicalBasesofHumanBehaviorThepurposeofthiscourseistoprovidestudentswithanunderstandingofthebiologicalfactorsunderlyinghumancognition andbehavior. Particular emphasis isplacedon themechanismsassociatedwith individualdifferences inhealthyfunctions(includingemotionregulation,stresssensitivity,highercognition,rewardsensitivity,impulsivity,andsocialfunctions)andtheirrelationswithpsychiatricandneurologicaldisorders.Biologicalfactorstobecoveredincludegenetic,neuroanatomical,neurophysiological,neurochemical,hormonal,andneuropsychologicalinfluences.Severaloftheinitialsessionsaredevotedtobasictopics(e.g.,neurons,neuronalsignaling,brainsystems),beforewebeginourdiscussionoftheneuralbasisofbehaviorandcognition.Wealsocoverseminalworkonanimalmodelsformechanisticinsights into the neurobiology of human behavior. Graduate studentswith any neuroscience research interest areencouragedtotakethiscourse.RequiredofPsychologyPh.D.studentsintheneurosciencearea.INP532,NeurobiologyofCorticalSystemsAn examination of the neural circuits that subserve sensory, motor, cognitive, and affective function, and theirrelationshipstohumandisorders.Acomparativespeciesapproachisusedtohighlighttheevolutionofneuralcircuitsand their functions. Additional discussion sessions for Neurobiology of Cortical Systems training grant trainees.RequiredoftraineesappointedtoNeurobiologyofCorticalSystemswhohavenottakenINP703.INP533,FunctionandDysfunctionoftheVisualSystem.Asurveycourseonthevisualsystem,coveringtheretina,centralvisualpathways,andvisualcenters.Topicsonthedevelopment,structure,function,dysfunction,andrepairofthevisualsystemwillbeintroducedbyfacultymembers


anddiscussedamongstudents,postdoctoralfellowsandfacultymembers.Theclasswillmeetforone1.5hrlectureandone1.5hrpaperdiscussionsessionperweek.INP540,HowtoGiveaTalkThiscourseisapracticalintroductiontotheartandscienceofgivingadata-basedneuroscienceseminar.Theabilitytogiveaclear,convincing,andengagingtalkaboutyourworkisoneofthekeycareerskillsofsuccessfulscientists.Content,visualpresentation,bodylanguage,anddeliveryallcombinetodetermineyourimpactonyouraudience.Thefocusinclassisonstudentpresentationskillsanddetailedfeedback,interspersedwithshortexampletalksbyinvitedguests.StudentsgiveatleasttwotalksoverthecourseofthetermandparticipateinweeklyQ&Aandfeedback.Gradingisbasedonclassparticipation.Enrollmentlimitedtoten.INP562/MCDB361/562,ModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topicsincludetime-dependentdynamicsinregulatory,signal-transduction,andneuronalnetworks;fluctuations,growth,andform;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalfitstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.INP580b,BioethicsinNeuroscienceThiscourseisanintroductiontoethicsandethicaldecision-makingintheNeurosciences.Formatforthecourseisaninformaldiscussion.Eachweek,wewillbejoinedbymembersoftheYalefacultyandcommunitywhocansharetheirexperiencesandexpertiseasitrelatestothetopicoftheweek.Thiscourseismandatoryforfirstyeargraduatestudentsin the Interdepartmental Neuroscience Program (INP). Grading is Sat/Unsat and is determined based onattendance/participation, weekly questions submitted based on assigned readings and a final term paper andpresentation.INP598ComputingandInformaticsforBiomedicalResearchHowdoesabiomedicalscientistnavigatethedynamicandrapidlyevolvinglandscapeofcomputingandinformationtechnologies for data operations that are of growing importance for cutting-edge research?This course lies at theintersection of modern computing architectures, data orchestration and software development. It is intended forstudentsacrossfieldsofneuroscience,biomedicalengineering,bioinformatics,psychology,andrelateddisciplineswhoaim todeveloppractical skillsand learn tools for computingand informaticsapplicable to cutting-edgebiomedicalresearch. Note that this course will not focus on analytics and/or statistics per se and will not require priorprogramming experience. Instead, scientific examples drawn from neuroimaging, genomics, computationalneuroscience,andbehavioral/psychologicalexperimentswillhelpthestudentdevelopatransferableknowledge-baseandtechnicalknow-howaroundaccessing,using,anddeployingcomputingtechnologiesandinformaticstoolsintheserviceofbiomedicalresearch.TopicswillincludetheLINUXshell,BASHscripting,leadingprogramminglanguagesforappliedscientificcomputing,IDEs,datatransferandinformationtechnologybasics,cloudcomputing,high-performancecomputing, modern database principles, git version control, containerization, software design and developmentprinciples, software documentation, licensing best practices, and research software distribution considerations.Collectively, the course aims to confer literacy and useful real-world skills around state-of-the-artcomputing/informaticstechnologiesthatarepracticallyrelevantforbiomedicalresearch.INP599,StatisticsandDataAnalysisinNeuroscienceThiscoursefocusesonpracticalapplicationsofvariousstatisticalmodelsandtestscommonlyusedinneuroscienceresearch.Itcoversbasicprobabilitytheory,hypothesistesting,andmaximumlikelihoodestimation,aswellasmodelcomparison.ThespecificmodelsandtestscoveredincludeANOVA,regression, timeseriesanalyses,anddimensionreductiontechniques(e.g.,PCA).ExamplesandhomeworkwillbegiveninMATLAB,whichwillbeintroducedatthebeginningofthecourse.Previousexperienceinprogrammingandbasicstatisticsisdesirablebutnotrequired.INP611/PSYC611/411,IntroductiontoSystemsNeuroscienceThiscourseprovidesanoverviewofthefundamentalprinciplesgoverningthecentralnervoussystem.Topicsincludethe anatomy of the central nervous system, the neuralmechanisms underlying cortical and subcortical control of


behavior, various neuroscience techniques, aswell as implications for nervous systemdisorders. The lectureswillcombinebasicknowledgeofthenervoussystemwiththekeyexperimentalfindingsthatledtonewdiscoveriesinbrainfunction.INP701,PrinciplesofNeuroscienceGeneralneuroscienceseminar:Lectures,readingsanddiscussionofselectedtopicsinneuroscience.Emphasiswillbeonhowapproachesatthemolecular,cellular,physiologicalandorganismallevelscanleadtounderstandingofneuronalandbrainfunction.Courseisrestrictedtograduatestudents.INP702,FoundationsofCellularandMolecularNeurobiologyThiswillbeaone-semestercoursefor1st-yearINPgraduatestudents(only).Thecoursewillmeetfor1.5hrsonT/F.Each classwill comprise lectures from faculty in the greater Neuroscience community, covering a comprehensiveoverviewofcellularandmolecularconceptsinneuroscience.Gradingwillbebasedonthreeexams.Eachexamwillcoveronethirdofthecourse(CellBiology,Electrophysiology,andSynapticFunction)andconsistofaone-week,take-homesetofshortanswer/essayquestions.INP703,FoundationsofSystemsNeuroscienceAn examination of the neural circuits that subserve sensory, motor, cognitive and affective function, and theirrelationshipstohumandisorders.Acomparativespeciesapproachwillbeusedtohighlight theevolutionofneuralcircuitsandtheirfunctions.INP704,ComparativeNeuroanatomyThis laboratory-based course will examine the fundamental structural organization of the brain in a comparativecontext.Forexample,principlesoftheorganizationofsystemsandcircuitswillbecomparedacrosshumanandnon-humanprimatesandrodents.Labswillalsoexploretheorganizationofthenervoussysteminzebrafish,drosophilaandc.elegans.ThecourseisintendedonlyforgraduatestudentsenrolledintheInterdepartmentalNeuroscienceGraduateProgramandwillcomplementalecture-basedcourseentitledFoundationsofSystemsNeuroscience.INP720/MCDB720,NeurobiologyExaminationoftheexcitabilityofthenervecellmembraneprovidesastartingpointforthestudyofmolecular,cellularandintracellularmechanismsunderlyingthegenerationandcontrolofbehavior.


MICROBIOLOGY http://catalog.yale.edu/gsas/degree-granting-departments-programs/microbiology/#coursestextMBIO530/MCDB530/IBIO530,BiologyoftheImmuneSystemThedevelopmentoftheimmunesystem.Cellularandmolecularmechanismsofimmunerecognition.Effectorresponsesagainst pathogens. Immunologic memory and vaccines. Human diseases including allergy, autoimmunity, cancer,immunodeficiency,HIV/AIDS.(Fall)MBIO601/IBIO601/CBB601,FundamentalsofResearch:ResponsibleConductofResearchAweeklyseminarpresentedbyfacultytrainersontopicsrelatingtoproperconductofresearch.RequiredoffirstyearImmunobiologystudents,first-yearCB&Bstudents,andtraininggrant-fundedpostdocs.(Spring)MBIO670,671,672,LaboratoryRotationsRotationinthreelaboratories.Requiredforallfirst-yeargraduatestudents.MBIO686,TheBiologyofBacterialPathogensIThe course provides an introduction to basic principles in bacterial pathogenesis. Topics focus on the bacterialdeterminantsmediatinginfectionandpathogenesis,aswellasstrategiestopreventandtreatdiseases.Eachweekalecture is given on the topic, followed by student presentations of seminal papers in the field. All participants arerequiredtoparticipateinthediscussionofpapers.(Fall)MBIO685,TheBiologyofBacterialPathogensIIThis interdisciplinarycourse focusesoncurrent topics related tohost-bacterial interactions.Eachweekalectureisgivenonthetopic,followedbystudentpresentationsofseminalpapersinthefield.Allparticipantsarerequiredtopresentapaper.(Spring)MBIO700,SeminalPapersontheFoundationsofModernMicrobiologyAllfirst-yearstudentsintheMicrobiologyprogramarerequiredtotakeMBIO700SeminalPapersontheFoundationsof Modern Microbiology directed by Priti Kumar. Students present and discuss papers describing fundamentaldiscoveriesinareasrelatedtomicrobiology.Thegoalistofamiliarizestudentswiththeprocessofscientificdiscovery,andwiththehistoryofmajordevelopmentsinthefield.Topicsincludeimportantdiscoveriesinvolvingmajorhumanpathogens,fundamentalprocessesinmolecularbiology,andthedevelopmentoftechnologythathasamajorimpactoncurrentbiomedicalresearch.Thisisanon-creditcourseofferedeverySpring.MBIO701,702,ResearchinProgressAllstudents,beginningintheirthirdyear,arerequiredtopresenttheirresearchonceayearattheGraduateStudentResearchinProgress.Thesepresentationsareintendedtogiveeachstudentpracticeinpresentingthestudent’sownworkbeforeasympatheticbutcriticalaudienceandtofamiliarizethefacultywiththeresearch.(Fall&Spring)MBIO703,704MicrobiologySeminarSeriesAllstudentsarerequiredtoattendallMicrobiologyseminarsscheduledthroughouttheacademicyear.Microbiologistsfromaroundtheworldareinvitedtodescribetheirresearch.(Fall&Spring)MBIO705,EvasionofHostDefensebyViruses,BacteriaandEukaryoticParasitesThe course, in student seminar format, is required for all first- and second-year Microbiology Graduate Programstudents.Subjectsincludestrategiesemployedbyviruses,bacteria,oreukaryoticparasitestoevadeeithercellintrinsicdefenses,suchasprogrammedcelldeathorinnateimmunesensing,orresponsesoperatingattheleveloftheorganism,suchastheadaptiveimmuneresponse.MBIO734/GENE734,MolecularBiologyofAnimalVirusesLecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cellinteractions.Prerequisite:graduatestandingorpermissionoftheinstructor.(Spring)


MOLECULARBIOPHYSICSANDBIOCHEMISTRY MB&B330/CB&B561/MCDB330/NSCI324ModelingBiologicalSystemsIStudy of the analytic and computational skills needed tomodel genetic networks and protein signaling pathways.Review of basic biochemical concepts including chemical reactions, ligand binding to receptors, cooperativity, andMichaelis-Menten enzyme kinetics.Deep exploration of biological systems including: kinetics of RNA and proteinsynthesisanddegradation;transcriptionactivatorsandrepressors;lyosogeny/lysisswitchoflambdaphageandtheroles of cooperativity and feedback; networkmotifs such as feed-forwardnetworks andhow they shape responsedynamics; cell signaling, MAP kinase networks and cell fate decisions; bacterial chemotaxis; and noise in geneexpressionandphenotypicvariability.Students learn tomodelusingMatLab inaseriesof in-classhackathons thatillustratebiologicalexamplesdiscussedinlectures.MB&B500a/MCDB500a,BiochemistryAn introduction to thebiochemistryof animals, plants, andmicroorganisms, emphasizing the relationsof chemicalprinciplesandstructuretotheevolutionandregulationoflivingsystems.MB&B517b/ENAS517b/MCDB517b/PHYS517b,MethodsandLogicinInterdisciplinaryResearch Thishalf-termPEBclassisintendedtointroducestudentstointegratedapproachestoresearch.Eachweek,thefirstoftwosessions is student-led,while thesecondsession is ledby facultywithcomplementaryexpertiseanddiscussespapersthatusedifferentapproachestothesametopic(forexample,physicalandbiologicalorexperimentandtheory).Counts as 0.5 credit towardMB&Bgraduate course requirements. ½Course cr;Required for students in IGPPEB.MB&B520a,BootCampBiology Anintensiveintroductiontobiologicalnomenclature,systems,processes,andtechniquesforgraduatestudentswithprevious backgrounds in non-biological fields including physics, engineering, and computer science who wish toperformgraduateresearchinthebiologicalsciences.Countsas0.5credittowardMB&Bgraduatecourserequirements. ½Coursecr;RequiredforstudentsinIGPPEB.MB&B523b/CB&B523b/ENAS541b/PHYS523b,BiologicalPhysics Thecoursehastwoaims:(1)tointroducestudentstothephysicsofbiologicalsystemsand(2)tointroducestudentstothebasicsofscientificcomputing.Thecoursefocusesonstudiesofabroadrangeofbiophysicalphenomenaincludingdiffusion, polymer statistics, protein folding,macromolecular crowding, cellmotion, and tissue development usingcomputationaltoolsandmethods.IntensivetutorialsareprovidedforMATLABincludingbasicsyntax,arrays,for-loops,conditionalstatements,functions,plotting,andimportingandexportingdata.MB&B529b/PHAR529b,StructuralBiologyandDrugDiscovery Acomprehensiveintroductiontotheconceptsandpracticalusesofstructuralbiologyandstructuralbiology-relatedtechniquesindrugdiscovery.Thefirsthalfofthecoursefocusesontechniquesusedtodiscoverandoptimizesmallandmacromoleculedrugs.Studentsareintroducedtotopicssuchassmallmoleculeleaddiscovery,X-raycrystallography,cryo-electronmicroscopy,andbiophysicaltechniques.Thefirsthalfofthecoursealsoincludesapracticalcomponentwhere students conduct hands-on structural biology experiments and learn about biophysical techniques in alaboratorysetting.Thesecondhalfofthecoursefocusesondrugdiscovery,particularlyforproteinkinases.Itincludesa field trip to theYaleCenter forDrugDiscovery,where thestudentsare introduced to the in-houseYalescreeningfacilitiesforsmallmoleculedrugdiscovery.Twohalf-creditcourses—PHAR530andPHAR531—arealsoofferedforthetwohalvesofPHAR529.MB&B561b/AMTH765b/CB&B562b/ENAS561b/INP562b/MCDB562b/PHYS562b,ModelingBiologicalSystemsII Thiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdo theyoscillateandgenerate spatialpatterns?Topics include time-dependentdynamics in regulatory, signal-transduction,andneuronalnetworks; fluctuations,growth,and form;mechanicsofcell shapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear, thecoursespendsroughlyhalf its timeonmechanicalsystemsat the


cellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.Prerequisite:a200-levelbiologycourseorpermissionoftheinstructor.MB&B562b/AMTH562b/CB&B562b/MCDB562b/PHYS562b,ModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topics includetime-dependentdynamics inregulatory,signal-transduction,andneuronalnetworks; fluctuations,growth,and form;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalf itstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.MB&B591a/ENAS991a/MCDB591a/PHYS991a,IntegratedWorkshop ThisrequiredcourseforstudentsinthePEBgraduateprograminvolvesaseriesofmodules,co-taughtbyfaculty, inwhich students fromdifferent academicbackgroundsand research skills collaborateonprojects at the interfaceofphysics,engineering,andbiology.ThemodulescoverabroadrangeofPEBresearchareasandskills.Thecoursestartswith an introduction to MATLAB, which is used throughout the course for analysis, simulations, and modeling.MB&B600a,PrinciplesofBiochemistryI Discussion of the physical, structural, and functional properties of proteins, lipids, and carbohydrates, threemajorclassesofmoleculesinlivingorganisms.Energymetabolism,hormonesignaling,andmusclecontractionasexamplesofcomplexbiologicalprocesseswhoseunderlyingmechanismscanbeunderstoodbyidentifyingandanalyzingthemoleculesresponsibleforthesephenomena.MB&B601b,PrinciplesofBiochemistryII AcontinuationofMB&B600thatconsidersthechemistryandmetabolismofnucleicacids,themechanismandregulationofproteinandnucleicacidsynthesis,andselectedtopicsinmacromolecularbiochemistry.MB&B602a/CBIO602a/MCDB602a,MolecularCellBiology A comprehensive introduction to themolecularandmechanistic aspectsof cellbiology forgraduate students inallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.Prerequisites:none,butsomeknowledgeofbasiccellbiologyandbiochemistryisassumed.Studentswhohavenot taken courses in theseareas canprepareby reading relevant sections inbasicmolecular cell biology texts.WerecommendPollardetal.,CellBiology(3rded.,2016),Albertsetal.,MolecularBiologyoftheCell(6thed.,2014),orLodishetal.,MolecularCellBiology(8thedition,2016).MB&B625a/GENE625a/MCDB625a,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapers illustratingtheverybestofgeneticanalysisanddissectthemindetail inthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.MB&B630b/MCDB630b,BiochemicalandBiophysicalApproachesinMolecularandCellularBiology Thiscourseintroducesthetheoryandapplicationofbiochemicalandbiophysicalmethodstostudythestructureandfunction of biologicalmacromolecules. The course considers the basic physical chemistry required in cellular andmolecular biology but does not require a previous course in physical chemistry. One class per week is a lectureintroducingatopic.Thesecondclassisadiscussionofoneortworesearchpapersutilizingthosemethods.DoesnotcountforgraduatecoursecreditforBQBSgraduatestudents.MB&B635a/ENAS518a,QuantitativeApproachesinBiophysicsandBiochemistry Thecourseoffersanintroductiontoquantitativemethodsrelevanttoanalysisandinterpretationofbiophysicalandbiochemical data. Topics covered include statistical testing, data presentation, and error analysis; introduction todynamical systems;analysisof largedatasets;andFourieranalysis insignal/imageprocessingandmacromolecularstructural studies. The course also includes an introduction to basic programming skills and data analysis usingMATLAB.RealdatafromresearchgroupsinMB&Bareusedforpractice.Prerequisites:MATH120andMB&B600orequivalents,orpermissionoftheinstructors.


MB&B650aand651b,LabRotationforBQBSFirst-YearStudentsRequiredofallfirst-yearBQBSgraduatestudents.Creditforfullyearonly.MB&B675a,SeminarforFirst-YearStudents Requiredofallfirst-yearBQBSgraduatestudents.MB&B676b,ResponsibleConductofResearch Designed for studentswho arebeginning todo scientific research. The course seeks to describe someof thebasicfeaturesoflifeincontemporaryresearchandsomeofthepersonalandprofessionalissuesthatresearchersencounterintheirwork.Approximatelysixsessions,runinaseminar/discussionformat.Requiredofallfirst-yearBQBSgraduatestudents.MB&B711b/C&MP711b,Practicalcryo-EMWorkshop Thislaboratorycourseprovideshands-ontraininginthepracticalaspectsofmacromolecularstructuredeterminationby cryo-electronmicroscopy (cryo-EM). Topics include cryo-EM data collection, image preparation and correction,single-particle picking and 2-D classification, 3-D classification, refinement and post-processing, model building,refinementandevaluation.Thecourseincludestrainingintheuseofcomputerprogramsusedtoperformthesecalculations.Prerequisite:MB&B710/C&MP710. ½CoursecreditMB&B720a,MacromolecularStructureandBiophysicalAnalysis Anin-depthanalysisofmacromolecularstructureanditselucidationusingmodernmethodsofstructuralbiologyandbiochemistry.Topicsincludearchitecturalarrangementsofproteins,RNA,andDNA;practicalmethodsinstructuralanalysis;andanintroductiontodiffractionandNMR.Prerequisites:physicalchemistry(maybetakenconcurrently)andbiochemistry.MB&B730a,MethodsandLogicinMolecularBiology The course examines fundamental concepts in molecular biology through intense critical analysis of the primaryliterature.Theobjectiveistodevelopprimaryliteraturereadingandcriticalthinkingskills.Requiredofandopenonlytofirst-yeargraduatestudentsinBQBS.MB&B734b/GENE734b/MBIO734b,MolecularBiologyofAnimalViruses Lecturecoursewithemphasisonmechanismsofviralreplication,oncogenictransformation,andvirus-hostcellinteractions.MB&B743b/GENE743b/MCDB743b,AdvancedEukaryoticMolecularBiology Selectedtopics in transcriptionalcontrol, regulationofchromatinstructure,mRNAprocessing,mRNAstability,RNAinterference,translation,proteindegradation,DNAreplication,DNArepair,site-specificDNArecombination,somatichypermutation.Prerequisite:biochemistryorpermissionoftheinstructor.MB&B749a,MedicalImpactofBasicScience Considerationofexamplesofrecentdiscoveriesinbasicsciencethathaveelucidatedthemolecularoriginsofdiseaseorthathavesuggestednewtherapiesfordisease.Emphasis isplacedonthefundamentalprinciplesonwhichtheseadvancesrely.Readingisfromtheprimaryscientificandmedicalliterature,withemphasisondevelopingtheabilitytoread this literature critically. Aimed primarily at undergraduates. Prerequisite: biochemistry or permission of theinstructor.MB&B752b/CB&B752b/CPSC752b/MCDB752b,BiomedicalDataScience:MiningandModeling Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generationsequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of proteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffunctionalgenomicsdatasets,andmachine-learningapproachestodataintegration.Prerequisites:biochemistryandcalculus,or


permissionoftheinstructor.MB&B753b,BiomedicalDataScience:Mining Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Thismoduleofthefull-termcourseMB&B752focusesonthefirstofthesetechniques,datamining.Specifictopics include sequence alignment, comparative genomics and phylogenetics, biological databases, microarraynormalization,andmachine-learningapproachestodataintegration.Countsas0.5credittowardMB&Bgraduatecourserequirements.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MB&B754b,BiomedicalDataScience:Modeling Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation. Thismodule of the full-term courseMB&B 752 focuses on the second of these techniques, simulation.Specific topics to be covered include geometric analysis of protein structure, molecular-dynamics simulation, andbiologicalnetworks.Countsas0.5credittowardMB&Bgraduatecourserequirements.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MB&B800a,AdvancedTopicsinMolecularMedicine Theseminar,whichcovers topics in themolecularmechanismsofdisease, illustrates timely issues inareassuchasproteinchemistryandenzymology,intermediarymetabolism,nucleicacidbiochemistry,geneexpression,andvirology.M.D.andM.D./Ph.D.studentsonly.Prerequisite:biochemistry(maybetakenconcurrently).


MOLECULAR,CELLULAR,ANDDEVELOPMENTALBIOLOGYMCDB321L/NSCI32L,LaboratoryforNeurobiologyIntroduction to the neurosciences. Projects include the study of neuronal excitability, sensory transduction, CNSfunction,synapticphysiology,andneuroanatomy.MCDB330/CB&B561/MB&B330/NSCI324ModelingBiologicalSystemsIStudy of the analytic and computational skills needed tomodel genetic networks and protein signaling pathways.Review of basic biochemical concepts including chemical reactions, ligand binding to receptors, cooperativity, andMichaelis-Menten enzyme kinetics.Deep exploration of biological systems including kinetics of RNA and proteinsynthesisanddegradation;transcriptionactivatorsandrepressors;lyosogeny/lysisswitchoflambdaphageandtheroles of cooperativity and feedback; networkmotifs such as feed-forwardnetworks andhow they shape responsedynamics; cell signaling, MAP kinase networks and cell fate decisions; bacterial chemotaxis; and noise in geneexpressionandphenotypicvariability.Students learn tomodelusingMatLab inaseriesof in-classhackathons thatillustratebiologicalexamplesdiscussedinlectures.MCDB500a/MB&B500a,BiochemistryAn introduction to thebiochemistryof animals, plants, andmicroorganisms, emphasizing the relationsof chemicalprinciplesandstructuretotheevolutionandregulationoflivingsystems.MCDB504,ResponsibleConductofResearchThiscoursemeetstheNIHrequirementthatstudentsreceivetrainingintheresponsibleconductofresearchatleasteveryfouryears.Twoninety-minutesessionsforMCDBstudents;additionalsessionsforfourthyearMCDBstudents.Attendance is taken, and students who attend both sessions receive a grade of Satisfactory. GradedSatisfactory/Unsatisfactory.MCDB517b/ENAS517b/MB&B517b/PHYS517b,MethodsandLogicinInterdisciplinaryResearchThishalf-termIGPPEBclassisintendedtointroducestudentstointegratedapproachestoresearch.Eachsessionisledby facultywithcomplementaryexpertiseanddiscussespapers thatusedifferentapproaches to thesametopic (forexample,physicalandbiologicalorexperimentandtheory).Countsas0.5credittowardgraduatecourserequirements.RequiredforstudentsinIGPPEB.MCDB530a/IBIO530a/MBIO530a,BiologyoftheImmuneSystemThedevelopmentoftheimmunesystem.Cellularandmolecularmechanismsofimmunerecognition.Effectorresponsesagainst pathogens. Immunologic memory and vaccines. Human diseases including allergy, autoimmunity, cancer,immunodeficiency,HIV/AIDS.MCDB550a/C&MP550a/ENAS550a/PHAR550a,PhysiologicalSystemsThecoursedevelopsafoundationinhumanphysiologybyexaminingthehomeostasisofvitalparameterswithinthebody,andthebiophysicalpropertiesofcells,tissues,andorgans.Basicconceptsincellandmembranephysiologyaresynthesizedthroughexploringthefunctionofskeletal,smooth,andcardiacmuscle.Thephysicalbasisofbloodflow,mechanismsofvascularexchange,cardiacperformance,andregulationofoverallcirculatoryfunctionarediscussed.Respiratoryphysiologyexploresthemechanicsofventilation,gasdiffusion,andacid-basebalance.Renalphysiologyexaminestheformationandcompositionofurineandtheregulationofelectrolyte,fluid,andacid-basebalance.Organsof thedigestive systemarediscussed from theperspectiveof substratemetabolismandenergybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.


MCDB560b/C&MP560b/ENAS570b/PHAR560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical, andphysiological levels.Students learnabout thedifferentclassesofmolecularmachines thatmediatemembrane transport, generate electrical currents, or performmechanical displacement. Emphasis is placed on therelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocell functionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.MCDB562/MCDB361/BENG465/MB&B562/AMTH765/CB&B562/INP562/PHYS562/ENAS561ModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topics includetime-dependentdynamics inregulatory,signal-transduction,andneuronalnetworks; fluctuations,growth,and form;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalf itstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.MCDB570b,BiotechnologyThe principles and applications of cellular,molecular, and chemical techniques that advance biotechnology. Topicsincludethemostrecenttoolsandstrategiesusedbygovernmentagencies,industriallabs,andacademicresearchtoadapt biological and chemical compounds as medical treatments, as industrial agents, or for the further study ofbiologicalsystems.MCDB585b,ResearchinMCDBforB.S./M.S.CandidatesAtwo-creditcoursetakeninthethird-to-lastterm(typicallythesecondtermofthejunioryear).Atthestartofthiscourse,eachstudentformsacommitteecomposedofhisorheradviserandtwofacultymembersthatmeetstodiscusstheresearchproject.Attheendofthiscourse,studentscompleteadetailedprospectusdescribingtheirthesisprojectand theworkcompleted thus far.Thecommitteeevaluatesanoralandwrittenpresentationof thisprospectus; theevaluationdetermineswhetherthestudentmaycontinueinthecombinedprogram.RequiredofstudentsinthejointB.S./M.S.programwithYaleCollege.MCDB591b/ENAS991b/MB&B591b/PHYS991b,IntegratedWorkshopThisrequiredcourseforstudentsinthePEBgraduateprograminvolvesaseriesofmodules,co-taughtbyfaculty,inwhichstudents fromdifferentacademicbackgroundsandresearchskills collaborateonprojectsat the interfaceofphysics,engineering,andbiology.ThemodulescoverabroadrangeofPEBresearchareasandskills.ThecoursestartswithanintroductiontoMATLAB,whichisusedthroughoutthecourseforanalysis,simulations,andmodeling.MCDB595ab,IntensiveResearchinMCDBforB.S./M.S.CandidatesAfour-credit,yearlongcourse(twocreditseachterm)thatissimilartoMCDB495/496andistakenduringthesenioryear.Duringthiscourse,studentsgiveanoralpresentationdescribingtheirwork.Attheendofthecourse,studentsareexpectedtopresenttheirworktothedepartmentintheformofaposterpresentation.Inaddition,studentsareexpectedto give an oral thesis defense, followed by a comprehensive examination of the thesis conducted by the thesiscommittee.Uponsuccessfulcompletionofthisexamination,aswellasotherrequirements,thestudentisawardedthecombinedB.S./M.S.degree.RequiredofstudentsinthejointB.S./M.S.programwithYaleCollege.MCDB602a/CBIO602a/MB&B602a,MolecularCellBiologyAcomprehensive introduction to themolecularandmechanisticaspectsof cellbiology forgraduatestudents inallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.


Prerequisites:none,butsomeknowledgeofbasiccellbiologyandbiochemistry isassumed.Studentswhohavenottaken courses in these areas can prepare by reading relevant sections in basic molecular cell biology texts. WerecommendPollardetal.,CellBiology(3rded.,2016),Albertsetal.,MolecularBiologyof theCell(6thed.,2014),orLodishetal.,MolecularCellBiology(8thedition,2016).MCDB603a/CBIO603a,SeminarinMolecularCellBiologyAgraduate-levelseminarinmoderncellbiology.Theclassisdevotedtothereadingandcriticalevaluationofclassicaland current papers. The topics are coordinated with theCBIO 602lecture schedule. Thus, concurrent enrollmentinCBIO602isrequired.MCDB625a/GENE625a/MB&B625aU,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapers illustratingtheverybestofgeneticanalysisanddissectthemindetail inthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.MCDB630b/MB&B630b,BiochemicalandBiophysicalApproachesinMolecularandCellularBiologyThiscourseintroducesthetheoryandapplicationofbiochemicalandbiophysicalmethodstostudythestructureandfunction of biologicalmacromolecules. The course considers the basic physical chemistry required in cellular andmolecular biology but does not require a previous course in physical chemistry. One class per week is a lectureintroducingatopic.Thesecondclassisadiscussionofoneortworesearchpapersutilizingthosemethods.DoesnotcountforgraduatecoursecreditforBBSBgraduatestudents.MCDB650EpigeneticsStudyofepigeneticstatesandthevariousmechanismsofepigeneticregulation,includinghistonemodification,DNAmethylation, nuclear organization, and regulation by noncoding RNAs. Detailed critique of papers from primaryliteratureanddiscussionofnoveltechnologies,withspecificattentiontotheroleofepigeneticsindevelopmentanditsimpactonhumanhealth.Prerequisite:permissionoftheinstructor.MCDB670,AdvancedSeminarinBiochemistryandGeneticsThisseminarisdesignedtoexpandstudents’abilitiestocriticallyreadandevaluatetheprimaryscientificliteraturerelevanttosomeofthemostactiveareasofbiochemicalandgeneticresearch.Specialemphasisisplacedontopicsthatdeal with recent discoveries in nucleic acids, such as catalytic RNA and DNA, functions of noncoding RNA, generegulation by RNA, and genomic processing and instability. Students read assigned papers in advance. Discussionfocusesonexperimentaldesignusedbytheauthors,resultsoftheexperiments,andconclusionsdrawnbytheauthors.MCDB677b/GENE777b,MechanismsofDevelopmentAnadvancedcourseonmechanismsofanimaldevelopmentfocusingonthegeneticspecificationofcellorganizationandidentityduringembryogenesisandsomaticdifferentiation.Theuseofevolutionarilyconservedsignalingpathwaystocarryoutdevelopmentaldecisionsinarangeofanimalsishighlighted.Courseworkincludesstudentparticipationincriticalanalysisofprimaryliteratureandaresearchproposaltermpaper.MCDB680a,AdvancesinPlantMolecularBiology The study of basic processes in plant growth and development to provide a foundation for addressing criticalagriculturalneedsinresponsetoachangingclimate.Topics includethe latestbreakthroughsinplantscienceswithemphasis on molecular, cellular, and developmental biology; biotic and abiotic plant interactions; development,genomics,proteomics,epigenetics,andchemicalbiologyinthecontextofplantbiology;andthecurrentsocietaldebatesaboutagrobiotechnology.MCDB720a/INP720a,NeurobiologyExaminationoftheexcitabilityofthenervecellmembraneasastartingpointforthestudyofmolecular,cellular,andintercellularmechanismsunderlyingthegenerationandcontrolofbehavior.


MCDB743b/GENE743b/MB&B743bu,AdvancedEukaryoticMolecularBiologySelectedtopics in transcriptionalcontrol, regulationofchromatinstructure,mRNAprocessing,mRNAstability,RNAinterference,translation,proteindegradation,DNAreplication,DNArepair,site-specificDNArecombination,somatichypermutation.Prerequisite:biochemistryorpermissionoftheinstructor.MCDB752b/MB&B752b/CBB752b/CPSC752b,BiomedicalDataScience:MiningandModelingBiomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generationsequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of proteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffunctionalgenomicsdatasets,andmachine-learningapproachestodataintegration.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MCDB900a/CBIO900a/GENE900a,ResearchSkillsandEthicsIThis course consists of seminars that covers ethics, grant writing, and training for scientific speaking forMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB901/CBIO901/GENE901b,ResearchSkillsandEthicsIIThis course consists of seminars that covers ethics, grant writing, and training for scientific speaking forMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB902&MCDB903AdvancedGraduateSeminarThecourseallowsstudentstohonetheirpresentationskillsthroughyearlypresentationoftheirdissertationwork.Twostudentseachgivethirty-minutepresentationsineachclasssession.Studentsarerequiredtopresenteveryyearbeginning in their thirdyear in theMCDBprogram.EachMCDBgraduate student is expected toattendat least80percentoftheclasssessions.Twofacultymembersco-directthecourse,attendtheseminars,andprovidefeedbacktothestudents.MCDB911a/CBIO911a/GENE911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB912a/CBIO912a/GENE912a,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB913b/CBIO913b/GENE913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB914b/CBIO914b/GENE914b,FourthLaboratoryRotation(optional)FourthlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB950aand951b,Second-YearResearchByarrangementwithfaculty.


PHARMACOLOGY http://medicine.yale.edu/pharm/graduate/courses.aspxPHAR502a/C&MP630a/PATH680a,SeminarinMolecularMedicine,Pharmacology,andPhysiologyReadingsanddiscussiononadiverserangeofcurrenttopicsinmolecularmedicine,pharmacology,andphysiology.Theclass emphasizes analysis of primary research literature and development of presentation and writing skills.Contemporaryarticlesareassignedonarelatedtopiceveryweek,andastudentleaddiscussionwithinputfromfacultywho are experts in the topic area. The overall goal is to cover a specific topic of medical relevance (e.g., cancer,neurodegeneration) from theperspectiveof threeprimarydisciplines (i.e., physiology: normal function; pathology:abnormalfunction;andpharmacology:intervention).PHAR504a,MolecularMechanismsofDrugActionsThis course covers themolecularmechanisms of therapeutics, which are presented in a conceptual framework toincreaseunderstandingbutdecreasememorization.Topicsinclude(butarenotlimitedto)receptoraffinity,efficacy,multiple equilibria, pharmacokinetics, and toxicity; enzyme kinetics and inhibition, drug discovery and design;molecular basis of antimicrobial therapy, cardiology drugs, anticancer and antiviral therapies; and therapeutics forinflammatorydisorders,asthma,andallergy.PHAR506aandb,MethodsinPharmacologicalResearch(Rotations) Studentsworkinlaboratoriesoffacultyoftheirchoice.Theperiodspentineachlaboratoryisoneterm.PHAR528b,PrinciplesofSignalTransductionThe regulation of intracellular signaling is of fundamental importance to the understanding of cell function andregulation.Thiscourseintroducesthebroadprinciplesofintracellularsignaltransduction.Moredetailedlecturesonspecificintracellularsignalingpathwaysaregiveninwhichstudentslearnboththebasicandmostrecentandcutting-edge concepts of intracellular signaling. Topics include regulation of signaling by protein phosphorylation, small Gproteins,G-protein-coupledreceptors,hormones,phospholipids,adhesion,andgasses.PHAR529b/MB&B529b,StructuralBiologyandDrugDiscoveryThegoalofthecourseistoshowstudentshowconceptsofstructuralbiologyareappliedtoareasofgreatimportancein pharmacology such as protein kinases, proteases, cell surface receptors, integrins and other membrane-boundenzymes,andtransportersandchannels,andhowtheseconceptsfacilitatedrugdevelopment.PHAR531b,ConceptsofStructuralBiologyandDrugDiscoveryThis0.5-creditcoursecoversthefirsthalfofthePHAR529bcourseandendsafterthe2ndexam.PHAR530b,TargetedUseofStructuralBiologyinDrugDiscoveryThis0.5-creditcoursebeginsinFebruary,joiningPHAR529b.PHAR537b,SystemsPharmacologyandIntegratedTherapeuticsThegoalofthiscourseistoprovideanin-depth,“hands-on”experienceindrugdesign,drugdiscovery,high-throughputscreening, state-of-the-art proteomics, and target validation. Required course for students in the PharmacologyTrainingProgram.PHAR550a/C&MP550a/ENAS550a/MCDB550a,PhysiologicalSystemsThecoursedevelopsafoundationinhumanphysiologybyexaminingthehomeostasisofvitalparameterswithinthebody,andthebiophysicalpropertiesofcells,tissues,andorgans.Basicconceptsincellandmembranephysiologyaresynthesizedthroughexploringthefunctionofskeletal,smooth,andcardiacmuscle.Thephysicalbasisofbloodflow,mechanismsofvascularexchange,cardiacperformance,andregulationofoverallcirculatoryfunctionarediscussed.Respiratoryphysiologyexploresthemechanicsofventilation,gasdiffusion,andacid-basebalance.Renalphysiology


examinestheformationandcompositionofurineandtheregulationofelectrolyte,fluid,andacid-basebalance.Organsof thedigestive systemarediscussed from theperspectiveof substratemetabolismand energybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.PHAR560b/C&MP560b/ENAS570b/MCDB560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical, andphysiological levels.Students learnabout thedifferentclassesofmolecularmachines thatmediatemembrane transport, generate electrical currents, or performmechanical displacement. Emphasis is placed on therelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocell functionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.PHAR580/C&MP650/PATH660,ResponsibleConductofResearch(RCR)Organized to foster discussion, the course is taught by faculty in the Pharmacology, Pathology, and Physiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.

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Course Guide 2021 - medicine.yale.edu