2024
Vazquez JM, Lauterbur ME, Mottaghinia S, Bucci M, Fraser D, Gray-Sandoval G, Gaucherand L, Haider ZR, Han M, Kohler W, Lama TM, Lecorf A, Maesen S, McMillan D, Li S, Lo J, Rey C, Capel SLR, Singer M, Slocum K, Thomas W, Tyburec JD, Santos Villa SG, Miller R, Buchalski M, Vazquez-Medina JP, Pfeffer S, Etienne L, Enard D, Sudmant PH. Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats. 2024. bioRxiv - https://doi.org/10.1101/2024.10.10.617725
Bolognini D*, Halgren A*, Lou RN*, Raveane A*, Rocha JL*, Guarracino A, Soranzo N, Chin CS, Garrison E†, Sudmant PH†. Recurrent evolution and selection shape structural diversity at the amylase locus. 2024. Nature - https://doi.org/10.1038/s41586-024-07911-1
Rocha JL, Lou RN, Sudmant PH. Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics. 2024. Curr Op Genetics Devel - https://doi.org/10.1016/j.gde.2024.102233
Swissa E, Monsonego U, Yang LT, Schori L, Kamintsky L, Mirloo S, Burger I, Uzzan S, Patel R, Sudmant PH, Prager O, Kaufer D, Friedman A. Cortical plasticity is associated with blood-brain barrier modulation. 2024. eLife - 39024007
Zhou AT, Owens GL, Larson WA, Lou RN†, Sudmant PH†. loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing. 2024. Bioinform Adv. - 39006965
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. The complete sequence and comparative analysis of ape sex chromosomes. 2024. Nature - 38811727
Allen KN, Torres-Velarde JM, Vazquez JM, Moreno-Santillán DD, Sudmant PH, Vázquez-Medina JP. Hypoxia exposure blunts angiogenic signaling and upregulates the antioxidant system in endothelial cells derived from elephant seals. 2024. BMC Biol - 38654271
Capel SLR, Hamilton NM, Fraser D, Escalona M, Nguyen O, Sacco S, Sahasradubhe R, Seligmann W, Vazquez JM, Sudmant PH, Morrison ML, Wayne RK, Buchalski MR. Reference genome of Townsend's big-eared bat, Corynorhinus townsendii. 2024. J of Heredity - 38092381
Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing. 2024. Nature Ecol & Evol - 38361161
Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. Population genomics of post-glacial western Eurasia. 2024. Nature - 38200295
Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. 2024. Nature - 38200293
Curti NJ, Fraser D, Escalona M, Fairbairn CW, Sacco S, Sahasradubhe R, Nguyen O, Seligmann W, Sudmant PH, Toffelmier E, Vazquez JM, Wayne R, Shaffer HB, Buchalski MR. A genome assembly of the Yuma myotis bat, Myotis yumanensis. 2024. J of Heredity - 37712349
2023
Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. 2023. Trends Genet - https://doi.org/10.1016/j.tig.2023.08.005
Sykes NTB, Kolora SRR, Sudmant PH, Owens GL. Rapid turnover and evolution of sex-determining regions among Sebastes rockfishes. 2023. Mol Ecol - https://doi.org/10.1111/mec.17090
Chin CS, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. 2023. Nat Methods - 37365340
L Rocha J, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, Godinho R. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. 2023. Nat Ecol Evol. - 37308700
Wang CL, Ohkubo R, Mu WC, Chen W, Fan JL, Song Z, Maruichi A, Sudmant PH, Pisco AO, Dubal DB, Ji N, Chen D. The mitochondrial unfolded protein response regulates hippocampal neural stem cell aging. 2023. Cell Metab. - 37146607
Karin BR, Arellano S, Wang L, Walzer K, Pomerantz A, Vasquez JM, Chatla K, Sudmant PH, Bach BH, Smith LL, McGuire JA. Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes. 2023. BMC Genomics - 37131128
Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Moses MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. Building pangenome graphs. 2023. bioRxiv - https://doi.org/10.1101/2023.04.05.535718
Long KP, Muroy SE, Sorooshyari S, Ko MJ, Jaques Y, Sudmant PH, Kaufer D. Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus. 2023. bioRxiv - https://doi.org/10.1101/2023.02.08.527777
2022
Ohkubo R, Mu WC, Wang CL, Song Z, Barthez M, Wang Y, Mitchener N, Abdullayev R, Lee YR, Ma Y, Curtin M, Srinivasan S, Zhang X, Yang F, Sudmant PH, Pisco AO, Neff N, Haynes CM, Chen D. The hepatic integrated stress response suppresses the somatotroph axis to control liver damage in nonalcoholic fatty liver disease. 2022. Cell Rep. - 36516757
Yamamoto R*, Chung R*, Vazquez JM, Sheng H, Steinberg PL, Ioannidis N†, Sudmant PH†. Tissue-specific impacts of aging and genetics on gene expression patterns in humans. 2022. Nature Communications - 36192477
Jin Y, Aguilar-Gómez D, Brandt DYC, Square TA, Li J, Liu Z, Wang T, Sudmant PH, Miller CT, Nielsen R. Population genomics of variegated toad-headed lizard Phrynocephalus versicolor and its adaptation to the colorful sand of the Gobi Desert. 2022. Genome Biol Evol. - 35679302
Sing TL, Conlon K, Lu SH, Madrazo N, Barker JC, Hollerer I, Brar GA, Sudmant PH†, Ünal E†. Comprehensive analysis of meiosis-derived cDNA libraries reveals gene isoforms and mitochondrial proteins important for competitive fitness. 2022. Genetics - 35471663
Xu P, Wang M, Song W, Wang Q, Yuan G, Sudmant PH, Zare H, Tu Z, Orr ME, Zhang B. The landscape of human tissue and cell type specific expression and co-regulation of senescence genes. 2022. Molecular Neurodegeneration - 35000600
2021
Dehkordi SK, Walker J, Sah E, Bennett E, Atrian F, Frost B, Woost B, Bennett RE, Orr TO, Zhou Y, Andhey PS, Colonna M, Sudmant PH, Xu P, Wang M, Zhang B, Zare H, Orr ME. Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. 2021. Nature Aging - 35531351
Kolora SRR*, Owens GL*, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH. Origins and evolution of extreme lifespan in Pacific Ocean rockfishes. 2021. Science - 34762458
- see perspective Long-lived fish in a big pond, also featured on the cover
Torres-Velarde JM, Kolora SRR, Khudyakov JI, Crocker DE, Sudmant PH, Vázquez-Medina JP. Elephant seal muscle cells adapt to sustained glucocorticoid exposure by shifting their metabolic phenotype. 2021. Am J Physiol Regul Integr Comp Physiol . - 34260302
2020
Sacramento E, Kirkpatrick JM, Mazzetto M, Baumgart M, Bartolome A, Di Sanzo S, Caterino C, Sanguanini M, Papaevgeniou N, Lefaki M, Childs D, Bagnoli S, Tozzini E, Di Fraia D, Romanov N, Sudmant PH, Huber W, Chondrogianni N, Vendruscolo M, Cellerino A, Ori A. Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation. 2020. Mol Syst Biol. - 32558274
Sandel MW, Fast KM, Albanese B, Popp A, Nensteil P, Sudmant PH. Complete mitochondrial genome of the imperiled Trispot Darter (Etheostoma trisella). 2020. Mitochondrial DNA Part B - 5 (2), 1523-1524
2019
Senatorov VV Jr, Friedman AR, Milikovsky DZ, Ofer J, Saar-Ashkenazy R, Charbash A, Jahan N,4, Chin G, Mihaly E, Lin JM, Ramsay HJ, Moghbel A, Preininger MK, Eddings CR, Harrison HV, Patel R, Shen Y, Ghanim H, Sheng H, Veksler R, Sudmant PH, Becker A, Hart B, Rogawski MA, Dillin A, Friedman 3,, Kaufer D. Blood-brain barrier dysfunction in aging induces hyperactivation of TGFβ signaling and chronic yet reversible neural dysfunction. 2019. Sci Transl Med. - 31801886
2018
Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB. Widespread accumulation of ribosome-isolated 3' UTRs in specific neuronal cell of the aging brain. 2018. Cell reports - 30485811.
2016
Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB, RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation. 2016. Molecular cell - 27720642.
Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE, Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. 2016. Nature - 27487209.
2015
Sudmant PH, Alexis MS, Burge CB, Meta-analysis of RNA-seq expression data across species, tissues and studies. 2015. Genome biology - 26694591.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO, An integrated map of structural variation in 2,504 human genomes. 2015. Nature - 26432246.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR, A global reference for human genetic variation. 2015. Nature - 26432245.
Etienne L, Bibollet-Ruche F, Sudmant PH, Wu LI, Hahn BH, Emerman M, The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys. 2015. PLoS pathogens - 26394054.
Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE, Global diversity, population stratification, and selection of human copy-number variation. 2015. Science - 26249230.
Xue Y*, Prado-Martinez J*, Sudmant PH*, Narasimhan V*, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A, Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. 2015. Science - 25859046.
Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C, MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. 2015. Genome research - 25659649.
Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE, Resolving the complexity of the human genome using single-molecule sequencing. 2015. Nature - 25383537.
2014
Antonacci F, Dennis MY, Huddleston J, Sudmant PH, Steinberg KM, Rosenfeld JA, Miroballo M, Graves TA, Vives L, Malig M, Denman L, Raja A, Stuart A, Tang J, Munson B, Shaffer LG, Amemiya CT, Wilson RK, Eichler EE, Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. 2014. Nature genetics - 25326701.
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J, Ancient human genomes suggest three ancestral populations for present-day Europeans. 2014. Nature - 25230663.
Falchi M, El-Sayed Moustafa JS, Takousis P, Pesce F, Bonnefond A, Andersson-Assarsson JC, Sudmant PH, Dorajoo R, Al-Shafai MN, Bottolo L, Ozdemir E, So HC, Davies RW, Patrice A, Dent R, Mangino M, Hysi PG, Dechaume A, Huyvaert M, Skinner J, Pigeyre M, Caiazzo R, Raverdy V, Vaillant E, Field S, Balkau B, Marre M, Visvikis-Siest S, Weill J, Poulain-Godefroy O, Jacobson P, Sjostrom L, Hammond CJ, Deloukas P, Sham PC, McPherson R, Lee J, Tai ES, Sladek R, Carlsson LM, Walley A, Eichler EE, Pattou F, Spector TD, Froguel P, Low copy number of the salivary amylase gene predisposes to obesity. 2014. Nature genetics - 24686848.
Mariotti M, Smith TF, Sudmant PH, Goldberger G, Pseudogenization of testis-specific Lfg5 predates human/Neanderthal divergence. 2014. Journal of human genetics - 24599118.
Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE, Reconstructing complex regions of genomes using long-read sequencing technology. 2014. Genome research - 24418700.
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S, The complete genome sequence of a Neanderthal from the Altai Mountains. 2014. Nature -24352235.
2013
Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE, Rates and patterns of great ape retrotransposition. 2013. Proceedings of the National Academy of Sciences of the United States of America - 23884656.
Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW, Baker C, Mohajeri K, Kondova I, Bontrop RE, Persengiev S, Antonacci F, Ventura M, Prado-Martinez J, Great Ape Genome Project, Marques-Bonet T, Eichler EE, Evolution and diversity of copy number variation in the great ape lineage. 2013. Genome research - 23825009.
Prado-Martinez J*, Sudmant PH*, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T, Great ape genetic diversity and population history. 2013. Nature- 23823723.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, An integrated map of genetic variation from 1,092 human genomes. 2012. Nature - 23128226.
2012
Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O'Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE, Estimating the human mutation rate using autozygosity in a founder population. 2012. Nature genetics -23001126.
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S, A high-coverage genome sequence from an archaic Denisovan individual. 2012. Science -22936568.
Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE, Structural diversity and African origin of the 17q21.31 inversion polymorphism. 2012. Nature genetics - 22751100.
Gidvani RD, Sudmant P, Li G, DaSilva LF, McConkey BJ, Duncker BP, Ingalls BP, A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. 2012. BMC systems biology -22738223.
Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, NHLBI Exome Sequencing Project, Quinlan AR, Nickerson DA, Eichler EE, Copy number variation detection and genotyping from exome sequence data. 2012. Genome research -22585873.
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, Eichler EE, Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. 2012. Cell - 22559943.
Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA, Wilson RK, Eichler EE, The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. 2012. Genome research - 22419167.
Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F, Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. 2012. International journal of cancer - 21796619.
2011
Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE, Population-genetic properties of differentiated human copy-number polymorphisms. 2011. American journal of human genetics - 21397061.
Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J, Haplotype-resolved genome sequencing of a Gujarati Indian individual. 2011. Nature biotechnology - 21170042.
2010
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE, Diversity of human copy number variation and multicopy genes. 2010. Science -21030649.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, A map of human genome variation from population-scale sequencing. 2010. Nature - 20981092.