Wen-Wei Liao, PhD
Postdoctoral AssociateCards
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Research
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Featured Publications
A draft human pangenome reference
Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Sirén J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Garrison N, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson N, Popejoy A, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Smith M, Sofia H, Abou Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Walenz B, Wood J, Zimin A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Wang T, Jarvis E, Miga K, Garrison E, Marschall T, Hall I, Li H, Paten B. A draft human pangenome reference. Nature 2023, 617: 312-324. PMID: 37165242, PMCID: PMC10172123, DOI: 10.1038/s41586-023-05896-x.Peer-Reviewed Original Research
2025
Highly accurate assembly polishing with DeepPolisher
Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook D, Nattestad M, Lucas J, Won T, Chang P, Carroll A, Paten B, Shafin K, Consortium A, Tayoun A, Albracht D, Allen J, Alsheikh-Ali A, Andrews C, Antipov D, Antonacci-Fulton L, Asri M, Ayllon M, Balacco J, Belter E, Bender H, Blair A, Buonaiuto S, Bolognini D, Bonini K, Boucher C, Bourque G, Cao S, Carroll A, Mc Cartney A, Cechova M, Chang P, Chang X, Cheema J, Cheng H, Ciofi C, Cody S, Colonna V, Conwell H, Cook-Deegan R, Diekhans M, Diroma M, Doerr D, Dong Z, Durbin R, Ebler J, Eichler E, Eizenga J, Eskandar P, Ferro E, Fiston-Lavier A, Ford S, Ford W, Formenti G, Frankish A, Freeberg M, Fu Q, Fullerton S, Fulton R, Gao Y, Garcia G, Garcia O, Gardner J, Garg S, Garrison E, Garrison N, Garza J, Ghorbani M, Graves-Lindsay T, Green R, Groza C, Guarracino A, Gymrek M, Haggerty L, Hall I, Hansen N, Hashmi M, Haeussler M, Haussler D, Hebbar P, Heringer P, Hickey G, Hillaker T, Hossain S, Huang N, Hunt S, Hunt T, Jafarzadeh N, Jain N, Jarvis E, Jiang J, LoTempio J, Kenny E, Kim J, Koo B, Koren S, Kremitzki M, Langmead B, Zhuo X, Lawson H, Li D, Li H, Liao W, Lin J, Liu T, Logsdon G, Lorig-Roach R, Loucks H, Loveland J, Lu J, Lu S, Lucas J, Macias-Velasco J, Marin M, Marsico F, Makova K, Markovic C, Marschall T, Martin F, Mastoras M, Mayoud C, McNulty B, Medico J, Menendez J, Miga K, Minkina A, Mitchell M, Mohanty S, Mokrab Y, Monlong J, Moosa S, Moreno-Ochando A, Morishita S, Mudge J, Munson K, Mwaniki N, Nassir N, Natali C, Negi S, Ni L, Novak A, Owa C, Paez S, Paten B, Clawson H, Peano C, Phillippy A, Pickett B, Pignata L, Pisanti N, Porubsky D, Prins P, Radhakrishnan A, Raney B, Rautiainen M, Raveane A, Ren L, Rhie A, Salehi F, Sacco S, Schatz M, Scheinfeldt L, Sehgal A, Seligmann W, Shabani M, Shafin K, Shahatit S, Shemirani R, Shivakumar V, Sinha S, Sirén J, Smeds L, Solar S, Sollitto M, Soranzo N, Stergachis A, Suner M, Suzuki Y, Söylev A, Tierney J, Tomlinson C, Tricomi F, Uddin M, Ungaro M, Varki R, Villani F, Vollger M, Walenz B, Wang C, Wang L, Wang T, Wenger A, Whelan C, Xin Z, Xu Z, Ye K, Yoo D, Zhang W, Zhou Y, Violich I, Zunino G. Highly accurate assembly polishing with DeepPolisher. Genome Research 2025, 35: 1595-1608. PMID: 40389286, PMCID: PMC12212083, DOI: 10.1101/gr.280149.124.Peer-Reviewed Original Research
2024
Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol 2024, 42: 663-673. PMID: 37165083, DOI: 10.1038/s41587-023-01793-w.Peer-Reviewed Original Research
2023
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Lee H, Greer S, Pavlichin D, Zhou B, Urban A, Weissman T, Consortium H, Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kolesnikov A, Korbel J, Kordosky J, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McDaniel J, Mountcastle J, Nattestad M, Olson N, Puiu D, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Wood J, Zimin A, Popejoy A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Jarvis E, Miga K, Wang T, Garrison E, Marschall T, Hall I, Li H, Paten B, Ji H. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell Reports Methods 2023, 3: 100543. PMID: 37671027, PMCID: PMC10475782, DOI: 10.1016/j.crmeth.2023.100543.Peer-Reviewed Original ResearchRecombination between heterologous human acrocentric chromosomes.
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E. Recombination between heterologous human acrocentric chromosomes. Nature 2023, 617: 335-343. PMID: 37165241, DOI: 10.1038/s41586-023-05976-y.Peer-Reviewed Original ResearchIncreased mutation and gene conversion within human segmental duplications.
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Human Pangenome Reference Consortium, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. Increased mutation and gene conversion within human segmental duplications. Nature 2023, 617: 325-334. PMID: 37165237, DOI: 10.1038/s41586-023-05895-y.Peer-Reviewed Original ResearchGaps and complex structurally variant loci in phased genome assemblies
Porubsky D, Vollger M, Harvey W, Rozanski A, Ebert P, Hickey G, Hasenfeld P, Sanders A, Stober C, Consortium H, Korbel J, Paten B, Marschall T, Eichler E, Abel H, Antonacci-Fulton L, Asri M, Baid G, Baker C, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson M, Chang P, Chang X, Cheng H, Chu J, Cody S, Colonna V, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler E, Eizenga J, Fairley S, Fedrigo O, Felsenfeld A, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton R, Gao Y, Garg S, Garrison E, Garrison N, Giron C, Green R, Groza C, Guarracino A, Haggerty L, Hall I, Harvey W, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis E, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Li H, Liao W, Lu S, Lu T, Lucas J, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin F, McCartney A, McDaniel J, Miga K, Mitchell M, Monlong J, Mountcastle J, Munson K, Mwaniki M, Nattestad M, Novak A, Nurk S, Olsen H, Olson N, Paten B, Pesout T, Phillippy A, Popejoy A, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sibbesen J, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tomlinson C, Tricomi F, Villani F, Vollger M, Wagner J, Walenz B, Wang T, Wood J, Zimin A, Zook J. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research 2023, 33: 496-510. PMID: 37164484, PMCID: PMC10234299, DOI: 10.1101/gr.277334.122.Peer-Reviewed Original ResearchConceptsProtein-coding genesGenome assemblyMbp of DNALinked-read dataLarge segmental duplicationsStrand-seqDiversity panelInversion polymorphismHaploid genomeSegmental duplicationsEuchromatic DNAMore haplotypesIdentical repeatsHaploid assembliesVariant lociDNAHaplotypesGenesFrequent expansionAssembly gapsImportant targetAssemblyHuman speciesHuman samplesMBP
2022
The Human Pangenome Project: a global resource to map genomic diversity
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison N, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D. The Human Pangenome Project: a global resource to map genomic diversity. Nature 2022, 604: 437-446. PMID: 35444317, PMCID: PMC9402379, DOI: 10.1038/s41586-022-04601-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHuman reference genomeReference genomeGenomic diversityGenomic variationHuman genomic variationGlobal genomic diversitySingle nucleotide variantsGene-disease associationsDiploid genomeGenetic resourcesGenomeGenomic researchFuture biomedical researchHigh-quality referenceStructural variantsHuman geneticsRoutine assemblyCommon variantsFunctional elementsPolymorphic regionDiversityBiomedical researchVariantsMajor updateGenetics
2018
TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma.
O'Neill K, Liao WW, Patel A, Hammell MG. TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Front Genet 2018, 9: 461. PMID: 30349559, DOI: 10.3389/fgene.2018.00461.Peer-Reviewed Original ResearchPrenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach.
Chen PY, Chu A, Liao WW, Rubbi L, Janzen C, Hsu FM, Thamotharan S, Ganguly A, Lam L, Montoya D, Pellegrini M, Devaskar SU. Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach. Reprod Sci 2018, 25: 523-539. PMID: 28693373, DOI: 10.1177/1933719117716779.Peer-Reviewed Original Research
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