Publications

Au EH, Fauci C, Luo Y, Mangan RJ, Snellings DA, Shoben CR, Weaver S, Simpson SK, Lowe CB. Gonomics: Uniting high performance and readability for genomics with Go.
Bioinformatics. 2023 Aug 25. btad516

Bartelt LC, Switonski PM, Carvalho J, Duvick LA, Scoles DR, Pulst SM, Orr HT, Hull C, Lowe CB, La Spada AR. Purkinje-enriched snRNA-seq in SCA7 cerebellum reveals Zebrin identity loss as a central feature of polyglutamine ataxias.
bioRxiv 2023 Mar 20;1-25.

Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution.
Nature Reviews Genetics. 2023 Feb 3;1-25.

Mangan RJ, Alsina FC, Mosti F, Sotelo-Fonseca JE, Snellings DA, Au EH, Carvalho J, Sathyan L, Johnson GD, Reddy TE, Silver DL, Lowe CB.
Adaptive sequence divergence forged new neurodevelopmental enhancers in humans
Cell. 2022 Nov 23; 185(24):4587-4603.

Saelens JW, Sweeney MI, Viswanathan G, Xet-Mull AM, Jurcic Smith KL, Sisk DM, Hu DD, Cronin RM, Hughes EJ, Brewer WJ, Coers J, Champion MM, Champion PA, Lowe CB, Smith CM, Lee S, Stout JE, Tobin DM.
An ancestral mycobacterial effector promotes dissemination of infection
Cell. 2022 Nov 23;185:1-19.

Wucherpfennig JI, Howes TR, Au JN, Au EH, Roberts Kingman GA, Brady SD, Herbert AL, Reimchen TE, Bell MA, Lowe CB, Dalziel AC, Kingsley DM. Evolution of stickleback spines through independent cis-regulatory changes at HOXDB.
Nature Ecology & Evolution. 2022 Sep 1; 6(1): 486-1552.

Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR.
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
Cell. 2019 Feb 7;176(4):743-756.e17.

Song J*, Lowe CB*, Kingsley DM.
Characterization of a human-specific tandem repeat associated with bipolar disorder and schizophrenia.
Am J Hum Genet. 2018 Jul 27. pii: S0002-9297(18)30238-6.

Lowe CB*, Sanchez-Luege N*, Howes TR, Brady SD, Richardson RR, Jones FC, Bell MA, Kingsley DM.
Detecting Copy Number Variation Associated With Phenotypic Classes.
Genome Res. 2018 Feb;28(2):256-265
PubMed

Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV.
Feather development genes and associated regulatory innovation predate the origin of Dinosauria.
Mol Biol Evol. 2015 Jan;32(1):23-8.
PubMed

Lowe CB, Haussler D.
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.
PLoS One. 2012;7(8):e43128.
PubMed

29 mammals sequencing and analysis consortium.
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature. 2011 Oct 12;478(7370):476-82.
PubMed

Anolis genome sequencing consortium.
The genome of the green anole lizard and a comparative analysis with birds and mammals.
Nature. 2011 Aug 31;477(7366):587-91.
PubMed

Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D.
Three periods of regulatory innovation during vertebrate evolution.
Science. 2011 Aug 19;333(6045):1019-24.
PubMed Interviewed by Joe Palca on NPR's All Things Considered

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. Cited 1000+
GREAT improves functional interpretation of cis-regulatory regions.
Nat Biotechnol. 2010 May;28(5):495-501.
PubMed

Lowe CB, Bejerano G, Salama SR, Haussler D. Stephen J. O'Brien Award
Endangered species hold clues to human evolution.
J Hered. 2010 Jul-Aug;101(4):437-47.
PubMed

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
Comparative genomics search for losses of long-established genes on the human lineage.
PLoS Comput Biol. 2007 Dec;3(12):e247.
PubMed

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D.
Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.
Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-8.
PubMed

Lowe CB, Bejerano G, Haussler D.
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
Proc Natl Acad Sci U S A. 2007 May 8;104(19):8005-10.
PubMed

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D.
A distal enhancer and an ultraconserved exon are derived from a novel retroposon.
Nature. 2006 May 4;441(7089):87-90.
PubMed