2024
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Cheng Y, Cai B, Li H, Zhang X, D’Souza G, Shrestha S, Edmonds A, Meyers J, Fischl M, Kassaye S, Anastos K, Cohen M, Aouizerat B, Xu K, Zhao H. HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data. Genome Biology 2024, 25: 273. PMID: 39407252, PMCID: PMC11476968, DOI: 10.1186/s13059-024-03411-7.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociQuantitative trait lociTrait lociMethylation dataFunctional annotation of genetic variantsAnnotation of genetic variantsGenetic variantsBisulfite sequencing dataEffects of genetic variantsBiologically relevant cell typesDNA methylation levelsCell typesFunctional annotationSequence dataComplex traitsMethylation datasetsRelevant cell typesMeQTLsMethylation levelsMethylation regulatorsReal data analysesLociVariantsMethylationDNA
2020
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood J, Ashenberg O, Cerami E, Coffey R, Demir E, Ding L, Esplin E, Ford J, Goecks J, Ghosh S, Gray J, Guinney J, Hanlon S, Hughes S, Hwang E, Iacobuzio-Donahue C, Jané-Valbuena J, Johnson B, Lau K, Lively T, Mazzilli S, Pe’er D, Santagata S, Shalek A, Schapiro D, Snyder M, Sorger P, Spira A, Srivastava S, Tan K, West R, Williams E, Network H, Aberle D, Achilefu S, Ademuyiwa F, Adey A, Aft R, Agarwal R, Aguilar R, Alikarami F, Allaj V, Amos C, Anders R, Angelo M, Anton K, Ashenberg O, Aster J, Babur O, Bahmani A, Balsubramani A, Barrett D, Beane J, Bender D, Bernt K, Berry L, Betts C, Bletz J, Blise K, Boire A, Boland G, Borowsky A, Bosse K, Bott M, Boyden E, Brooks J, Bueno R, Burlingame E, Cai Q, Campbell J, Caravan W, Cerami E, Chaib H, Chan J, Chang Y, Chatterjee D, Chaudhary O, Chen A, Chen B, Chen C, Chen C, Chen F, Chen Y, Chheda M, Chin K, Chiu R, Chu S, Chuaqui R, Chun J, Cisneros L, Coffey R, Colditz G, Cole K, Collins N, Contrepois K, Coussens L, Creason A, Crichton D, Curtis C, Davidsen T, Davies S, de Bruijn I, Dellostritto L, De Marzo A, Demir E, DeNardo D, Diep D, Ding L, Diskin S, Doan X, Drewes J, Dubinett S, Dyer M, Egger J, Eng J, Engelhardt B, Erwin G, Esplin E, Esserman L, Felmeister A, Feiler H, Fields R, Fisher S, Flaherty K, Flournoy J, Ford J, Fortunato A, Frangieh A, Frye J, Fulton R, Galipeau D, Gan S, Gao J, Gao L, Gao P, Gao V, Geiger T, George A, Getz G, Ghosh S, Giannakis M, Gibbs D, Gillanders W, Goecks J, Goedegebuure S, Gould A, Gowers K, Gray J, Greenleaf W, Gresham J, Guerriero J, Guha T, Guimaraes A, Guinney J, Gutman D, Hacohen N, Hanlon S, Hansen C, Harismendy O, Harris K, Hata A, Hayashi A, Heiser C, Helvie K, Herndon J, Hirst G, Hodi F, Hollmann T, Horning A, Hsieh J, Hughes S, Huh W, Hunger S, Hwang S, Iacobuzio-Donahue C, Ijaz H, Izar B, Jacobson C, Janes S, Jané-Valbuena J, Jayasinghe R, Jiang L, Johnson B, Johnson B, Ju T, Kadara H, Kaestner K, Kagan J, Kalinke L, Keith R, Khan A, Kibbe W, Kim A, Kim E, Kim J, Kolodzie A, Kopytra M, Kotler E, Krueger R, Krysan K, Kundaje A, Ladabaum U, Lake B, Lam H, Laquindanum R, Lau K, Laughney A, Lee H, Lenburg M, Leonard C, Leshchiner I, Levy R, Li J, Lian C, Lim K, Lin J, Lin Y, Liu Q, Liu R, Lively T, Longabaugh W, Longacre T, X. C, Macedonia M, Madison T, Maher C, Maitra A, Makinen N, Makowski D, Maley C, Maliga Z, Mallo D, Maris J, Markham N, Marks J, Martinez D, Mashl R, Masilionais I, Mason J, Massagué J, Massion P, Mattar M, Mazurchuk R, Mazutis L, Mazzilli S, McKinley E, McMichael J, Merrick D, Meyerson M, Miessner J, Mills G, Mills M, Mondal S, Mori M, Mori Y, Moses E, Mosse Y, Muhlich J, Murphy G, Navin N, Nawy T, Nederlof M, Ness R, Nevins S, Nikolov M, Nirmal A, Nolan G, Novikov E, Oberdoerffer P, O’Connell B, Offin M, Oh S, Olson A, Ooms A, Ossandon M, Owzar K, Parmar S, Patel T, Patti G, Pe’er D, Pe'er I, Peng T, Persson D, Petty M, Pfister H, Polyak K, Pourfarhangi K, Puram S, Qiu Q, Quintanal-Villalonga Á, Raj A, Ramirez-Solano M, Rashid R, Reeb A, Regev A, Reid M, Resnick A, Reynolds S, Riesterer J, Rodig S, Roland J, Rosenfield S, Rotem A, Roy S, Rozenblatt-Rosen O, Rudin C, Ryser M, Santagata S, Santi-Vicini M, Sato K, Schapiro D, Schrag D, Schultz N, Sears C, Sears R, Sen S, Sen T, Shalek A, Sheng J, Sheng Q, Shoghi K, Shrubsole M, Shyr Y, Sibley A, Siex K, Simmons A, Singer D, Sivagnanam S, Slyper M, Snyder M, Sokolov A, Song S, Sorger P, Southard-Smith A, Spira A, Srivastava S, Stein J, Storm P, Stover E, Strand S, Su T, Sudar D, Sullivan R, Surrey L, Suvà M, Tan K, Terekhanova N, Ternes L, Thammavong L, Thibault G, Thomas G, Thorsson V, Todres E, Tran L, Tyler M, Uzun Y, Vachani A, Van Allen E, Vandekar S, Veis D, Vigneau S, Vossough A, Waanders A, Wagle N, Wang L, Wendl M, West R, Williams E, Wu C, Wu H, Wu H, Wyczalkowski M, Xie Y, Yang X, Yapp C, Yu W, Yuan Y, Zhang D, Zhang K, Zhang M, Zhang N, Zhang Y, Zhao Y, Zhou D, Zhou Z, Zhu H, Zhu Q, Zhu X, Zhu Y, Zhuang X. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell 2020, 181: 236-249. PMID: 32302568, PMCID: PMC7376497, DOI: 10.1016/j.cell.2020.03.053.Commentaries, Editorials and LettersConceptsSingle-cell genomic technologiesSingle-cell resolutionDynamic tumor ecosystemRelevant cell typesGenomic approachesCell statesGenomic technologiesTumor ecosystemBulk sequencingThree-dimensional atlasesCancer biologyCell typesCellular interactionsTumor initiationUnprecedented resolutionTumor transitionTherapeutic discoveryDiverse setCancer transitionComplex interactionsPrecision medicine treatmentBiologyCrucial transitionEcosystemsSequencing
2019
In vivo Imaging-Driven Approaches to Study Virus Dissemination and Pathogenesis
Uchil PD, Haugh KA, Pi R, Mothes W. In vivo Imaging-Driven Approaches to Study Virus Dissemination and Pathogenesis. Annual Review Of Virology 2019, 6: 1-24. PMID: 31283440, PMCID: PMC7217087, DOI: 10.1146/annurev-virology-101416-041429.Peer-Reviewed Original Research
2015
Genetic basis of autoimmunity
Marson A, Housley WJ, Hafler DA. Genetic basis of autoimmunity. Journal Of Clinical Investigation 2015, 125: 2234-2241. PMID: 26030227, PMCID: PMC4497748, DOI: 10.1172/jci78086.Peer-Reviewed Original ResearchConceptsGenetic basisInterpretation of GWASMultiple genomic datasetsWide association studyCommon human autoimmune diseasesRelevant cell typesCellular conditionsCellular phenotypesGenomic datasetsGene expressionDense genotypingBiological pathwaysAssociation studiesHuman autoimmune diseasesNucleotide variantsCell typesAutoimmune diseasesPrimary immune cellsUnbiased viewMonogenic mutationsPolygenic risk factorsEssential mechanismComplex disorderEnvironmental factorsNovel diagnosticsIntegrative analysis of 111 reference human epigenomes
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller M, Amin V, Whitaker J, Schultz M, Ward L, Sarkar A, Quon G, Sandstrom R, Eaton M, Wu Y, Pfenning A, Wang X, ClaussnitzerYaping Liu M, Coarfa C, Alan Harris R, Shoresh N, Epstein C, Gjoneska E, Leung D, Xie W, David Hawkins R, Lister R, Hong C, Gascard P, Mungall A, Moore R, Chuah E, Tam A, Canfield T, Scott Hansen R, Kaul R, Sabo P, Bansal M, Carles A, Dixon J, Farh K, Feizi S, Karlic R, Kim A, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer T, Neph S, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari R, Siebenthall K, Sinnott-Armstrong N, Stevens M, Thurman R, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes M, Bates D, Bell R, Bennett D, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso M, Charnecki T, Chen H, Chen Z, Cheng J, Cho S, Chu A, Chung W, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass I, Gnirke A, Gormley M, Gu H, Gu J, Hafler D, Hangauer M, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson A, Jia H, Jiang P, Johnson A, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee A, Lee K, Li J, Li N, Li Y, Ligon K, Lin S, Lin Y, Liu J, Liu Y, Luckey C, Ma Y, Maire C, Marson A, Mattick J, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukame E, Nagarajan R, Neri F, Nery J, Nguyen T, O’Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson N, Raghuraman S, Raney B, Raubitschek A, Reynolds A, Richards H, Riehle K, Rinaudo P, Robinson J, Rockweiler N, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian S, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won K, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen C, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet A, Boyer L, De Jager P, Farnham P, Fisher S, Haussler D, Jones S, Li W, Marra M, McManus M, Sunyaev S, Thomson J, Tlsty T, Tsai L, Wang W, Waterland R, Zhang M, Chadwick L, Bernstein B, Costello J, Ecker J, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos J, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 2015, 518: 317-330. PMID: 25693563, PMCID: PMC4530010, DOI: 10.1038/nature14248.Peer-Reviewed Original ResearchConceptsHuman epigenomeHuman diseasesIntegrative analysisReference human genome sequenceDiverse human traitsRoadmap Epigenomics ConsortiumHuman genome sequenceHistone modification patternsRelevant cell typesEpigenomic informationEpigenomic marksDNA accessibilityRegulatory modulesGene regulationEpigenomic studiesGenome sequenceDNA methylationGenetic variationRegulatory elementsCellular differentiationMolecular basisModification patternsEpigenomeHuman traitsCell types
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