Preprints

Local genetic adaptation to habitat in wild chimpanzees.

Ostridge HJ^, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM^. bioRxiv. 2024. doi: 10.1101/2024.07.09.601734 [Dennis lab analysis on zenodo]

m6A-mRNA reader YTHDF2 identified as a potential risk gene in autism with disproportionate megalencephaly.

Nishizaki SS, Haghani NK, La GN, Mariano NAF, Uribe-Salazar JM, Kaya G, Regester M, Andrews GS, Nordahl CW, Amaral DG, Dennis MY^. medRxiv. 2024. doi: 10.1101/2022.12.21.22283275v2

Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development.

Uribe-Salazar JM, Kaya G, Weyenberg KB, Radke B, Hino K, Soto DC, Shiu J, Wenzhu Z, Ingamells C, Haghani NK, Xu E, Rosas J, Simó S, Miesfeld J, Glaser T, Baraban SC, Jao L, Dennis MY^. bioRxiv. 2024. doi: 10.1101/2024.09.11.612570

Gene expansions contributing to human brain evolution.

Soto DC*, Uribe-Salazar JM*, Kaya G, Valdarrago R, Sekar A, Haghani NK, Hino K, La GN, Mariano NAF, Ingamells C, Baraban AE, Turner TN, Green ED, Simó S, Quon G, Andrés AM, Dennis MY^. bioRxiv. 2024. doi: 10.1101/2024.09.26.615256v1

2024

Deciphering the role of structural variation in human evolution: A functional perspective.

Karageorgiou C, Gokcumen O, Dennis MY^. Curr Opin Genet Dev. Review. doi: 10.1016/j.gde.2024.102240

Pluripotency of a founding field: rebranding developmental biology.

Rogers CD^, Amemiya C, Arur S, Babonis L, Barresi M, Bartlett M, Behringer R, Benham-Pyle B, Bergmann D, Blackman B, Brown CT, Browne B, Camacho J, Chabu CY, Chow I, Cleaver O, Cool J, Dennis MY, Dickinson AJ, Di Talia S, Frank M, Gillmor S, Haag ES, Hariharan I, Harland R, Husbands A, Jerome-Majewska L, Koenig K, Labonne C, Layden M, Lowe C, Mani M, Martik M, McKown K, Moens C, Mosimann C, Onyenedum J, Reed R, Rivera A, Rokhsar D, Royer L, Rutaganira F, Shahan R, Sinha N, Swalla B, Van Norman JM, Wagner DE, Wikramanayake A, Zebell S, Brady SM^. Development. Perspective. doi: 10.1242/dev.202342

Transforming our understanding of species-specific gene regulation.

Dennis MY^. Cell Genomics. Preview. doi: 10.1016/j.xgen.2024.100540 [Original Research Article from Hodges and Capra labs]

2023

LRRC37B is a human modifier of voltage-gated sodium channels and axon excitability in cortical neurons.

Libé-Philippot B, Lejeune A, Wierda K, Louros N, Erkol E, Vlaeminck I, Beckers S, Gaspariunaite V, Bilheu A, Konstantoulea K, Nyitrai H, De Vleeschouwer M, Vennekens KM, Vidal N, Bird TW, Soto DC, Jaspers T, Dewilde M, Dennis MY, Rosseau F, Comoletti D, Schymkowitz J, Theys T, de Wit J, Vanderhaeghen P^. Cell. doi: 10.1016/j.cell.2023.11.028

Translational Neuroscience Approaches to Understanding Autism.

Veenstra-VanderWeele J, O'Reilly KC, Dennis MY, Uribe-Salazar JM, Amaral DG. Am J Psychiatry. Review. doi: 10.1176/appi.ajp.20230153

FixItFelix: improving genomic analysis by fixing reference errors.

Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM^, Sedlazeck FJ^. Genome Biology. 2023. doi: 10.1101/2022.07.18.500506

Genomic structural variation: A complex but important driver of human evolution.

Soto DC*, Uribe-Salazar JM*, Shew CJ*, Sekar A, McGinty SP, Dennis MY^. Am J Biol Anthropol. Review. doi: 10.1002/ajpa.24713

2022

Effects of pairing on color change and central gene expression in lined seahorses.

Mederos SL, Duarte RC, Mastoras M, Dennis MY, Settles ML, Lau AR, Scott A, Woodward K, Johnson C, Seelke AH, Bales KL^. Genes Brain Behav. doi: 10.1111/gbb.12812

A complete reference genome improves analysis of human genetic variation.

Aganezov S*, Yan SM*, Soto DC*, Kirsche M*, Zarate S*, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC^, Dennis MY^, Zook JM^, Schatz MC^. Science. doi: 10.1126/science.abl3533 [Dennis lab analysis on github]

Complete genomic and epigenetic maps of human centromeres.

Altemose N, Logsdon GA*, Bzikadze AV*, Sidhwani P*, Langley SA*, Caldas GV*, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA^, Miga KH^. Science. doi: 10.1126/science.abl4178

The complete sequence of a human genome.

Nurk S*, Koren S*, Rhie A*, Rautiainen M*, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE^, Miga KH^, Phillippy AM^. Science. doi: 10.1126/science.abj6987 [Telomere-to-Telomere Consortium github][UCSC Genome Browser CHM13 hub] [Our T2T Commentary in Genome Research]

Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism.

Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, Dennis MY, Benke KS, Bakulski KM, Dou J, Marathe R, Jianu JM, Williams LA, Gutierrez Fugón OJ, Walker CK, Ozonoff S, Daniels J, Grosvenor LP, Volk HE, Feinberg JI, Fallin MD, Hertz-Picciotto I, Schmidt RJ, Yasui DH, LaSalle JM^. Genome Biol. doi: 10.1186/s13059-022-02613-1

Evaluation of CRISPR gene-editing tools in zebrafish.

Uribe-Salazar JM, Kaya G, Sekar A, Weyenberg KB, Ingamells C, Dennis MY^. BMC Genomics. doi: 10.1186/s12864-021-08238-1 [Data available at ENA]

2021

RapID Cell Counter: Semi-automated and mid-throughput estimation of cell density within diverse cortical layers.

Sekar A*, Sanches T*, Hino K, Kumar M, Wang J, Ha E, Durbin-Johnson B, Simo S^, Dennis MY^. eNeuro. doi: 10.1523/ENEURO.0185-21.2021 [RapID on github]

Diverse molecular mechanisms contribute to differential expression of human duplicated genes.

Shew CJ, Carmona-Mora P, Soto DC, Mastoras M, Roberts E, Rosas J, Jagannathan D, Kaya G, O’Geen H, Dennis MY^. Mol Biol Evol. doi: 10.1093/molbev/msab131 [ChIP-seq data analysis snakemake] [UCSC track hub] [Data available at ENA]

2020

Assessment of autism zebrafish mutant models using a high-throughput larval phenotyping platform.

Colón-Rodríguez A, Uribe-Salazar JM, Weyenberg KB, Sriram A, Quezada A, Kaya G, Jao E, Radke B, Lein PJ, Dennis MY^. Front Cell Dev Biol: Zebrafish Models for Human Disease Studies. doi: 10.3389/fcell.2020.586296 [Data available on github][Data available on ENA]

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.

Maggiolini FAM, Sanders AD, Shew CJ, Sulovari A, Mao Y, Puig M, Catacchio CR, Dellino M, Palmisano D, Mercuri L, Bitonto M, Porubský D, Cáceres M, Eichler EE, Ventura M, Dennis MY, Korbel JO, Antonacci F^. Genome Res. doi: 10.1101/gr.265322.120 [Rhesus Hi-C data available at ENA]

Telomere-to-telomere assembly of a complete human X chromosome.

Miga KH*^, Koren S*, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Lindsay TAG, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM^. Nature. doi: 10.1038/s41586-020-2547-7

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.

Soto DC*, Shew C*, Mastoras M, Schmidt JM, Sahasrabudhe R, Kaya G, Andrés AM, Dennis MY^. Genes (Basel). doi: 10.3390/genes11030276 [Data available on github][Data available at ENA]

2018

Psychedelics Promote Structural and Functional Neural Plasticity.

Ly C, Greb AC,Cameron LP, Wong JM, Barragan EV, Wilson PC, Burbach KF, Zarandi SS, Sood A, Paddy MR, Duim WC, Dennis MY, McAllister AK, Ori-McKenney KM, Gray JA, Olson DE^. Cell Reports. doi: 10.1016/j.celrep.2018.05.022

Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.

Key FM, Abdul-Aziz MA, Mundry R, Peter B, Sekar A, Amato MD, Dennis MY, Schmidt JM, Andres AM^. PLOS Genet. doi: 10.1371/journal.pgen.1007298

2017

The birth of a human-specific neural gene by incomplete duplication and gene fusion.

Dougherty ML*, Nuttle X*, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE^. Genome Biology. doi: 10.1186/s13059-017-1163-9

The evolution and population diversity of human-specific segmental duplications.

Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HA, Nuttle X, Hoekzema K, Graves TA, Wilson RK, Eichler EE^. Nat Ecol Evol. doi: 10.1038/s41559-016-0069 [Supplementary Information] [Supplementary Tables] [Supplementary Data][1KG data available at NCBI]

2016

Human adaptation and evolution by segmental duplication.

Dennis MY and Eichler EE^. Curr Opin Genet Dev. Review. doi: 10.1016/j.gde.2016.08.001

2011-2015

Epigenetics of autism-related impairment: Copy number variation and maternal infection.

Mazina V, Gerdts J, Ankenman K, Ward T, Dennis MY, Girirajan S, Eichler EE^, and Bernier R^. JDBP 2015. doi: 10.1097/DBP.0000000000000126

Resolving the complexity of the human genome using single-molecule sequencing.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin J, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE^. Nature 2015. doi: 10.1038/nature13907

Palindromic GOLGA8 core duplicons promote 15q13.3 microdeletion and evolutionary instability.

Antonacci F*, Dennis MY*, Huddleston J, Sudmant PH, Meltz Steinberg K, Graves TA, Vives L, Malig M, Denman L, Baker C, Amemiya CT, Stuart A, Tang J, Muson B, Rosenfeld JA, Shaffer LG, Wilson RK, and Eichler EE^. Nat Genet. 2014. doi: 10.1038/ng.3120

Selection on a variant associated with improved viral clearance induced local, adaptive pseudogenization of interferon lambda 4 (IFNL4).

Key FM, Peter B, Dennis MY, Huerta-Sanchez E, Tang W, Nielsen R, Prokunina-Olsson L, and Andres AM^. PLOS Genet. 2014. doi: 10.1371/journal.pgen.1004681

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston JH, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, and Eichler EE^. Genome Res. 2014. doi: 10.1101/gr.168450.113

Refinement and discovery of new hotspots of copy number variation associated with autism spectrum disorder.

Girirajan S*, Dennis MY*, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, and Eichler EE^. AJHG 2013. doi: 10.1016/j.ajhg.2012.12.016

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication.

Dennis MY*, Nuttle X*, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, and Eichler EE^. Cell 2012. doi: 10.1016/j.cell.2012.03.033 [Preview in Cell] [Research Highlight in Nature] [Research Highlight in Nature Review Genetics]

Detection of structural variants and indels within exome data.

Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, and Eichler EE^. Nat Methods 2011. doi: 10.1038/nmeth.1810