concertedsosos

YuanXue(Soso)Single-celldatascience,biochemistry,machinelearning,BioengineeringPh.
D.
Candidate@Quakelab,Stanfordyuanxue@stanford.
edugithub/xuesosolinkedin/yuan-xuexuesoso.
github.
ioBackgroundstatementIhaveoveradecadelongexperienceinlifesciencesresearch.
Ihaveexpertiseinmostmodernexperimentalandanalyticalmethodsforhigh-throughputmeasurement,dataprocessing,andsystematicanalysis.
Ialsohaveresearchexperienceinproteinchemistry,infectiousmicrobiology,andcellularbiology.
EducationStanfordUniversity-nowPh.
D.
Bioengineering.
Thesisadvisers:StephenQuake,JohnBoothroydStanford,CA,USAStanfordUniversity-M.
S.
BioengineeringStanford,CA,USAUTSouthwesternMedicalCenter-Biophysics(enrolledinPh.
D.
program)Dallas,TX,USAReedCollege-B.
A.
Biology.
Thesisadviser:JayMelliesPortland,OR,USALaSalleCatholicCollegePreparatory-Portland,OR,USADiocesanBoys'School-HongKong,PRCAwards&HonorsStanfordBio-XTravelAwardStanfordBio-XSIGFFellowOneofstudentsawardedwithathree-yearfellowshiptoconductinterdisciplinaryresearchonthetopicsofparasitologyandsingle-cellbioinformaticsco-advisedbyprofessorsJohnBoothroydandStephenQuakeReedCollegeLarryRubenPostbac.
ResearchFellowReedCollegeSummerExperienceAwardeeReedCollegeIndependentResearchAwardeeiGEMCompetitionTeamGoldMedalistProjectsLife-cycleofToxoplasmagondiiandco-transcriptomicanalysisofhostinfection-nowProducedtherstsingle-cellatlasofToxoplasma.
BuiltaninteractivevisualizationwebsitewithApache,Flask,Bokeh.
ComparativeanalysistoPlasmodiumbergheirevealedconcertedgeneticprogramtolife-cycle.
Anovelsingle-cellanalysisalgorithm:self-assemblingmanifolds(SAM)-Single-cellsequencingrevealsnovelgermcellpopulationinaparasiticatworm,Schistosomamansoni.
TemperatureeectonDNApolymerasedelity-CharacterizederrorrateofDNApolymeraseadaptedtoawiderangeoftemperature.
Foundtheirpolymerasedelityisdierentiallysensitivetochangesinreactiontemperature.
Manuscriptcurrentlyinpreparation.
Publications.
PengyangLi,DaniaNanesSarfati,YuanXue,XiYu,AlexanderTarashansky,StephenR.
Quake,JohnBoothroyd.
Single-cellanalysisofSchistosomamansonirevealsaconservedgeneticprogramcontrollinggermlinestemcellfate.
Submitted().
equalcontribution.
SuchitaRastogi,YuanXue,StephenR.
Quake,JohnBoothroyd.
DierentialImpactsonHostTranscriptionbyROPandGRAEectorsfromtheIntracellularParasiteToxoplasmagondii.
Submitted.
AcceptedonmBio().
bioRxivpreprintequalcontribution.
YuanXue,StephenR.
Quake.
TemperatureeectonDNApolymerasedelity.
Inpreparation().
.
YuanXue,TerenceTheisen,SuchiRastogi,AbelFerrel,StephenR.
Quake,JohnBoothroyd.
Asingle-parasitetranscriptionalatlasofToxoplasmagondiirevealsnovelcontrolofantigenexpression.
eLife().
article,bioRxivpreprintequalcontribution.
AlexanderTarashansky,YuanXue,PengyangLi,StephenR.
Quake,BoWang.
Self-assemblingManifoldsinSingle-cellRNASequencingData.
Elife().
article,bioRxivpreprint.
TheTabulaMurisConsortium,StephenR.
Quake,TonyWyss-Coray,SpyrosDarmanis.
Single-celltranscriptomicsofmouseorganscreatesaTabulaMuris.
Nature().
article,bioRxivpreprint.
YuanXue,JossefOsborn,AnandPanchal,JayL.
Mellies.
TheRpoEstressresponsepathwaymediatesreductionofenteropathogenicEscherichiacolivirulencebyzinc.
AppliedandEnvironmentalMicrobiology().
spotlightresearcharticle.
JingZhou,Shi-HaoTan,ValerieNicolas,ChantalBauvy,Nai-DiYang,JianbinZhang,YuanXue,PatriceCodogno,Han-MingShen.
ActivationoflysosomalfunctioninthecourseofautophagyviamTORCsuppressionandautophagosome-lysosomefusion.
CellResearch().
articleTeachingExperienceTAinmicrouidicdevicelaboratory(BioED)@StanfordUniversityTAinintroductiontobioengineering(BioE)@StanfordUniversityTAinmicrobiology@ReedCollegeAcademictutorincellularbiologyandchemistry@ReedCollege-Poster&ConferenceBuildingasingle-cellatlasofToxoplasmainteractomeInvitedspeakeratNationalUniversityofSingaporeYuanXueetal.
Buildingasingle-cellatlasofToxoplasmainteractomeInvitedspeakeratCellSymposiaSingleCells:FromTechnologytoBiologyYuanXueetal.
Single-cellco-transcriptomicmeasurementresolvesparasiticlifecycleandhostinteractionsPosterpresenter@StanfordBioengineeringdepartmentretreatYuanXueetal.
Buildingasingle-cellatlasoftheToxoplasmainteractomeInvitedspeaker@StanfordMicrobiology&ImmunologydepartmentretreatYuanXueetal.
CoolbiochemistrymeasuredwithahottoolPosterpresenter@StanfordBioengineeringdepartmentretreatYuanXue,StephenR.
QuakeTemperatureadaptationandpolymerasedelityPosterpresenter@GordonResearchConference(GRC):NucleicAcidsYuanXue,StephenR.
QuakeSkillsLanguagesEnglish,Cantonese,Mandarin,Japanese,Python,R,C++,Bash,LATEXVisualizationmatplotlib,plotly,seaborn,bokeh,networkX,graphviz,graph-toolMachinelearningnumpy,pandas,sklearn,scikit-learn,tensorow,kerasWorkowssnakemake,cloudcomputing(e.
g.
AWS,Slurm)WebdevelopmentFlask-RESTapi,ApacheBioinformaticsSTARRNAaligner,htseq-count,salmon,velocyto,samtools,cellranger,scanpyExperimentalSmart-seq,X'featurebarcoding,molecularcloning,HPLCproteinpurication,gel-basedassay,FACS,tissueculturing,uorescenceimaging,viraltransfection,high-throughputliquid-handlingMaintainedpackagessingleCell_snakeAsnakemakepipelineforlocal/SlurmsubmissionofsinglecelldataalignmentandtranscriptcountingDensityPlotApythonpackageforgeneratingdensityplotcommonlyseeninFACSanalysisbag_of_velocytoASlurmsubmissionscriptforparallelsubmissionofRNAvelocityalignmentnheatmapAmulti-levelheatmapplottingtoolwiththeoptiontoperformhierarchicalclustering.