Harold Smith, Ph.D.
Photo of Harold Smith
Scientific Focus Areas: Cell Biology, Computational Biology, Developmental Biology, Genetics and Genomics, Systems Biology

Publications

A selection of recent and significant publications can be viewed below.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.
Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§., Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP.
Science (2022 Mar 4) 375:eabk2432. Abstract/Full Text
Mutation Mapping and Identification by Whole-Genome Sequencing.
Smith HE.
Methods Mol Biol (2022) 2468:257-269. Abstract/Full Text
The MLK-1/SCD-4 Mixed Lineage Kinase/MAP3K functions to promote dauer formation upstream of DAF-2/InsR.
Rasmussen NR, Smith HE, Reiner DJ.
MicroPubl Biol (2021 Jun 15) 2021. Abstract/Full Text
A complement factor H homolog, heparan sulfation, and syndecan maintain inversin compartment boundaries in C. elegans cilia.
Acker N, Smith H, Devine C, Oltjen SL, Tsiropoulou S, Smit-McBride Z, Lange K, Blacque OE, Matsubara JA, Gordus A, Golden A, Vogel BE.
Proc Natl Acad Sci U S A (2021 Apr 20) 118. Abstract/Full Text
An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing.
Montemayor C, Simone A, Long J, Montemayor O, Delvadia B, Rivera R, Lewis KL, Shahsavari S, Gandla D, Dura K, Krishnan US, Wendzel NC, Elavia N, Grissom S, Karagianni P, Bueno M, Loy D, Cacanindin R, McLaughlin S, Tynuv M, Brunker PAR, Roback J, Adams S, Smith H, Biesecker L, Klein HG.
Vox Sang (2021 Apr) 116:451-463. Abstract/Full Text
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community.
Lee HK, Knabl L, Pipperger L, Volland A, Furth PA, Kang K, Smith HE, Knabl L Sr, Bellmann R, Bernhard C, Kaiser N, Gänzer H, Ströhle M, Walser A, von Laer D, Hennighausen L.
Sci Rep (2021 Feb 19) 11:4243. Abstract/Full Text
Dynamic sex chromosome expression in Drosophila male germ cells.
Mahadevaraju S, Fear JM, Akeju M, Galletta BJ, Pinheiro MMLS, Avelino CC, Cabral-de-Mello DC, Conlon K, Dell'Orso S, Demere Z, Mansuria K, Mendonça CA, Palacios-Gimenez OM, Ross E, Savery M, Yu K, Smith HE, Sartorelli V, Yang H, Rusan NM, Vibranovski MD, Matunis E, Oliver B.
Nat Commun (2021 Feb 9) 12:892. Abstract/Full Text
Mutation of NEKL-4/NEK10 and TTLL genes suppress neuronal ciliary degeneration caused by loss of CCPP-1 deglutamylase function.
Power KM, Akella JS, Gu A, Walsh JD, Bellotti S, Morash M, Zhang W, Ramadan YH, Ross N, Golden A, Smith HE, Barr MM, O'Hagan R.
PLoS Genet (2020 Oct) 16:e1009052. Abstract/Full Text
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community.
Lee HK, Knabl L, Pipperger L, Volland A, Furth P, Kang K, Smith H, Knabl L, Bellmann R, Bernhard C, Kaiser N, Gänzer H, Ströhle M, Walser A, Von Laer D, Hennighausen L.
Res Sq (2020 Sep 23) Abstract/Full Text
Identification of Suppressors of top-2 Embryonic Lethality in Caenorhabditis elegans.
Bhandari N, Rourke C, Wilmoth T, Bheemreddy A, Schulman D, Collins D, Smith HE, Golden A, Jaramillo-Lambert A.
G3 (Bethesda) (2020 Apr 9) 10:1183-1191. Abstract/Full Text
Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos.
Lee HK, Smith HE, Liu C, Willi M, Hennighausen L.
Commun Biol (2020 Jan 9) 3:19. Abstract/Full Text
Simultaneous targeting of linked loci in mouse embryos using base editing.
Lee HK, Willi M, Smith HE, Miller SM, Liu DR, Liu C, Hennighausen L.
Sci Rep (2019 Feb 7) 9:1662. Abstract/Full Text
Mutation frequency is not increased in CRISPR-Cas9-edited mice.
Willi M, Smith HE, Wang C, Liu C, Hennighausen L.
Nat Methods (2018 Oct) 15:756-758. Abstract/Full Text
A Genetic Analysis of the Caenorhabditis elegans Detoxification Response.
Fukushige T, Smith HE, Miwa J, Krause MW, Hanover JA.
Genetics (2017 Jun) 206:939-952. Abstract/Full Text
A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter.
Davison JR, Lohith KM, Wang X, Bobyk K, Mandadapu SR, Lee SL, Cencic R, Nelson J, Simpkins S, Frank KM, Pelletier J, Myers CL, Piotrowski J, Smith HE, Bewley CA.
Antimicrob Agents Chemother (2017 Jun) 61. Abstract/Full Text
Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice.
Lee HK, Willi M, Wang C, Yang CM, Smith HE, Liu C, Hennighausen L.
Nucleic Acids Res (2017 May 5) 45:4606-4618. Abstract/Full Text
Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing.
Smith HE, Yun S.
PLoS One (2017) 12:e0174446. Abstract/Full Text
The Identification of a Novel Mutant Allele of topoisomerase II in Caenorhabditis elegans Reveals a Unique Role in Chromosome Segregation During Spermatogenesis.
Jaramillo-Lambert A, Fabritius AS, Hansen TJ, Smith HE, Golden A.
Genetics (2016 Dec) 204:1407-1422. Abstract/Full Text
Mapping Challenging Mutations by Whole-Genome Sequencing.
Smith HE, Fabritius AS, Jaramillo-Lambert A, Golden A.
G3 (Bethesda) (2016 May 3) 6:1297-304. Abstract/Full Text
The Paired-box protein PAX-3 regulates the choice between lateral and ventral epidermal cell fates in C. elegans.
Thompson KW, Joshi P, Dymond JS, Gorrepati L, Smith HE, Krause MW, Eisenmann DM.
Dev Biol (2016 Apr 15) 412:191-207. Abstract/Full Text
The E2F-DP1 Transcription Factor Complex Regulates Centriole Duplication in Caenorhabditis elegans.
Miller JG, Liu Y, Williams CW, Smith HE, O'Connell KF.
G3 (Bethesda) (2016 Jan 15) 6:709-20. Abstract/Full Text
Forward Genetics Identifies a Requirement for the Izumo-like Immunoglobulin Superfamily spe-45 Gene in Caenorhabditis elegans Fertilization.
Singaravelu G, Rahimi S, Krauchunas A, Rizvi A, Dharia S, Shakes D, Smith H, Golden A, Singson A.
Curr Biol (2015 Dec 21) 25:3220-4. Abstract/Full Text
Promotion of bone morphogenetic protein signaling by tetraspanins and glycosphingolipids.
Liu Z, Shi H, Szymczak LC, Aydin T, Yun S, Constas K, Schaeffer A, Ranjan S, Kubba S, Alam E, McMahon DE, He J, Shwartz N, Tian C, Plavskin Y, Lindy A, Dad NA, Sheth S, Amin NM, Zimmerman S, Liu D, Schwarz EM, Smith H, Krause MW, Liu J.
PLoS Genet (2015 May) 11:e1005221. Abstract/Full Text
Rapid and Efficient Identification of Caenorhabditis elegans Legacy Mutations Using Hawaiian SNP-Based Mapping and Whole-Genome Sequencing.
Jaramillo-Lambert A, Fuchsman AS, Fabritius AS, Smith HE, Golden A.
G3 (Bethesda) (2015 Mar 4) 5:1007-19. Abstract/Full Text
Library Construction for Mutation Identification by Whole-Genome Sequencing.
Smith HE.
Methods Mol Biol (2015) 1327:1-9. Abstract/Full Text
Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes.
Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B.
Dev Cell (2014 Dec 22) 31:761-73. Abstract/Full Text
Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 Sites in Caenorhabditis elegans.
Paix A, Wang Y, Smith HE, Lee CY, Calidas D, Lu T, Smith J, Schmidt H, Krause MW, Seydoux G.
Genetics (2014 Dec) 198:1347-56. Abstract/Full Text
Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.
Genome Res (2014 Jul) 24:1209-23. Abstract/Full Text
Nematode sperm motility.
Smith HE.
WormBook (2014 Apr 4) 1-15. Abstract/Full Text
Identification of suppressors of mbk-2/DYRK by whole-genome sequencing.
Wang Y, Wang JT, Rasoloson D, Stitzel ML, O' Connell KF, Smith HE, Seydoux G.
G3 (Bethesda) (2014 Feb 19) 4:231-41. Abstract/Full Text
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).
Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.
BMC Bioinformatics (2013 Nov 9) 14:320. Abstract/Full Text
Drosophila ryanodine receptors mediate general anesthesia by halothane.
Gao S, Sandstrom DJ, Smith HE, High B, Marsh JW, Nash HA.
Anesthesiology (2013 Mar) 118:587-601. Abstract/Full Text
Simplification and desexualization of gene expression in self-fertile nematodes.
Thomas CG, Li R, Smith HE, Woodruff GC, Oliver B, Haag ES.
Curr Biol (2012 Nov 20) 22:2167-72. Abstract/Full Text
Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes.
Zhu BM, Kang K, Yu JH, Chen W, Smith HE, Lee D, Sun HW, Wei L, Hennighausen L.
Nucleic Acids Res (2012 May) 40:4461-72. Abstract/Full Text
Mediation of Drosophila autosomal dosage effects and compensation by network interactions.
Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B.
Genome Biol (2012 Apr 24) 13:r28. Abstract/Full Text
SPE-44 implements sperm cell fate.
Kulkarni M, Shakes DC, Guevel K, Smith HE.
PLoS Genet (2012) 8:e1002678. Abstract/Full Text
Identifying insertion mutations by whole-genome sequencing.
Smith HE.
Biotechniques (2011 Feb) 50:96-7. Abstract/Full Text