Li C, Bonder MJ, Syed S, Jensen M; Human Genome Structural Variation Consortium (HGSVC); HGSVC Functional Analysis Working Group; Gerstein MB, Zody MC, Chaisson MJP, Talkowski ME, Marschall T, Korbel JO, Eichler EE, Lee C, Shi X. (2024). An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Res Dec 23;34(12):2304-2318.
Blog Archives
Identification and annotation of centromeric hypomethylated regions with CDR-Finder
Mastrorosa FK, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA. (2024). Identification and annotation of centromeric hypomethylated regions with CDR-Finder. Bioinformatics Nov 28;40(12):btae733. doi: 10.1093/bioinformatics/btae733.
Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. (2024). Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans. Genome Res Nov 20;34(11):1798-1810.
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves CE, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal C, Zakarian C, Goodwin S, Jensen TD, Robb E; 1000 Genomes ONT Sequencing Consortium; University of Washington Center for Rare Disease Research (UW-CRDR); Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. (2024). High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res Nov 20;34(11):2061-2073.
Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling
Duan W, Huang G, Sui Y, Wang K, Yu Y, Chu X, Cao X, Chen L, Liu J, Eichler EE, Xiong B. (2024). Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling. Proc Natl Acad Sci U S A Nov 5;121(45):e2404173121. doi: 10.1073/pnas.2404173121. Epub 2024 Oct 29.
3-hour genome sequencing and targeted analysis to rapidly assess genetic risk
Zalusky MP, Gustafson JA, Bohaczuk SC, Mallory B, Reed P, Wenger T, Beckman E, Chang IJ, Paschal CR, Buchan JG, Lockwood CM, Puia-Dumitrescu M, Garalde DR, Guillory J, Markham AJ, Bamshad MJ, Eichler EE, Stergachis AB, Miller DE. (2024). 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. Genet Med 2024;2:101833. doi: 10.1016/j.gimo.2024.101833. Epub 2024 Feb 24.
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Henglin M, Ghareghani M, Harvey WT, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. (2024). Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing. Genome Biol Oct 10;25(1):265.
AGAP duplicons associate with structural diversity at Chromosome 10q11.22
Fornezza S, Delvecchio VS, Harvey WT, Dishuck PC, Eichler EE, Giannuzzi G. (2024). AGAP duplicons associate with structural diversity at Chromosome 10q11.22. Genome Res Oct 29;34(10):1487–1499.
Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B
Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. (2024). Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. Am J Hum Genet Aug 8;111(8):1700-1716.
The complete sequence and comparative analysis of ape sex chromosomes
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler EE, Phillippy AM. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature Jun;630(8016):401-411.
Embryonic origin of two ASD subtypes of social symptom severity: the larger the brain cortical organoid size, the more severe the social symptoms
Courchesne E, Taluja V, Nazari S, Aamodt CM, Pierce K, Duan K, Stophaeros S, Lopez L, Barnes CC, Troxel J, Campbell K, Wang T, Hoekzema K, Eichler EE, Nani JV, Pontes W, Sanchez SS, Lombardo MV, de Souza JS, Hayashi MAF, Muotri AR. (2024). Embryonic origin of two ASD subtypes of social symptom severity: the larger the brain cortical organoid size, the more severe the social symptoms. Mol Autism May 25;15(1):22.

