BBS COURSE GUIDE - Yale School of Medicine 2019... · 2019-09-28 · CBIO 655a/GENE 655a, Stem Cells: Biology and Application This course is designed for first-year or second-year

BBSCOURSEGUIDEYaleUniversity

AcomprehensivelistingofgraduatelevelcoursesaffiliatedwiththeYaleCombinedProgramintheBiological&BiomedicalSciences

LastupdatedAugust7,2019

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Thisguidecontainsallcoursesofferedbythe11Ph.D.programsaffiliatedwiththeYaleBBSProgram.

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

VisittheOnlineCourseInformationsystemathttps://courses.yale.edu/tofindcoursetimes,dates,andlocations.CELLBIOLOGYhttps://medicine.yale.edu/cellbio/graduate/courses.aspxCBIO501a/502b,MoleculestoSystemsThiscourseisdesignedtoprovidemedicalstudentswithacurrentandcomprehensivereviewofbiologicstructureandfunctionatthecellular,tissue,andorgansystemlevels.Areascoveredincludestructureandorganizationofcells;regulationofthecellcycleandmitosis;proteinbiosynthesisandmembranetargeting;cellmotilityandthecytoskeleton;signaltransduction;celladhesion;cellandtissueorganizationoforgansystems.Clinicalcorrelationsessions,whichillustratethecontributionsofcellbiologytospecificmedicalproblems,areinterspersedinthelectureschedule.Histophysiologylaboratoriesprovidepracticalexperiencewithanunderstandingofexploringcellandtissuestructure.ThecourseisofferedonlytoM.D.andM.D./Ph.D.students.ItrunsforthreetermsfromSeptembertoDecemberofthenextacademicyeartocoincidewiththeSchoolofMedicinecurriculum.Registrationandthereleaseofgradestakesplaceinthethirdterm.Thecourseisequivalenttotwograduatecredits. CBIO600a/601b,FrontiersinMedicine“FrontiersinMedicine,”agraduatecreditcourseforfirst-yearMD-PhDstudentsandanelectivecourseformedicalstudents,emphasizestheconnectionsbetweenbasicandclinicalscience,humanphysiologyanddisease.ItparallelsthecontentofYaleMedicalSchool’sfirst-yearcoursesandisdesignedforstudentswhoareconsideringacareerinmedicalresearchorwhochoosetoexplorescientifictopicsindepth,learnaboutcutting-edgeresearchandimprovetheirpresentationskills.Discussionscoverthechallengesfacedinresearch,selectingyourtopicandpursuinganacademiccareer.EnrollmentislimitedtothosewhohavetakenoraretakingtheMastersCourses.Selecttopicsarepresentedbyeminentfacultywhoserveasexcellentrolemodelsforyouracademiccareers.Inmostsessions,twostudentsreviewrelevantmanuscriptsundertheguidanceofafacultymentorandpresentthematerialtothegroup.Priortothestartofclass,studentsarerequiredtosubmitquestionsconcerningtechniquesandconceptsthatmaynotbeclearfromtheassignedpapers.Thesequestionswillthenbeaddressedduringthepresentation.Studentevaluationsaregradedonattendance,participationingroupdiscussionsandformalpresentations.ThecourserunsfromSeptembertomid-Mayandprovidesgraduatecreditifneeded.Itisequivalenttotwograduatecredits.CBIO602a/MB&B602a/MCDB602a,MolecularCellBiologyAcomprehensiveintroductiontothemolecularandmechanisticaspectsofcellbiologyforgraduatestudentsinallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.CBIO603a/MCDB603a,SeminarinMolecularCellBiologyAgraduate-levelseminarcourseinmoderncellbiology.Theclassisdevotedtothereadingandcriticalevaluationofclassicalandcurrentpapers.ThetopicsarecoordinatedwiththeCBIO602alectureschedule.Thus,concurrentenrollmentinCBIO602aisrequired.CBIO604b,SystemsCellBiologyIntroductiontotheorganizationandfunctionofcellswithincomplexmulticellularsystemsasencounteredinthe

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humanbody.Coversmajortissuesandorgansaswellasthecardiovascular,immune,andnervoussystems,withspecialemphasisonthemolecularandcellularbasesofdevelopmentalprocessesandhumandiseases.Lecturessupplementedbyelectronic-basedtutorialsonthehistologyoftissuesandorgans.CBIO606b,AdvancedTopicsinCellBiologyThisseminarcourse,whichmeetsonceweekly,coversadvancedtopicsincellbiology.Eachtopicisspreadovertwoorthreesessions,whichstartwithanintroductoryoverviewandarefollowedbyadiscussionofkeypapersledbyanexpertinthefield.CBIO655a/GENE655a,StemCells:BiologyandApplicationThiscourseisdesignedforfirst-yearorsecond-yearstudentstolearnthefundamentalsofstemcellbiologyandtogainfamiliaritywithcurrentresearchinthefield.Thecourseispresentedinalectureanddiscussionformatbasedonprimaryliterature.Topicsincludestemcellconcepts,methodologiesforstemcellresearch,embryonicstemcells,adultstemcells,cloningandstemcellreprogramming,andclinicalapplicationsofstemcellresearch.Prerequisites:undergraduate-levelcellbiology,molecularbiology,andgenetics.CBIO701b,IlluminatingCellularFunctionIntroductiontotheprinciplesandpracticalmethodsoflivecellimaging.Coversprinciplesoffluorescentmicroscopy(includinggeneticallyencodedprobesandphysiologicalindicators),imageformation,imagedetection,andimageanalysis.Includeshands-ondemonstrationsofstate-of-the-artinstrumentation,suchasvideo-rateconfocaland super-resolution "nanoscopes." The course is equivalent to ½ graduate credit.CBIO900a/GENE900a/MCDB900a,First-YearIntroductiontoResearchandRotationsScientificwritingandlaboratoryrotationtalksforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO901b/GENE901b/MCDB901b,First-YearIntroductiontoResearch—Ethics:ScientificIntegrityinBiomedicalResearchEthicsandlaboratoryrotationtalksforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO903aorb,ReadingCourseinCellBiologyIndependentstudyofspecifictopicsincellbiologythroughdirectedreadingoftheliteratureunderfacultysupervision.StudentmaychooseanytopicandanyYalefacultysubjecttoapprovalbytheCellBiologyDGS.OpentoCellBiologystudents,andtostudentsinotherdepartmentswithapprovalfromtheirrespectiveDGS.Termpaperrequired.CBIO911a/GENE911a/MCDB911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO912b/GENE912b/MCDB912b,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.CBIO913b/GENE913b/MCDB913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,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.Organsofthedigestivesystemarediscussedfromtheperspectiveofsubstratemetabolismandenergybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.C&MP560b/ENAS570b/MCDB560b/PHAR560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical,andphysiologicallevels.Studentslearnaboutthedifferentclassesofmolecularmachinesthatmediatemembranetransport,generateelectricalcurrents,orperformmechanicaldisplacement.Emphasisisplacedontherelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocellfunctionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.C&MP570,MitochondrialBioenergeticsandIntermediaryMetabolism.Thecoursewillpresentacomprehensiveintroductiontothefundamentalsofmitochondrialphysiologyandpathophysiology,withtopicsincludingglucose,lipid,aminoacid,andcholesterolmetabolism;mitochondrialbioenergetics;fluxmodeling;inheritedandacquiredmetabolicdisorders;andcommonmethodsusedtocharacterizemetabolism.Inadditiontothesekeytopics,studentswillgainexperienceinreviewingpapersandcriticallyevaluatingexperimentaldesignandimplementation.Thematerialwillbepresentedinamixedlecture/discussionformat.TheclasswillbeofferedWednesdaysandFridaysfrom10:30-11:45thissemester.Pleasecontacteitheroftheinstructors([email protected],[email protected])ifyouhaveanyquestions.C&MP570b,SensoryPhysiologyThecourseprovidesanoverviewofthemammalianspecialsensorysystems,includingmolecularandcellularbasesofvision,audition,taste,olfaction,andsomatosensation.Facultywithfocusinthoseareasleadpresentationsanddiscussionsonperipheralandcentralmechanisms.Psychophysicalaspectsofsensationareintroduced.C&MP600,MedicalPhysiologyCaseConferences(openonlytoMD/PhD&MRSPstudents)Two-termcoursetaughtingroupsoftentotwelvestudentsbythesamegroupleader(s)throughouttheyear.Workshopformatpermitsstudentstoapplybasicconceptsofphysiologytoclinicalsyndromesanddiseaseprocesses.Studentsareexpectedtoparticipateactivelyinaweeklydiscussionofaclinicalcasethatillustratesprinciplesofhumanphysiologyandpathophysiologyatthewhole-body,system,organ,cellular,ormolecularlevel.Prerequisites:C&MP550aandpermissionoftheinstructor.Creditforfullyearonly.C&MP610,MedicalResearchScholarsProgram:MentoredClinicalExperience(openonlytoMRSPstudents)

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ThegoalsofthecoursearetointroduceMRSPstudentstoaspectsofclinicallyimportanthumandiseases.Studentsexploreeachdiseaseoverthreeone-and-one-half-hoursessionsledbyaclinician-scientistwhoisanexpertintherelevantorgansystem.Studentsexploretwodiseaseprocessesperterm.Thefirstofthethreesessionsisdevotedtoadiscussionoftheclinicalpresentation,naturalhistory,pathology,epidemiology,treatment,andprognosisofthediseaseprocess.DuringthissessionstudentshavetheopportunitytoviewgrossormicroscopicspecimensofdiseasedtissueinassociationwithmembersofthePathologyfaculty.Studentsareassignedreadingsinpathology,pathophysiology,andclinicaltextstoprepareforthefirstclasssession.Thesecondsessionfocusesontranslationalaspectsofthediseaseprocess.Studentsreadandpresentpapersrelevanttothemolecularbasisofthediseaseandcutting-edgeapproachestoitstherapy.Inthethirdsessionstudentsmeetwithpatientswhohaveexperiencedthediseaseand/orvisitandexplorefacilitiesassociatedwithdiagnosisandtreatmentofthediseaseprocess.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.Theclassemphasizesanalysisofprimaryresearchliteratureanddevelopmentofpresentationandwritingskills.Contemporaryarticlesareassignedonarelatedtopiceveryweek,andastudentleadsdiscussionswithinputfromfacultywhoareexpertsinthetopicarea.Theoverallgoalistocoveraspecifictopicofmedicalrelevance(e.g.,cancer,neurodegeneration)fromtheperspectiveofthreeprimarydisciplines(i.e.,physiology:normalfunction;pathology:abnormalfunction;andpharmacology:intervention).C&MP650/PATH660/PHAR580,EthicsOrganizedtofosterdiscussion,thecourseistaughtbyfacultyinthePharmacology,Pathology,andPhysiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.C&MP710b/MB&B710b4,ElectronCryo-MicroscopyforProteinStructureDeterminationUnderstandingcellularfunctionrequiresstructuralandbiochemicalstudiesatanever-increasinglevelofcomplexity.Thecourseisanintroductiontotheconceptsandapplicationsofhigh-resolutionelectroncryo-microscopy.Thisrapidlyemergingnewtechniqueistheonlymethodthatallowsbiologicalmacromoleculestobestudiedatalllevelsofresolutionfromcellularorganizationtonearatomicdetail.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,polymerstatistics,proteinfolding,macromolecularcrowding,cellmotion,andtissuedevelopmentusingcomputationaltoolsandmethods.WewillprovideintensivetutorialsforMatlabincludingbasicsyntax,arrays,for-loops,conditionalstatements,functions,plotting,andimportingandexportingdata.CB&B555a/CPSC453a/GENE555a/CPSC553a,MachineLearningforBiologyThiscourseintroducesbiologyasasystemsanddatasciencetocomputerscienceandbiomedicalsciencestudentsthroughopencomputationalproblemsinbiology,thetypesofhigh-throughputdatathatarebeingproducedbymodernbiologicaltechnologies,andcomputationalapproachesthatmaybeusedtotacklesuchproblems.Wewillcoverapplicationsofmachinelearningmethodsintheanalysisofhigh-throughputbiologicaldata,especiallyfocusingongenomicandproteomicdata.Thiswillincludemethodsfordenoisingdata,non-lineardimensionalityreductionforvisualizationandprogressionanalysis,unsupervisedclustering,andinformationtheoreticanalysisofgeneregulatoryandsignalingnetworks.Students’gradeswillbebasedonprogrammingassignments,amid-term,paperpresentationandafinalproject.CB&B561/MB&B330/NSCI324,ModelingBiologicalSystemsIStudyoftheanalyticandcomputationalskillsneededtomodelgeneticnetworksandproteinsignalingpathways.Reviewofbasicbiochemicalconceptsincludingchemicalreactions,ligandbindingtoreceptors,cooperativity,andMichaelis-Mentenenzymekinetics.Deepexplorationofbiologicalsystemsincluding:kineticsofRNAandproteinsynthesisanddegradation;transcriptionactivatorsandrepressors;lyosogeny/lysisswitchoflambdaphageandtherolesofcooperativityandfeedback;networkmotifssuchasfeed-forwardnetworksandhowtheyshaperesponsedynamics;cellsignaling,MAPkinasenetworks,andcellfatedecisions;bacterialchemotaxis;andnoiseingeneexpressionandphenotypicvariability.StudentslearntomodelusingMATLABinaseriesofin-classhackathonsthatillustratebiologicalexamplesdiscussedinlectures.CB&B562b/AMTH562b/MB&B562b/MCDB562b/PHYS562bModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topicsincludetime-dependentdynamicsinregulatory,signal-transduction,andneuronalnetworks;fluctuations,growth,andform;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalfitstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.CB&B601b/IBIO601b,FundamentalsofResearch:ResponsibleConductofResearch Aweeklyseminarpresentedbyfacultytrainersontopicsrelatingtoproperconductofresearch.Requiredforfirst-yearCB&Bstudents,first-yearImmunobiologystudents,andtraininggrant-fundedpostdocs.Pass/Fail.CB&B645b/BIS692b/STAT645b,StatisticalMethodsinGeneticsandBioinformatics(Courseofferedeveryotheryear)Introductiontoproblems,algorithms,anddataanalysisapproachesincomputationalbiologyandbioinformatics;stochasticmodelingandstatisticalmethodsappliedtoproblemssuchasmappingdisease-associatedgenes,analyzinggeneexpressionmicroarraydata,sequencealignment,andSNPanalysis.Statisticalmethodsincludemaximumlikelihood,EM,Bayesianinference,MarkovchainMonteCarlo,andsomemethodsofclassificationandclustering;modelsincludehiddenMarkovmodels,Bayesiannetworks,andthecoalescent.Thelimitationsofcurrentmodels,andthefutureopportunitiesformodelbuilding,arecriticallyaddressed.Prerequisite:STAT538a,542b,or661a.Priorknowledgeofbiologyisnotrequired,butsomeinterestinthesubjectandawillingnesstocarryoutcalculationsusingRisassumed.

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CB&B647b/GENE645b/BIS645b,StatisticalMethodsinHumanGenetics(Courseofferedeveryotheryear)Probabilitymodelingandstatisticalmethodologyfortheanalysisofhumangeneticsdataarepresented.Topicsincludepopulationgenetics,singlelocusandpolygenicinheritance,linkageanalysis,quantitativetraitanalysis,associationanalysis,haplotypeanalysis,populationstructure,wholegenomegenotypingplatforms,copynumbervariation,pathwayanalysis,andgeneticriskpredictionmodels.CB&B711a,712b,713b,LabRotations Three2.5–3-monthresearchrotationsinfacultylaboratoriesarerequiredduringthefirstyearofgraduatestudy.Theserotationsarearrangedbyeachstudentwithindividualfacultymembers.CB&B740a,ClinicalandTranslationalInformatics Thecourseprovidesanintroductiontoclinicalandtranslationalinformatics.Topicsinclude(1)overviewofbiomedicalinformatics,(2)design,function,andevaluationofclinicalinformationsystems,(3)clinicaldecisionmakingandpracticeguidelines,(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.Theseminarisbasedonstudentpresentationsanddiscussionsofrecentprominentpublicationsfromleadingjournalsandconferencesinthefield.Prerequisite:basicconceptsindataanalysis(e.g.,CPSC545or563)orpermissionoftheinstructor.CB&B750b,CoreTopicsinBiomedicalInformaticsThecoursefocusesonprovidinganintroductiontocommonunifyingthemesthatserveasthefoundationfordifferentareasofbiomedicalinformatics,includingclinical,neuro-,andgenomeinformatics.Thecourseisdesignedforstudentswithsignificantcomputerexperienceandcourseworkwhoplantobuilddatabasesandcomputationaltoolsforuseinbiomedicalresearch.Emphasisisonunderstandingbasicprinciplesunderlyinginformaticsapproachestointeroperationamongbiomedicaldatabasesandsoftwaretools,standardizedbiomedicalvocabulariesandontologies,biomedicalnaturallanguageprocessing,modelingofbiologicalsystems,highperformancecomputationinbiomedicine,andotherrelatedtopics.CB&B752b/MB&B752b,BiologicalDataScience:Mining&ModelingBiomedicaldatascienceencompassestheanalysisofgenesequences,macromolecularstructures,andfunctionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Specifictopicstobecoveredincludesequencealignment,large-scaleprocessing,next-generationsequencingdata,comparativegenomics,phylogenetics,biologicaldatabasedesign,geometricanalysisofproteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffunctionalgenomicsdatasets,andmachine-learningapproachestodataintegration.

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EXPERIMENTALPATHOLOGYhttp://catalog.yale.edu/gsas/degree-granting-departments-programs/experimental-pathology/#coursestextNote:Pathology600,616,617,and618bareprimarilygearedtowardmedicalstudents,butmaybetakenbygraduatestudentswiththepermissionoftheDirectorofMedicalStudies.PATH620,621,622,LaboratoryRotationsinExperimentalPathologyLaboratoryrotationsforfirst-yeargraduatestudents.PATH625,PathobiologyofNeurodegenerationThiscourseexploresdementiawithanemphasisonAlzheimer'sdisease(AD)andwhatweknowaboutitscauses,itscomplications,andtherationalebehindthetreatmentsthatarenowavailable.Topicstobecoveredincludetheamyloidhypothesis,toxicmutations,animalmodels,immunetherapy,ApoE4,bloodvesseldamage,Inflammation,memory,braintraining,protectivelifestyles,falsealarmsanduncertainclaims,andeconomicsofdementia.Thisisanewlydesignedcoursethatwillfocusontheanalysisofprimaryresearchdatathatwillrequireaworkingknowledgeofmolecularandcellbiologyandproteinbiochemistry.Itwillbegearedtotheinterestsofstudentsplanningacareerinbrain-relatedresearcheitherinacademicsorindustry.1.5hrweeklysessionswillinvolvestudentpresentationsofcriticalpublicationsfollowedbydiscussionbyalltheparticipants.PATH630b/ENAS535b,Biomaterial-TissueInteractionsThecourseaddressestheinteractionsbetweentissuesandbiomaterials,withanemphasisontheimportanceofmolecular-andcellular-leveleventsindictatingtheperformanceandlongevityofclinicallyrelevantdevices.Inaddition,specificareassuchasbiomaterialsfortissueengineeringandtheimportanceofstem/progenitorcells,andbiomaterial-mediatedgeneanddrugdeliveryareaddressed.PATH640a/BBS640a,DevelopingandWritingaScientificResearchProposalThecoursewillcovertheintricaciesofscientificwritingandguidestudentsinthedevelopmentofascientificresearchproposalonthetopicoftheirresearch.AllelementsofanNIHfellowshipapplicationwillbecoveredandeligiblestudentswillsubmittheirapplicationsforfunding.PATH650b,CellularandMolecularBiologyofCancerAcomprehensivesurveyofcancerresearchfromthecellulartotheclinicallevel.Therelationofcancertointracellularandintercellularregulationofcellproliferationisemphasized,asareanimalmodelsforcancerresearch.Backgroundinmoleculargeneticsandcellbiologyisassumed.Opentoadvancedundergraduateswithpermissionoftheorganizers.PATH660/C&MP650/PHAR580,EthicsOrganizedtofosterdiscussion,thecourseistaughtbyfacultyinthePharmacology,Pathology,andPhysiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.PATH670b/MCDB315BiologicalMechanismsofReactiontoInjuryAnintroductiontohumanbiologyanddiseaseasamanifestationofreactiontoinjury.Topicsincludeorganstructureandfunction,cellinjury,circulatoryandinflammatoryresponses,disorderedphysiology,andneoplasia.PATH680a/C&MP630a/PHAR502a,SeminarinMolecularMedicine,Pharmacology,andPhysiologyReadingsanddiscussiononadiverserangeofcurrenttopicsinmolecularmedicine,pharmacology,andphysiology.Theclassemphasizesanalysisofprimaryresearchliteratureanddevelopmentofpresentationandwritingskills.Contemporaryarticlesareassignedonarelatedtopiceveryweek,andastudentleadsdiscussionswithinputfromfacultywhoareexpertsinthetopicarea.Theoverallgoalistocoveraspecifictopicofmedicalrelevance(e.g.,

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cancer,neurodegeneration)fromtheperspectiveofthreeprimarydisciplines(i.e.,physiology:normalfunction;pathology:abnormalfunction;andpharmacology:intervention).PATH681a/BBS681a,AdvancedTopicsinCancerBiologyThisadvancedgraduatelevelcoursefocusesonreadingsanddiscussionon3-4majortopicsincancerbiology,suchastargetedtherapy,tumorimmunology,tumormetabolism,andgenomicevolutionofcancer.Foreachtopic,theclassstartswithaninteractivelecture,followedbycriticalanalysisofprimaryresearchliterature.Recentresearcharticlesareassignedonthesetopics,andastudentleadsdiscussionswithinputfromfacultywhoareexpertsinthetopicarea.Pre-requisites:PATH650boratthediscretionoftheinstructor.PATH682b,CancerClinicalTranslationThiscoursewillcombinebasiccancerbiologyknowledgewithreal-worldclinicaloncologyissuesthroughdidacticsessionsandworkshopdiscussions.Thefirsthalfofthecoursewillemphasizepracticalissuesinmovingresearchideasintotheclinic,designandexecutionofstandardandnovelformsofclinicaltrials,andstatisticalanalysisofclinicaltrialdata.Inthesecondhalf,clinicalexpertswilldiscussforemostclinicalandbiologicalchallengesforcancerresearch.Classsizeislimited,withpriorityforCancerBiologyTrainingProgramtrainees.Path650bisrecommendedasaprerequisite.Advancedundergraduatesorgraduatestudentsmaybeadmittedwithpermissionoftheorganizers.PATH690a,MolecularMechanismsofDiseaseThiscoursecoversaspectsofthefundamentalmolecularandcellularmechanismsunderlyingvarioushumandiseases.Manyofthedisordersdiscussedrepresentmajorformsofinfectious,degenerative,vascular,neoplastic,andinflammatorydisease.Additionally,certainrarerdiseasesthatillustrategoodmodelsforinvestigationand/orapplicationofbasicbiologicprinciplesarecoveredinthecourse.Theobjectiveistohighlightadvancesinexperimentalandmolecularmedicineastheyrelatetounderstandingthepathogenesisofdiseaseandtheformulationoftherapies.

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GENETICShttp://catalog.yale.edu/gsas/degree-granting-departments-programs/genetics/#coursestextGENE555a/CB&B555a/CPSC453a/553a,ComputationalMethodsforAnalysisandModelingofBiologicalData.Thiscourseintroducesbiologyasasystemsanddatasciencetocomputerscienceandbiomedicalsciencestudentsthroughopencomputationalproblems inbiology, the typesofhigh-throughputdata thatarebeingproducedbymodernbiologicaltechnologies,andcomputationalapproachesthatmaybeusedtotacklesuchproblems.Wewillcover applications of machine learning methods in the analysis of high-throughput biological data, especiallyfocusingongenomicandproteomicdata.Thiswillincludemethodsfordenoisingdata,non-lineardimensionalityreductionforvisualizationandprogressionanalysis,unsupervisedclustering,andinformationtheoreticanalysisofgeneregulatoryandsignalingnetworks.Students’gradeswillbebasedonprogrammingassignments,amid-term,paperpresentationandafinalproject.Prerequisite:GENE760orpermissionoftheinstructorGENE625a/MB&B625a/MCDB625a,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapersillustratingtheverybestofgeneticanalysisanddissectthemindetailinthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.GENE655a/CBIO655a,StemCells:BiologyandApplicationThiscourseisdesignedforfirst-yearorsecond-yearstudentstolearnthefundamentalsofstemcellbiologyandtogainfamiliaritywithcurrentresearchinthefield.Thecourseispresentedinalectureanddiscussionformatbasedonprimaryliterature.Topicsincludestemcellconcepts,methodologiesforstemcellresearch,embryonicstemcells,adultstemcells,cloningandstemcellreprogramming,andclinicalapplicationsofstemcellresearch.Prerequisites:undergraduate-levelcellbiology,molecularbiology,andgenetics.GENE675and676,GraduateStudentSeminar:CriticalAnalysisandPresentationofScientificLiteratureStudentsgainexperienceinpreparinganddeliveringseminarsandindiscussingpresentationsbyotherstudents.Avarietyoftopicsinmolecular,cellular,developmental,andpopulationgeneticsarecovered.Requiredforallsecond-yearstudentsinGenetics.GradedSatisfactory/Unsatisfactory.GENE734b/MBIO734b,MolecularBiologyofAnimalVirusesLecturecoursewithemphasisonmechanismsofviralreplication,oncogenictransformation,andvirus-hostcellinteractions.GENE743b/MB&B743b/MCDB743b,AdvancedEukaryoticMolecularBiologySelectedtopicsintranscriptionalcontrol,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.Thiscourseisintendedonlyforgraduatestudentswhoareinterestedingenomicapproachesbutwhohavehadlittlepriorexperienceingenomicsorbioinformatics.Enrollmentlimitedtotwenty.Prerequisite:permissionoftheinstructor.GENE777b/MCDB677b,MechanismsofDevelopmentAnadvancedcourseonmechanismsofanimalandplantdevelopmentfocusingonthegeneticspecificationofcellorganizationandidentityduringembryogenesisandsomaticdifferentiation.Theuseofevolutionarilyconserved


signalingpathwaystocarryoutdevelopmentaldecisionsinarangeofanimalsishighlighted.Courseworkincludesstudentparticipationincriticalanalysisofprimaryliteratureandaresearchproposaltermpaper.GENE900a/CBIO900a/MCDB900a,First-YearIntroductiontoResearchandRotationsScientificwritingandlaboratoryrotationtalksforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE901b/CBIO901b/MCDB901b,First-YearIntroductiontoResearch—Ethics:ScientificIntegrityinBiomedicalResearchEthicsandlaboratoryrotationtalksforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE911a/CBIO911a/MCDB911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE912a/CBIO912a/MCDB912a,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE913b/CBIO913b/MCDB913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.GENE921aandb,ReadingCourseinGeneticsandMolecularBiologyDirectedreadingwithfaculty.Termpaperrequired.Prerequisite:permissionofGeneticsDGS.


IMMUNOBIOLOGYhttp://medicine.yale.edu/immuno/programs/courses.aspxIBIO503b,ResponsibleConductinResearch,RefresherCourseNIHrequirement,4thyearstudentstoreceivetrainingintheresponsibleconductofresearchevery4years,andImmunobiolgy503bmeetsthisrequirement.Thecoursehastwocomponents:

1. Onelarge-groupsessionwillbeheldforall4thyearstudentsthroughtheBBS.ThemaintopicswillbeScientificMisconductandAuthorship.

2. TwoImmunobiologyfacultyfacilitatediscussionsbasedonRCRtopicswhicharegatheredinadvancefromthestudents.Theseanonymous-hypotheticalstoriesareselectedbythefacultyanddiscussed.Aworkshopenvironmentwherestudentsarethenaskedtoanalyzeeachcaseandsuggestcoursesofactions.

IBIO530a,BiologyoftheImmuneSystem,Thedevelopmentoftheimmunesystem.Cellularandmolecularmechanismsofimmunerecognition.Effectorresponsesagainstpathogens;autoimmunity.IBIO531b,AdvancedImmunologyThehistoricaldevelopmentandcentralparadigmsofkeyareasinimmunology.Thecourseattemptstodevelopaclearunderstandingofhowtheseparadigmswereestablishedexperimentally.Landmarkstudiesarediscussedtodeterminehowtheconclusionswereobtainedandwhytheywereimportantatthetimetheyweredone.Lectureanddiscussionformat;readingsofprimaryresearchpapersandreviewarticles.Prerequisite:IBIO530aorequivalent.Enrollmentlimitedtofifteen.RequiredforallfirstyearBBS/ImmunologyStudents.IBIO532b,InflammationThiscoursewillcoverfundamentalsofinflammationfromabroadbiologicalperspective.Bothphysiologicalandpathologicalaspectsofinflammationwillbethefocusofthiscourse. IBIO536a,ImmunoSeminar:Neuroimmunology.Thiscoursewillexplorethediversearrayofinteractionsbetweentheimmuneandnervoussystems,bothinhomeostasisanddiseasesettings,includingbutnotlimitedtoneurodegenerative,vascularandmalignantdiseases.LIMITEDTO22Students.PreferencetoImmunobiologystudentstakingfordegreerequirement.Prerequisites:IBIO530aandIBIO531borequivalentIBIO537b,ImmunoSeminar:TranslationalImmunobiologyThiscourseisdesignedtointroduceimmunobiologyPh.D.studentstotranslationalresearchandmedicine.Eachweeklyseminarwillfocusonaspecificdiseasewithaconspicuousimmunologicalcomponent.In-classperiodswillconsistofveryinteractive,didacticsectionscoveringdiseasephenotype,underlyingimmunobiologyandpathology,andmechanismsoftreatmentapproaches,includinglimitations.Discussionsareledbyprincipalinvestigatorswhofocusonhumantranslationalimmunologyandbyclinician-scientistswhoseepatientsinassociatedclinics.Examplesoftopicsinclude:TandBcellcontributionstotheunderlyingpathophysiologyofmultiplesclerosis,type1diabetes,systemiclupuserythematosus,myastheniagravis,andotherautoimmunediseases;immuneresponsestoacutebraininjury;inheritedimmunedisorders;paradigmsgoverninghowanti-tumorimmuneresponsesarepromotedorsuppressed;andcurrentapproachesinimmunotherapy-basedclinicaltrials.Assignmentswillchallengestudentstothinkcreativelyaboutsolutionstoproblemsthatobstructtheprogresstowardunderstandingdiseasemechanismsanddevelopingtherapeutics.Atermassignment,intheformofaresearchproposal,willfocusonindependentstudyofatranslationalimmunobiologyproblemofeachstudent’schoosing.Studentswillbeprovidedwithelectiveopportunitiesforexperientiallearningthroughclinicvisitswithcoursefacultyinstructors.Thecombinationofmedicalknowledgeandinteractionwithtranslationalandclinician-scientistsprovidesanewperspectivetoIBIOPh.D.studentsthatwillbroadentheirbasicsciencetraining.Theexposuretothepracticeofmedicinewillenableimmunobiology(andother)graduatestudentstoworkmoreconfidentlyattheinterfaceofresearchandmedicineandfacilitatecollaborationswithclinicalinvestigators.Prerequisites:IBIO531aorasimilarcoursethatprovidesasolidfoundationinfundamentalimmunologyisrecommended.Prerequisitecouldbewaivedforhighlymotivatedstudents.


IBIO600a,IntroductiontoResearch,Introductiontotheresearchinterestsofthefaculty.RequiredforallfirstyearImmunology/BBSstudents.Pass/Fail.IBIO601b/CB&B601b,FundamentalsofResearch:ResponsibleConductofResearch Facultyledpresentationsontopicsrelatingtoproperconductofresearch.RequiredforfirstyearImmunobiologystudents.Pass/Fail;Requiredforallfirstyearstudents.IBIO611a,ResearchRotation1Intensiveexperienceinthedesignandexecutionofexperimentsinimmunologyorotherareasofbiology.Studentsdesignafocusedresearchprojectinconsultationwithafacultymentorandexecutethedesignedexperimentsinthementor'slaboratory.Studentsareexpectedtoreadrelevantbackgroundpapersfromtheliterature,designandperformexperiments,interprettheresultingdata,andproposefollowupexperiments.Studentsarealsoexpectedtoattendthementor'sweeklylabmeeting(s)aswellasweeklyImmunobiologydepartmentalseminarsandResearchinProgressseminars.ThecourseconcludeswiththestudentgivingabriefpresentationoftheworkperformedatRotationTalks,attendedbyotherfirstyearImmunologyTrackgraduatestudents.Evaluationisbythementorandtrainee.StudentsmustsubmitaprioritizedlistoffourpossiblementorstoBarbaraCottonintheofficeoftheDirectorofGraduateStudiesatleastoneweekpriortothebeginningofthecourse.RotationassignmentsareorganizedandchosenbytheDGS.GradedPass/Fail.(1coursecredit;minimumof20hours/week).RequiredforallfirstyearImmunology/BBSstudents.IBIO612b,ResearchRotation2SeedescriptionunderIBIO611a.IBIO613b,ResearchRotation3SeedescriptionunderIBIO611a.


INTERDEPARTMENTALNEUROSCIENCEPROGRAMhttps://medicine.yale.edu/inp/academics/courses.aspxINP507,CellularandMolecularMechanismsofNeurologicalDiseasesThiscoursefocusesondiseasessuchasAlzheimer’s,Parkinson’s,Schizophrenia,MultipleSclerosis,andEpilepsy,inwhichmodernneurosciencehasadvancedmechanisticexplanationsforclinicalconditions.Thecoursewillhighlightrecentgenetic,molecular,electrophysiological,andimagingexperimentsinparsingdiseasemechanisms.INP510,StructuralandFunctionalOrganizationoftheHumanNervousSystemAnintegrativeoverviewofthestructureandfunctionofthehumanbrainpertainingtomajorneurologicalandpsychiatricdisorders.Neuroanatomy,neurophysiology,andclinicalcorrelationsareinterrelatedtoprovideessentialbackgroundintheneurosciences.Lecturesinneurocytologyandneuroanatomysurveyneuronalorganizationinthehumanbrain,withemphasisonlongfibertractsrelatedtoclinicalneurology.Weeklythree-hourlaboratorysectionsinclosecollaborationwithfacultymembers.Lecturesinneurophysiologycovervariousaspectsofneuralfunctionatthecellularlevel,withastrongemphasisonthemammaliannervoussystem.Clinicalcorrelationsconsistoffivesessionsgivenbyoneortwofacultymembersrepresentingbothbasicandclinicalsciences.Thesesessionsrelateneurologicalsymptomstocellularprocessesinvariousdiseasesofthebrain.Variableclassschedule;contactcourseinstructor.Registrationforthiscourseisbypermissionoftheinstructor.INP511/INP512,LabRotationforFirst-YearStudentsRequiredforallfirst-yearNeurosciencegraduatestudents.Rotationperiodisoneterm.GradingisSat/UnsatbasedonPI’srotationevaluation.INP513/INP514,SecondYearThesisResearchRequiredforallsecond-yearINPgraduatestudents.Bothtermsrequired.GradingisSat/UnsatbasedonPI’scertification.INP519,TutorialByarrangementwithfacultyandapprovalofDGS.INP530/PSYC530,FoundationsofNeuroscience:BiologicalBasesofHumanBehaviorThepurposeofthiscourseistoprovidestudentswithanunderstandingofthebiologicalfactorsunderlyinghumancognitionandbehavior.Particularemphasisisplacedonthemechanismsassociatedwithindividualdifferencesinhealthyfunctions(includingemotionregulation,stresssensitivity,highercognition,rewardsensitivity,impulsivity,andsocialfunctions)andtheirrelationswithpsychiatricandneurologicaldisorders.Biologicalfactorstobecoveredincludegenetic,neuroanatomical,neurophysiological,neurochemical,hormonal,andneuropsychologicalinfluences.Severaloftheinitialsessionsaredevotedtobasictopics(e.g.,neurons,neuronalsignaling,brainsystems),beforewebeginourdiscussionoftheneuralbasisofbehaviorandcognition.Wealsocoverseminalworkonanimalmodelsformechanisticinsightsintotheneurobiologyofhumanbehavior.Graduatestudentswithanyneuroscienceresearchinterestareencouragedtotakethiscourse.RequiredofPsychologyPh.D.studentsintheneurosciencearea.INP532,NeurobiologyofCorticalSystemsAnexaminationoftheneuralcircuitsthatsubservesensory,motor,cognitive,andaffectivefunction,andtheirrelationshipstohumandisorders.Acomparativespeciesapproachisusedtohighlighttheevolutionofneuralcircuitsandtheirfunctions.AdditionaldiscussionsessionsforNeurobiologyofCorticalSystemstraininggranttrainees.RequiredoftraineesappointedtoNeurobiologyofCorticalSystemswhohavenottakenINP703.INP533,FunctionandDysfunctionoftheVisualSystem.Asurveycourseonthevisualsystem,coveringtheretina,centralvisualpathways,andvisualcenters.Topicsonthedevelopment,structure,function,dysfunction,andrepairofthevisualsystemwillbeintroducedbyfaculty


membersanddiscussedamongstudents,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.ThiscourseismandatoryforfirstyeargraduatestudentsintheInterdepartmentalNeuroscienceProgram(INP).GradingisSat/Unsatandisdeterminedbasedonattendance/participation,weeklyquestionssubmittedbasedonassignedreadingsandafinaltermpaperandpresentation.INP599,StatisticsandDataAnalysisinNeuroscienceThiscoursefocusesonpracticalapplicationsofvariousstatisticalmodelsandtestscommonlyusedinneuroscienceresearch.Itcoversbasicprobabilitytheory,hypothesistesting,andmaximumlikelihoodestimation,aswellasmodelcomparison.ThespecificmodelsandtestscoveredincludeANOVA,regression,timeseriesanalyses,anddimensionreductiontechniques(e.g.,PCA).ExamplesandhomeworkwillbegiveninMATLAB,whichwillbeintroducedatthebeginningofthecourse.Previousexperienceinprogrammingandbasicstatisticsisdesirablebutnotrequired.INP611/PSYC611/411,IntroductiontoSystemsNeuroscienceThiscourseprovidesanoverviewofthefundamentalprinciplesgoverningthecentralnervoussystem.Topicsincludetheanatomyofthecentralnervoussystem,theneuralmechanismsunderlyingcorticalandsubcorticalcontrolofbehavior,variousneurosciencetechniques,aswellasimplicationsfornervoussystemdisorders.Thelectureswillcombinebasicknowledgeofthenervoussystemwiththekeyexperimentalfindingsthatledtonewdiscoveriesinbrainfunction.INP701,PrinciplesofNeuroscienceGeneralneuroscienceseminar:Lectures,readingsanddiscussionofselectedtopicsinneuroscience.Emphasiswillbeonhowapproachesatthemolecular,cellular,physiologicalandorganismallevelscanleadtounderstandingofneuronalandbrainfunction.Courseisrestrictedtograduatestudents.INP702,FoundationsofCellularandMolecularNeurobiologyThiswillbeaone-semestercoursefor1st-yearINPgraduatestudents(only).Thecoursewillmeetfor1.5hrsonT/F.EachclasswillcompriselecturesfromfacultyinthegreaterNeurosciencecommunity,coveringacomprehensiveoverviewofcellularandmolecularconceptsinneuroscience.Gradingwillbebasedonthreeexams.Eachexamwillcoveronethirdofthecourse(CellBiology,Electrophysiology,andSynapticFunction)andconsistofaone-week,take-homesetofshortanswer/essayquestions.


INP703,FoundationsofSystemsNeuroscienceAnexaminationoftheneuralcircuitsthatsubservesensory,motor,cognitiveandaffectivefunction,andtheirrelationshipstohumandisorders.Acomparativespeciesapproachwillbeusedtohighlighttheevolutionofneuralcircuitsandtheirfunctions.INP704,ComparativeNeuroanatomyThislaboratorybasedcoursewillexaminethefundamentalstructuralorganizationofthebraininacomparativecontext.Forexample,principlesoftheorganizationofsystemsandcircuitswillbecomparedacrosshumanandnon-humanprimatesandrodents.Labswillalsoexploretheorganizationofthenervoussysteminzebrafish,drosophilaandc.elegans.ThecourseisintendedonlyforgraduatestudentsenrolledintheInterdepartmentalNeuroscienceGraduateProgramandwillcomplementalecturebasedcourseentitledFoundationsofSystemsNeuroscience.INP720/MCDB720,NeurobiologyExaminationoftheexcitabilityofthenervecellmembraneprovidesastartingpointforthestudyofmolecular,cellularandintracellularmechanismsunderlyingthegenerationandcontrolofbehavior.


MICROBIOLOGY http://catalog.yale.edu/gsas/degree-granting-departments-programs/microbiology/#coursestextMBIO530/MCDB530/IBIO530,BiologyoftheImmuneSystemThedevelopmentoftheimmunesystem.Cellularandmolecularmechanismsofimmunerecognition.Effectorresponsesagainstpathogens.Immunologicmemoryandvaccines.Humandiseasesincludingallergy,autoimmunity,cancer,immunodeficiency,HIV/AIDS.(Fall)MBIO561/MCDB561IntroductiontoDynamicalSystemsinBiologyStudyoftheanalyticandcomputationalskillsneededtomodelgeneticnetworksandproteinsignalingpathways.Reviewofbasicbiochemicalconceptsincludingchemicalreactions,ligandbindingtoreceptors,cooperativity,andMichaelis-Mentenenzymekinetics.Deepexplorationofbiologicalsystemsincluding:kineticsofRNAandproteinsynthesisanddegradation;transcriptionactivatorsandrepressors;lyosogeny/lysisswitchoflambdaphageandtherolesofcooperativityandfeedback;networkmotifssuchasfeed-forwardnetworksandhowtheyshaperesponsedynamics;cellsignaling,MAPkinasenetworksandcellfatedecisions;bacterialchemotaxis;andnoiseingeneexpressionandphenotypicvariability.StudentslearntomodelusingMATLABinaseriesofin-classhackathonsthatillustratebiologicalexamplesdiscussedinlectures.(Fall)MBIO601/IBIO601/CBB601,FundamentalsofResearch:ResponsibleConductofResearchAweeklyseminarpresentedbyfacultytrainersontopicsrelatingtoproperconductofresearch.Requiredoffirst-yearImmunobiologystudents,first-yearCB&Bstudents,andtraininggrant-fundedpostdocs.(Spring)MBIO670,671,672,LaboratoryRotationsRotationinthreelaboratories.Requiredforallfirst-yeargraduatestudents.MBIO680/EMD680,MolecularandCellularProcessesofParasiticEukaryotesAnintroductorytopic-basedcourseinmodernparasitology.Foreachtopicthereisanintroductorylecturefollowedbyajournalclub-likediscussionsessionofrelevantpapersselectedfromtheliterature.Thecourseprovidesanintroductiontobasicbiologicalconceptsofparasiticeukaryotescausingdiseasesinhumans.Topicsincludestrategiesusedbyparasiticeukaryotestoestablishinfectionsinthehostandapproachestodiseasecontrol,througheitherchemotherapy,vaccines,orgenomics.Inaddition,emphasisisplacedonevaluatingthequalityandlimitationofscientificpublicationsanddevelopingskillsinscientificcommunication.Prerequisite:permissionoftheinstructor.(Spring)MBIO685,TheBiologyofBacterialPathogensIIThis interdisciplinary course focuses on foundational topics related to host-bacterial interactions. Each week a lecture is given on the topic, followed by student presentations of seminal papers in the field. All participants are required to present a paper.(Spring) MBIO686,TheBiologyofBacterialPathogensIThecourseprovidesanintroductiontobacterialphysiology,geneticsandpathogenesis.Thecoursediscusseshowtoidentifyandstudybacterialdeterminantsmediatingsurvivaltodifferentstressconditionsandtheabilitytoestablishcommensalorpathogenicinteractionswitheukaryotichosts.OnThursday,alectureisgivenonaspecifictopic,andonapaper(s)onthattopicisdiscussed.Allparticipantsarerequiredtoparticipateinthediscussionofpapers.(Fall)MBIO700,SeminalPapersontheFoundationsofModernMicrobiologyThecourse,instudentseminarformat,isrequiredforallfirstandsecondyearMicrobiologyGraduateProgramstudents.Subjectstobediscussedincludestrategiesemployedbyviruses,bacteriaoreukaryoticparasitestoevadeeithercellintrinsicdefenses,suchasprogrammedcelldeathorinnateimmunesensing,orresponsesoperatingattheleveloftheorganism,suchastheadaptiveimmuneresponse.(Spring,oddyears)MBIO701,702,ResearchinProgressAllstudents,beginningintheirthirdyear,arerequiredtopresenttheirresearchonceayearattheGraduate


StudentResearchinProgress.Thesepresentationsareintendedtogiveeachstudentpracticeinpresentinghisorherownworkbeforeasympatheticbutcriticalaudienceandtofamiliarizethefacultywiththeresearch.(Fall&Spring)MBIO703,704MicrobiologySeminarSeriesAllstudentsarerequiredtoattendallMicrobiologyseminarsscheduledthroughouttheacademicyear.Microbiologistsfromaroundtheworldareinvitedtodescribetheirresearch.(Fall&Spring)MBIO705,EvasionofHostDefensebyViruses,BacteriaandEukaryoticParasitesThecourse,instudentseminarformat,isrequiredforallfirstandsecondyearMicrobiologyGraduateProgramstudents.Subjectstobediscussedincludestrategiesemployedbyviruses,bacteriaoreukaryoticparasitestoevadeeithercellintrinsicdefenses,suchasprogrammedcelldeathorinnateimmunesensing,orresponsesoperatingattheleveloftheorganism,suchastheadaptiveimmuneresponse.(Spring,evenyears)MBIO734/GENE734,MolecularBiologyofAnimalVirusesLecture-basedcourseprovidingthefoundationsofmolecularvirology,emphasizingmedically-relevantviruses,mechanismsofviralreplication,oncogenictransformation,andvirus-hostcellinteractions.Prerequisite:graduatestandingorpermissionoftheinstructor.(Spring)


MOLECULARBIOPHYSICSANDBIOCHEMISTRY MB&B500a/MCDB500a,BiochemistryAnintroductiontothebiochemistryofanimals,plants,andmicroorganisms,emphasizingtherelationsofchemicalprinciplesandstructuretotheevolutionandregulationoflivingsystems.MB&B517b/ENAS517b/MCDB517b/PHYS517b,MethodsandLogicinInterdisciplinaryResearch Thishalf-termPEBclassisintendedtointroducestudentstointegratedapproachestoresearch.Eachweek,thefirstoftwosessionsisstudent-led,whilethesecondsessionisledbyfacultywithcomplementaryexpertiseanddiscussespapersthatusedifferentapproachestothesametopic(forexample,physicalandbiologicalorexperimentandtheory).Countsas0.5credittowardMB&Bgraduatecourserequirements. ½Coursecr;RequiredforstudentsinIGPPEB.MB&B520a,BootCampBiology Anintensiveintroductiontobiologicalnomenclature,systems,processes,andtechniquesforgraduatestudentswithpreviousbackgroundsinnon-biologicalfieldsincludingphysics,engineering,andcomputersciencewhowishtoperformgraduateresearchinthebiologicalsciences.Countsas0.5credittowardMB&Bgraduatecourserequirements. ½Coursecr;RequiredforstudentsinIGPPEB.MB&B523b/CB&B523b/ENAS541b/PHYS523b,BiologicalPhysics Thecoursehastwoaims:(1)tointroducestudentstothephysicsofbiologicalsystemsand(2)tointroducestudentstothebasicsofscientificcomputing.Thecoursefocusesonstudiesofabroadrangeofbiophysicalphenomenaincludingdiffusion,polymerstatistics,proteinfolding,macromolecularcrowding,cellmotion,andtissuedevelopmentusingcomputationaltoolsandmethods.IntensivetutorialsareprovidedforMATLABincludingbasicsyntax,arrays,for-loops,conditionalstatements,functions,plotting,andimportingandexportingdata.MB&B529b/PHAR529b,StructuralBiologyandDrugDiscovery Acomprehensiveintroductiontotheconceptsandpracticalusesofstructuralbiologyandstructuralbiology-relatedtechniquesindrugdiscovery.Thefirsthalfofthecoursefocusesontechniquesusedtodiscoverandoptimizesmallandmacromoleculedrugs.Studentsareintroducedtotopicssuchassmallmoleculeleaddiscovery,X-raycrystallography,cryo-electronmicroscopy,andbiophysicaltechniques.Thefirsthalfofthecoursealsoincludesapracticalcomponentwherestudentsconducthands-onstructuralbiologyexperimentsandlearnaboutbiophysicaltechniquesinalaboratorysetting.Thesecondhalfofthecoursefocusesondrugdiscovery,particularlyforproteinkinases.ItincludesafieldtriptotheYaleCenterforDrugDiscovery,wherethestudentsareintroducedtothein-houseYalescreeningfacilitiesforsmallmoleculedrugdiscovery.Twohalf-creditcourses—PHAR530andPHAR531—arealsoofferedforthetwohalvesofPHAR529.MB&B562b/AMTH765b/CB&B562b/ENAS561b/INP562b/MCDB562b/PHYS562b,ModelingBiologicalSystemsII Thiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topicsincludetime-dependentdynamicsinregulatory,signal-transduction,andneuronalnetworks;fluctuations,growth,andform;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalfitstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.Prerequisite:a200-levelbiologycourseorpermissionoftheinstructor.MB&B591a/ENAS991a/MCDB591a/PHYS991a,IntegratedWorkshop ThisrequiredcourseforstudentsinthePEBgraduateprograminvolvesaseriesofmodules,co-taughtbyfaculty,inwhichstudentsfromdifferentacademicbackgroundsandresearchskillscollaborateonprojectsattheinterfaceofphysics,engineering,andbiology.ThemodulescoverabroadrangeofPEBresearchareasandskills.ThecoursestartswithanintroductiontoMATLAB,whichisusedthroughoutthecourseforanalysis,simulations,andmodeling.


MB&B600a,PrinciplesofBiochemistryI Discussionofthephysical,structural,andfunctionalpropertiesofproteins,lipids,andcarbohydrates,threemajorclassesofmoleculesinlivingorganisms.Energymetabolism,hormonesignaling,andmusclecontractionasexamplesofcomplexbiologicalprocesseswhoseunderlyingmechanismscanbeunderstoodbyidentifyingandanalyzingthemoleculesresponsibleforthesephenomena.MB&B601b,PrinciplesofBiochemistryII AcontinuationofMB&B600thatconsidersthechemistryandmetabolismofnucleicacids,themechanismandregulationofproteinandnucleicacidsynthesis,andselectedtopicsinmacromolecularbiochemistry.MB&B602a/CBIO602a/MCDB602a,MolecularCellBiology Acomprehensiveintroductiontothemolecularandmechanisticaspectsofcellbiologyforgraduatestudentsinallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.Prerequisites:none,butsomeknowledgeofbasiccellbiologyandbiochemistryisassumed.Studentswhohavenottakencoursesintheseareascanpreparebyreadingrelevantsectionsinbasicmolecularcellbiologytexts.WerecommendPollardetal.,CellBiology(3rded.,2016),Albertsetal.,MolecularBiologyoftheCell(6thed.,2014),orLodishetal.,MolecularCellBiology(8thedition,2016).MB&B625a/GENE625a/MCDB625a,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapersillustratingtheverybestofgeneticanalysisanddissectthemindetailinthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.MB&B630b/MCDB630b,BiochemicalandBiophysicalApproachesinMolecularandCellularBiology Thiscourseintroducesthetheoryandapplicationofbiochemicalandbiophysicalmethodstostudythestructureandfunctionofbiologicalmacromolecules.Thecourseconsidersthebasicphysicalchemistryrequiredincellularandmolecularbiologybutdoesnotrequireapreviouscourseinphysicalchemistry.Oneclassperweekisalectureintroducingatopic.Thesecondclassisadiscussionofoneortworesearchpapersutilizingthosemethods.DoesnotcountforgraduatecoursecreditforBQBSgraduatestudents.MB&B635a/ENAS518a,QuantitativeApproachesinBiophysicsandBiochemistry Thecourseoffersanintroductiontoquantitativemethodsrelevanttoanalysisandinterpretationofbiophysicalandbiochemicaldata.Topicscoveredincludestatisticaltesting,datapresentation,anderroranalysis;introductiontodynamicalsystems;analysisoflargedatasets;andFourieranalysisinsignal/imageprocessingandmacromolecularstructuralstudies.ThecoursealsoincludesanintroductiontobasicprogrammingskillsanddataanalysisusingMATLAB.RealdatafromresearchgroupsinMB&Bareusedforpractice.Prerequisites:MATH120andMB&B600orequivalents,orpermissionoftheinstructors.MB&B650aand651b,LabRotationforBQBSFirst-YearStudentsRequiredofallfirst-yearBQBSgraduatestudents.Creditforfullyearonly.MB&B675a,SeminarforFirst-YearStudents Requiredofallfirst-yearBQBSgraduatestudents.MB&B676b,ResponsibleConductofResearch Designedforstudentswhoarebeginningtodoscientificresearch.Thecourseseekstodescribesomeofthebasicfeaturesoflifeincontemporaryresearchandsomeofthepersonalandprofessionalissuesthatresearchersencounterintheirwork.Approximatelysixsessions,runinaseminar/discussionformat.Requiredofallfirst-yearBQBSgraduatestudents.MB&B711b/C&MP711b,Practicalcryo-EMWorkshop Thislaboratorycourseprovideshands-ontraininginthepracticalaspectsofmacromolecularstructuredeterminationbycryo-electronmicroscopy(cryo-EM).Topicsincludecryo-EMdatacollection,imagepreparation


andcorrection,single-particlepickingand2-Dclassification,3-Dclassification,refinementandpost-processing,modelbuilding,refinementandevaluation.Thecourseincludestrainingintheuseofcomputerprogramsusedtoperformthesecalculations.Prerequisite:MB&B710/C&MP710. ½CoursecreditMB&B720a,MacromolecularStructureandBiophysicalAnalysis Anin-depthanalysisofmacromolecularstructureanditselucidationusingmodernmethodsofstructuralbiologyandbiochemistry.Topicsincludearchitecturalarrangementsofproteins,RNA,andDNA;practicalmethodsinstructuralanalysis;andanintroductiontodiffractionandNMR.Prerequisites:physicalchemistry(maybetakenconcurrently)andbiochemistry.MB&B730a,MethodsandLogicinMolecularBiology Thecourseexaminesfundamentalconceptsinmolecularbiologythroughintensecriticalanalysisoftheprimaryliterature.Theobjectiveistodevelopprimaryliteraturereadingandcriticalthinkingskills.Requiredofandopenonlytofirst-yeargraduatestudentsinBQBS.MB&B734b/GENE734b/MBIO734b,MolecularBiologyofAnimalViruses Lecturecoursewithemphasisonmechanismsofviralreplication,oncogenictransformation,andvirus-hostcellinteractions.MB&B743b/GENE743b/MCDB743b,AdvancedEukaryoticMolecularBiology Selectedtopicsintranscriptionalcontrol,regulationofchromatinstructure,mRNAprocessing,mRNAstability,RNAinterference,translation,proteindegradation,DNAreplication,DNArepair,site-specificDNArecombination,somatichypermutation.Prerequisite:biochemistryorpermissionoftheinstructor.MB&B749a/GENE749a,MedicalImpactofBasicScience Considerationofexamplesofrecentdiscoveriesinbasicsciencethathaveelucidatedthemolecularoriginsofdiseaseorthathavesuggestednewtherapiesfordisease.Emphasisisplacedonthefundamentalprinciplesonwhichtheseadvancesrely.Readingisfromtheprimaryscientificandmedicalliterature,withemphasisondevelopingtheabilitytoreadthisliteraturecritically.Aimedprimarilyatundergraduates.Prerequisite:biochemistryorpermissionoftheinstructor.MB&B752b/CB&B752b/CPSC752b/MCDB752b,BiomedicalDataScience:MiningandModeling Biomedicaldatascienceencompassestheanalysisofgenesequences,macromolecularstructures,andfunctionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Specifictopicstobecoveredincludesequencealignment,large-scaleprocessing,next-generationsequencingdata,comparativegenomics,phylogenetics,biologicaldatabasedesign,geometricanalysisofproteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffunctionalgenomicsdatasets,andmachine-learningapproachestodataintegration.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MB&B753b,BiomedicalDataScience:Mining Biomedicaldatascienceencompassestheanalysisofgenesequences,macromolecularstructures,andfunctionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Thismoduleofthefull-termcourseMB&B752focusesonthefirstofthesetechniques,datamining.Specifictopicsincludesequencealignment,comparativegenomicsandphylogenetics,biologicaldatabases,microarraynormalization,andmachine-learningapproachestodataintegration.Countsas0.5credittowardMB&Bgraduatecourserequirements.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MB&B754b,BiomedicalDataScience:Modeling Biomedicaldatascienceencompassestheanalysisofgenesequences,macromolecularstructures,andfunctionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Thismoduleofthefull-termcourseMB&B752focusesonthesecondofthesetechniques,simulation.Specifictopicstobecoveredincludegeometricanalysisofproteinstructure,molecular-dynamicssimulation,andbiologicalnetworks.Countsas0.5credittowardMB&Bgraduatecourserequirements.


Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MB&B800a,AdvancedTopicsinMolecularMedicine Theseminar,whichcoverstopicsinthemolecularmechanismsofdisease,illustratestimelyissuesinareassuchasproteinchemistryandenzymology,intermediarymetabolism,nucleicacidbiochemistry,geneexpression,andvirology.M.D.andM.D./Ph.D.studentsonly.Prerequisite:biochemistry(maybetakenconcurrently).


MOLECULAR,CELLULAR,ANDDEVELOPMENTALBIOLOGYhttp://catalog.yale.edu/gsas/degree-granting-departments-programs/molecular-cellular-developmental-biology/#coursestext MCDB321L/NSCI32L,LaboratoryforNeurobiologyIntroductiontotheneurosciences.Projectsincludethestudyofneuronalexcitability,sensorytransduction,CNSfunction,synapticphysiology,andneuroanatomy.MCDB330/CB&B561/MB&B330/NSCI324ModelingBiologicalSystemsIStudyoftheanalyticandcomputationalskillsneededtomodelgeneticnetworksandproteinsignalingpathways.Reviewofbasicbiochemicalconceptsincludingchemicalreactions,ligandbindingtoreceptors,cooperativity,andMichaelis-Mentenenzymekinetics.Deepexplorationofbiologicalsystemsincluding:kineticsofRNAandproteinsynthesisanddegradation;transcriptionactivatorsandrepressors;lyosogeny/lysisswitchoflambdaphageandtherolesofcooperativityandfeedback;networkmotifssuchasfeed-forwardnetworksandhowtheyshaperesponsedynamics;cellsignaling,MAPkinasenetworksandcellfatedecisions;bacterialchemotaxis;andnoiseingeneexpressionandphenotypicvariability.StudentslearntomodelusingMatLabinaseriesofin-classhackathonsthatillustratebiologicalexamplesdiscussedinlectures.MCDB500a/MB&B500a,BiochemistryAnintroductiontothebiochemistryofanimals,plants,andmicroorganisms,emphasizingtherelationsofchemicalprinciplesandstructuretotheevolutionandregulationoflivingsystems.MCDB504,ResponsibleConductofResearchThiscoursemeetstheNIHrequirementthatstudentsreceivetrainingintheresponsibleconductofresearchatleasteveryfouryears.Twoninety-minutesessionsforMCDBstudents;additionalsessionsforfourth-yearMCDBstudents.Attendanceistaken,andstudentswhoattendbothsessionsreceiveagradeofSatisfactory.GradedSatisfactory/Unsatisfactory.MCDB517b/ENAS517b/MB&B517b/PHYS517b,MethodsandLogicinInterdisciplinaryResearchThishalf-termIGPPEBclassisintendedtointroducestudentstointegratedapproachestoresearch.Eachsessionisledbyfacultywithcomplementaryexpertiseanddiscussespapersthatusedifferentapproachestothesametopic(forexample,physicalandbiologicalorexperimentandtheory).Countsas0.5credittowardgraduatecourserequirements.RequiredforstudentsinIGPPEB.MCDB530a/IBIO530a/MBIO530a,BiologyoftheImmuneSystemThedevelopmentoftheimmunesystem.Cellularandmolecularmechanismsofimmunerecognition.Effectorresponsesagainstpathogens.Immunologicmemoryandvaccines.Humandiseasesincludingallergy,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.Organsofthedigestivesystemarediscussedfromtheperspectiveofsubstratemetabolismandenergybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.


MCDB560b/C&MP560b/ENAS570b/PHAR560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical,andphysiologicallevels.Studentslearnaboutthedifferentclassesofmolecularmachinesthatmediatemembranetransport,generateelectricalcurrents,orperformmechanicaldisplacement.Emphasisisplacedontherelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocellfunctionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.MCDB562/MCDB361/BENG465/MB&B562/AMTH765/CB&B562/INP562/PHYS562/ENAS561ModelingBiologicalSystemsIIThiscoursecoversadvancedtopicsincomputationalbiology.Howdocellscompute,howdotheycountandtelltime,howdotheyoscillateandgeneratespatialpatterns?Topicsincludetime-dependentdynamicsinregulatory,signal-transduction,andneuronalnetworks;fluctuations,growth,andform;mechanicsofcellshapeandmotion;spatiallyheterogeneousprocesses;diffusion.Thisyear,thecoursespendsroughlyhalfitstimeonmechanicalsystemsatthecellularandtissuelevel,andhalfonmodelsofneuronsandneuralsystemsincomputationalneuroscience.MCDB570b,BiotechnologyTheprinciplesandapplicationsofcellular,molecular,andchemicaltechniquesthatadvancebiotechnology.Topicsincludethemostrecenttoolsandstrategiesusedbygovernmentagencies,industriallabs,andacademicresearchtoadaptbiologicalandchemicalcompoundsasmedicaltreatments,asindustrialagents,orforthefurtherstudyofbiologicalsystems.MCDB585b,ResearchinMCDBforB.S./M.S.CandidatesAtwo-creditcoursetakeninthethird-to-lastterm(typicallythesecondtermofthejunioryear).Atthestartofthiscourse,eachstudentformsacommitteecomposedofhisorheradviserandtwofacultymembersthatmeetstodiscusstheresearchproject.Attheendofthiscourse,studentscompleteadetailedprospectusdescribingtheirthesisprojectandtheworkcompletedthusfar.Thecommitteeevaluatesanoralandwrittenpresentationofthisprospectus;theevaluationdetermineswhetherthestudentmaycontinueinthecombinedprogram.RequiredofstudentsinthejointB.S./M.S.programwithYaleCollege.MCDB591b/ENAS991b/MB&B591b/PHYS991b,IntegratedWorkshopThisrequiredcourseforstudentsinPEBinvolveshands-onlaboratorymoduleswithstudentsworkinginpairs.Abiologystudentispairedwithaphysicsorengineeringstudent;acomputation/theorystudentispairedwithanexperimentalstudent.Themodulesaredevisedsothatarangeofskillsisacquired,andstudentslearnfromeachother.Modulesarehostedinfacultylaboratories.MCDB595ab,IntensiveResearchinMCDBforB.S./M.S.CandidatesAfour-credit,yearlongcourse(twocreditseachterm)thatissimilartoMCDB495/496andistakenduringthesenioryear.Duringthiscourse,studentsgiveanoralpresentationdescribingtheirwork.Attheendofthecourse,studentsareexpectedtopresenttheirworktothedepartmentintheformofaposterpresentation.Inaddition,studentsareexpectedtogiveanoralthesisdefense,followedbyacomprehensiveexaminationofthethesisconductedbythethesiscommittee.Uponsuccessfulcompletionofthisexamination,aswellasotherrequirements,thestudentisawardedthecombinedB.S./M.S.degree.RequiredofstudentsinthejointB.S./M.S.programwithYaleCollege.MCDB602a/CBIO602a/MB&B602a,MolecularCellBiology


Acomprehensiveintroductiontothemolecularandmechanisticaspectsofcellbiologyforgraduatestudentsinallprograms.Emphasizesfundamentalissuesofcellularorganization,regulation,biogenesis,andfunctionatthemolecularlevel.Prerequisites:none,butsomeknowledgeofbasiccellbiologyandbiochemistryisassumed.Studentswhohavenottakencoursesintheseareascanpreparebyreadingrelevantsectionsinbasicmolecularcellbiologytexts.WerecommendPollardetal.,CellBiology(3rded.,2016),Albertsetal.,MolecularBiologyoftheCell(6thed.,2014),orLodishetal.,MolecularCellBiology(8thedition,2016).MCDB603a/CBIO603a,SeminarinMolecularCellBiologyAgraduate-levelseminarcourseinmoderncellbiology.Theclassisdevotedtothereadingandcriticalevaluationofclassicalandcurrentpapers.ThetopicsarecoordinatedwiththeMCDB602alectureschedule.Thus,concurrentenrollmentinMCDB602aisrequired.MCDB625a/GENE625a/MB&B625aU,BasicConceptsofGeneticAnalysisTheuniversalprinciplesofgeneticanalysisineukaryotesarediscussedinlectures.Studentsalsoreadasmallselectionofprimarypapersillustratingtheverybestofgeneticanalysisanddissectthemindetailinthediscussionsections.WhileotherYalegraduatemoleculargeneticscoursesemphasizemolecularbiology,thiscoursefocusesontheconceptsandlogicunderlyingmoderngeneticanalysis.MCDB630b/MB&B630b,BiochemicalandBiophysicalApproachesinMolecularandCellularBiologyThiscourseintroducesthetheoryandapplicationofbiochemicalandbiophysicalmethodstostudythestructureandfunctionofbiologicalmacromolecules.Thecourseconsidersthebasicphysicalchemistryrequiredincellularandmolecularbiologybutdoesnotrequireapreviouscourseinphysicalchemistry.Oneclassperweekisalectureintroducingatopic.Thesecondclassisadiscussionofoneortworesearchpapersutilizingthosemethods.DoesnotcountforgraduatecoursecreditforBBSBgraduatestudents.MCDB650EpigeneticsStudyofepigeneticstatesandthevariousmechanismsofepigeneticregulation,includinghistonemodification,DNAmethylation,nuclearorganization,andregulationbynoncodingRNAs.Detailedcritiqueofpapersfromprimaryliteratureanddiscussionofnoveltechnologies,withspecificattentiontotheroleofepigeneticsindevelopmentanditsimpactonhumanhealth.MCDB670,AdvancedSeminarinBiochemistryandGeneticsThisseminarisdesignedtoexpandstudents’abilitiestocriticallyreadandevaluatetheprimaryscientificliteraturerelevanttosomeofthemostactiveareasofbiochemicalandgeneticresearch.Specialemphasisisplacedontopicsthatdealwithrecentdiscoveriesinnucleicacids,suchascatalyticRNAandDNA,functionsofnoncodingRNA,generegulationbyRNA,andgenomicprocessingandinstability.Studentsreadassignedpapersinadvance.Discussionfocusesonexperimentaldesignusedbytheauthors,resultsoftheexperiments,andconclusionsdrawnbytheauthors.MCDB677b/GENE777b,MechanismsofDevelopmentAnadvancedcourseonmechanismsofanimaldevelopmentfocusingonthegeneticspecificationofcellorganizationandidentityduringembryogenesisandsomaticdifferentiation.Theuseofevolutionarilyconservedsignalingpathwaystocarryoutdevelopmentaldecisionsinarangeofanimalsishighlighted.Courseworkincludesstudentparticipationincriticalanalysisofprimaryliteratureandaresearchproposaltermpaper.MCDB680a,AdvancesinPlantMolecularBiology Thestudyofbasicprocessesinplantgrowthanddevelopmenttoprovideafoundationforaddressingcriticalagriculturalneedsinresponsetoachangingclimate.Topicsincludethelatestbreakthroughsinplantscienceswithemphasisonmolecular,cellular,anddevelopmentalbiology;bioticandabioticplantinteractions;development,genomics,proteomics,epigenetics,andchemicalbiologyinthecontextofplantbiology;andthecurrentsocietaldebatesaboutagrobiotechnology.


MCDB720a/INP720a,NeurobiologyExaminationoftheexcitabilityofthenervecellmembraneasastartingpointforthestudyofmolecular,cellular,andintercellularmechanismsunderlyingthegenerationandcontrolofbehavior.MCDB743b/GENE743b/MB&B743bu,AdvancedEukaryoticMolecularBiologySelectedtopicsintranscriptionalcontrol,regulationofchromatinstructure,mRNAprocessing,mRNAstability,RNAinterference,translation,proteindegradation,DNAreplication,DNArepair,site-specificDNArecombination,somatichypermutation.Prerequisite:biochemistryorpermissionoftheinstructor.MCDB752b/MB&B752b/CBB752b/CPSC752b,BiomedicalDataScience:MiningandModelingBiomedicaldatascienceencompassestheanalysisofgenesequences,macromolecularstructures,andfunctionalgenomicsdataonalargescale.Itrepresentsamajorpracticalapplicationformoderntechniquesindataminingandsimulation.Specifictopicstobecoveredincludesequencealignment,large-scaleprocessing,next-generationsequencingdata,comparativegenomics,phylogenetics,biologicaldatabasedesign,geometricanalysisofproteinstructure,molecular-dynamicssimulation,biologicalnetworks,normalizationofmicroarraydata,miningoffunctionalgenomicsdatasets,andmachine-learningapproachestodataintegration.Prerequisites:biochemistryandcalculus,orpermissionoftheinstructor.MCDB900a/CBIO900a/GENE900a,First-YearIntroductiontoResearch–GrantWritingScientificCommunicationGrantwriting,scientificcommunication,andlaboratoryrotationtalksforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB901/CBIO901/GENE901ResearchSkillsandEthicsIIThiscourseconsistsofaweeklyseminarthatcoversethics,writing,andresearchmethodsincellularandmolecularbiologyaswellasstudentpresentations(“rotationtalks”)ofworkcompletedinthethirdlaboratoryrotation.MCDB902&MCDB903AdvancedGraduateSeminarThecourseallowsstudentstohonetheirpresentationskillsthroughyearlypresentationoftheirdissertationwork.Twostudentseachgivethirty-minutepresentationsineachclasssession.StudentsarerequiredtopresenteveryyearbeginningintheirthirdyearintheMCDBprogram.EachMCDBgraduatestudentisexpectedtoattendatleast80percentoftheclasssessions.Twofacultymembersco-directthecourse,attendtheseminars,andprovidefeedbacktothestudents.MCDB911a/CBIO911a/GENE911a,FirstLaboratoryRotationFirstlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB912a/CBIO912a/GENE912a,SecondLaboratoryRotationSecondlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB913b/CBIO913b/GENE913b,ThirdLaboratoryRotationThirdlaboratoryrotationforMolecularCellBiology,Genetics,andDevelopmenttrackstudents.MCDB950aand951b,Second-YearResearchByarrangementwithfaculty.


PHARMACOLOGY http://medicine.yale.edu/pharm/graduate/courses.aspxPHAR502a/C&MP630a/PATH680a,SeminarinMolecularMedicine,Pharmacology,andPhysiologyReadingsanddiscussiononadiverserangeofcurrenttopicsinmolecularmedicine,pharmacology,andphysiology.Theclassemphasizesanalysisofprimaryresearchliteratureanddevelopmentofpresentationandwritingskills.Contemporaryarticlesareassignedonarelatedtopiceveryweek,andastudentleadsdiscussionswithinputfromfacultywhoareexpertsinthetopicarea.Theoverallgoalistocoveraspecifictopicofmedicalrelevance(e.g.,cancer,neurodegeneration)fromtheperspectiveofthreeprimarydisciplines(i.e.,physiology:normalfunction;pathology:abnormalfunction;andpharmacology:intervention).PHAR504a,MolecularMechanismsofDrugActionsThiscoursecoversthemolecularmechanismsoftherapeutics,whicharepresentedinaconceptualframeworktoincreaseunderstandingbutdecreasememorization.Topicsinclude(butarenotlimitedto)receptoraffinity,efficacy,multipleequilibria,pharmacokinetics,andtoxicity;enzymekineticsandinhibition,drugdiscoveryanddesign;molecularbasisofantimicrobialtherapy,cardiologydrugs,anticancerandantiviraltherapies;andtherapeuticsforinflammatorydisorders,asthma,andallergy.PHAR506aandb,MethodsinPharmacologicalResearch(Rotations) Studentsworkinlaboratoriesoffacultyoftheirchoice.Theperiodspentineachlaboratoryisoneterm.PHAR528b,PrinciplesofSignalTransductionTheregulationofintracellularsignalingisoffundamentalimportancetotheunderstandingofcellfunctionandregulation.Thiscourseintroducesthebroadprinciplesofintracellularsignaltransduction.Moredetailedlecturesonspecificintracellularsignalingpathwaysaregiveninwhichstudentslearnboththebasicandmostrecentandcutting-edgeconceptsofintracellularsignaling.Topicsincluderegulationofsignalingbyproteinphosphorylation,smallGproteins,G-protein-coupledreceptors,hormones,phospholipids,adhesion,andgasses.PHAR529b,StructuralBiologyandDrugDiscoveryThegoalofthecourseistoshowstudentshowconceptsofstructuralbiologyareappliedtoareasofgreatimportanceinpharmacologysuchasproteinkinases,proteases,cellsurfacereceptors,integrinsandothermembrane-boundenzymes,andtransportersandchannels,andhowtheseconceptsfacilitatedrugdevelopment.PHAR531b,ConceptsofStructuralBiologyandDrugDiscoveryThis0.5-creditcoursecoversthefirsthalfofthePHAR529bcourseandendsafterthe2ndexam.PHAR530b,TargetedUseofStructuralBiologyinDrugDiscoveryThis0.5-creditcoursebeginsinFebruary,joiningPHAR529b.PHAR537b,SystemsPharmacologyandIntegratedTherapeuticsThegoalofthiscourseistoprovideanin-depth,“hands-on”experienceindrugdesign,drugdiscovery,high-throughputscreening,state-of-the-artproteomics,andtargetvalidation.RequiredcourseforstudentsinthePharmacologyTrainingProgram.PHAR550a/C&MP550a/ENAS550a/MCDB550a,PhysiologicalSystemsThecoursedevelopsafoundationinhumanphysiologybyexaminingthehomeostasisofvitalparameterswithinthebody,andthebiophysicalpropertiesofcells,tissues,andorgans.Basicconceptsincellandmembranephysiologyaresynthesizedthroughexploringthefunctionofskeletal,smooth,andcardiacmuscle.Thephysicalbasisofbloodflow,mechanismsofvascularexchange,cardiacperformance,andregulationofoverallcirculatoryfunctionarediscussed.Respiratoryphysiologyexploresthemechanicsofventilation,gasdiffusion,andacid-basebalance.Renalphysiologyexaminestheformationandcompositionofurineandtheregulationofelectrolyte,fluid,andacid-basebalance.Organsofthedigestivesystemarediscussedfromtheperspectiveofsubstratemetabolism


andenergybalance.Hormonalregulationisappliedtometaboliccontrolandtocalcium,water,andelectrolytebalance.Thebiologyofnervecellsisaddressedwithemphasisonsynaptictransmissionandsimpleneuronalcircuitswithinthecentralnervoussystem.Thespecialsensesareconsideredintheframeworkofsensorytransduction.Weeklydiscussionsectionsprovideaforumforin-depthexplorationoftopics.Graduatestudentsevaluateresearchfindingsthroughliteraturereviewandweeklymeetingswiththeinstructor.PHAR560b/C&MP560b/ENAS570b/MCDB560b,CellularandMolecularPhysiology:MolecularMachinesinHumanDiseaseThecoursefocusesonunderstandingtheprocessesthattransfermoleculesacrossmembranesatthecellular,molecular,biophysical,andphysiologicallevels.Studentslearnaboutthedifferentclassesofmolecularmachinesthatmediatemembranetransport,generateelectricalcurrents,orperformmechanicaldisplacement.Emphasisisplacedontherelationshipbetweenthemolecularstructuresofmembraneproteinsandtheirindividualfunctions.Theinteractionsamongtransportproteinsindeterminingthephysiologicalbehaviorsofcellsandtissuesarealsostressed.Molecularmotorsareintroducedandtheirmechanicalrelationshiptocellfunctionisexplored.Studentsreadpapersfromthescientificliteraturethatestablishtheconnectionsbetweenmutationsingenesencodingmembraneproteinsandawidevarietyofhumangeneticdiseases.PHAR580/C&MP650/PATH660,ResponsibleConductofResearch(RCR)Organizedtofosterdiscussion,thecourseistaughtbyfacultyinthePharmacology,Pathology,andPhysiologydepartmentsandtwoorthreeseniorgraduatestudents.Eachsessionisbasedoncasestudiesfromprimaryliterature,reviews,andtwotexts:FrancisMacrina’sScientificIntegrityandKathyBarker’sAttheBench.Eachweek,studentsarerequiredtosubmitareactionpaperdiscussingthereadingassignment.Studentstaketurnsleadingtheclassdiscussion;afinalshortpaperonahottopicinbioethicsisrequired.

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BBS COURSE GUIDE - Yale School of Medicine 2019... · 2019-09-28 · CBIO 655a/GENE 655a, Stem Cells: Biology and Application This course is designed for first-year or second-year