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Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans.

Qin Z, Johnsen R, Yu S, Chu JS, Baillie DL, Chen N.

G3 (Bethesda). 2018 Mar 2;8(3):981-997. doi: 10.1534/g3.117.300338.


Systematic functional analysis of the Ras GTPase family unveils a conserved network required for anterograde protein trafficking.

Caruso ME, Jenna S, Baillie DL, Bossé R, Simpson JC, Chevet E, Taouji S.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600302.


Degenerin channel activation causes caspase-mediated protein degradation and mitochondrial dysfunction in adult C. elegans muscle.

Gaffney CJ, Shephard F, Chu J, Baillie DL, Rose A, Constantin-Teodosiu D, Greenhaff PL, Szewczyk NJ.

J Cachexia Sarcopenia Muscle. 2016 May;7(2):181-92. doi: 10.1002/jcsm.12040. Epub 2015 Jun 4.


The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis.

Hench J, Henriksson J, Abou-Zied AM, Lüppert M, Dethlefsen J, Mukherjee K, Tong YG, Tang L, Gangishetti U, Baillie DL, Bürglin TR.

PLoS One. 2015 May 29;10(5):e0126947. doi: 10.1371/journal.pone.0126947. eCollection 2015.


let-65 is cytoplasmic methionyl tRNA synthetase in C. elegans.

Alriyami MZ, Jones MR, Johnsen RC, Banerjee Y, Baillie DL.

Meta Gene. 2014 Nov 9;2:819-30. doi: 10.1016/j.mgene.2014.08.006. eCollection 2014 Dec.


High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans.

Chu JS, Chua SY, Wong K, Davison AM, Johnsen R, Baillie DL, Rose AM.

BMC Genomics. 2014 May 12;15:361. doi: 10.1186/1471-2164-15-361.


Identification of 526 conserved metazoan genetic innovations exposes a new role for cofactor E-like in neuronal microtubule homeostasis.

Frédéric MY, Lundin VF, Whiteside MD, Cueva JG, Tu DK, Kang SY, Singh H, Baillie DL, Hutter H, Goodman MB, Brinkman FS, Leroux MR.

PLoS Genet. 2013;9(10):e1003804. doi: 10.1371/journal.pgen.1003804. Epub 2013 Oct 3.


The ortholog of the human proto-oncogene ROS1 is required for epithelial development in C. elegans.

Jones MR, Rose AM, Baillie DL.

Genesis. 2013 Aug;51(8):545-61. doi: 10.1002/dvg.22405. Epub 2013 Jun 27.


Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.

Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FS.

Int J Antimicrob Agents. 2012 Sep;40(3):246-51. doi: 10.1016/j.ijantimicag.2012.05.009. Epub 2012 Jul 20.


RNA-seq analysis of the C. briggsae transcriptome.

Uyar B, Chu JS, Vergara IA, Chua SY, Jones MR, Wong T, Baillie DL, Chen N.

Genome Res. 2012 Aug;22(8):1567-80. doi: 10.1101/gr.134601.111. Epub 2012 Jul 6.


Oligoarray comparative genomic hybridization-mediated mapping of suppressor mutations generated in a deletion-biased mutagenesis screen.

Jones MR, Rose AM, Baillie DL.

G3 (Bethesda). 2012 Jun;2(6):657-63. doi: 10.1534/g3.112.002238. Epub 2012 Jun 1.


The atm-1 gene is required for genome stability in Caenorhabditis elegans.

Jones MR, Huang JC, Chua SY, Baillie DL, Rose AM.

Mol Genet Genomics. 2012 Apr;287(4):325-35. doi: 10.1007/s00438-012-0681-0. Epub 2012 Feb 18.


Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs.

Chu JS, Johnsen RC, Chua SY, Tu D, Dennison M, Marra M, Jones SJ, Baillie DL, Rose AM.

Genetics. 2012 Apr;190(4):1225-33. doi: 10.1534/genetics.111.137208. Epub 2012 Jan 20.


Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans.

Chu JS, Tarailo-Graovac M, Zhang D, Wang J, Uyar B, Tu D, Trinh J, Baillie DL, Chen N.

Nucleic Acids Res. 2012 Jan;40(1):53-64. doi: 10.1093/nar/gkr690. Epub 2011 Sep 8.


The two actin-interacting protein 1 genes have overlapping and essential function for embryonic development in Caenorhabditis elegans.

Ono S, Nomura K, Hitosugi S, Tu DK, Lee JA, Baillie DL, Ono K.

Mol Biol Cell. 2011 Jul 1;22(13):2258-69. doi: 10.1091/mbc.E10-12-0934. Epub 2011 May 5.



Johnsen RC, Baillie DL.

In: Riddle DL, Blumenthal T, Meyer BJ, Priess JR, editors. C. elegans II. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. No abstract available. Chapter 4.


Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing.

Shin H, Lee H, Fejes AP, Baillie DL, Koo HS, Jones SJ.

BMC Res Notes. 2011 Feb 8;4:34. doi: 10.1186/1756-0500-4-34.


Duplication of cyb-3 (cyclin B3) suppresses sterility in the absence of mdf-1/MAD1 spindle assembly checkpoint component in Caenorhabditis elegans.

Tarailo-Graovac M, Wang J, Tu D, Baillie DL, Rose AM, Chen N.

Cell Cycle. 2010 Dec 15;9(24):4858-65. Epub 2010 Dec 15.


xnd-1 regulates the global recombination landscape in Caenorhabditis elegans.

Wagner CR, Kuervers L, Baillie DL, Yanowitz JL.

Nature. 2010 Oct 14;467(7317):839-43. doi: 10.1038/nature09429.


Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans.

Chu JS, Baillie DL, Chen N.

BMC Evol Biol. 2010 May 4;10:130. doi: 10.1186/1471-2148-10-130.


Protein phosphatase 2A cooperates with the autophagy-related kinase UNC-51 to regulate axon guidance in Caenorhabditis elegans.

Ogura K, Okada T, Mitani S, Gengyo-Ando K, Baillie DL, Kohara Y, Goshima Y.

Development. 2010 May;137(10):1657-67. doi: 10.1242/dev.050708. Epub 2010 Apr 14.


A strawberry notch homolog, let-765/nsh-1, positively regulates lin-3/egf expression to promote RAS-dependent vulval induction in C. elegans.

Simms CL, Baillie DL.

Dev Biol. 2010 May 15;341(2):472-85. doi: 10.1016/j.ydbio.2010.03.004. Epub 2010 Mar 15.


Characterization of the octamer, a cis-regulatory element that modulates excretory cell gene-expression in Caenorhabditis elegans.

Mah AK, Tu DK, Johnsen RC, Chu JS, Chen N, Baillie DL.

BMC Mol Biol. 2010 Mar 8;11:19. doi: 10.1186/1471-2199-11-19.


Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern.

Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ.

BMC Genomics. 2010 Feb 23;11:131. doi: 10.1186/1471-2164-11-131.


Characterization of the astacin family of metalloproteases in C. elegans.

Park JO, Pan J, Möhrlen F, Schupp MO, Johnsen R, Baillie DL, Zapf R, Moerman DG, Hutter H.

BMC Dev Biol. 2010 Jan 28;10:14. doi: 10.1186/1471-213X-10-14.


Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.

Sleumer MC, Mah AK, Baillie DL, Jones SJ.

Nucleic Acids Res. 2010 May;38(9):2990-3004. doi: 10.1093/nar/gkq003. Epub 2010 Jan 25.


Characterizing the transcriptional regulation of let-721, a Caenorhabditis elegans homolog of human electron flavoprotein dehydrogenase.

Chew DS, Mah AK, Baillie DL.

Mol Genet Genomics. 2009 Dec;282(6):555-70. doi: 10.1007/s00438-009-0485-z. Epub 2009 Sep 23.


Evaluation of the therapeutic potential of carbonic anhydrase inhibitors in two animal models of dystrophin deficient muscular dystrophy.

Giacomotto J, Pertl C, Borrel C, Walter MC, Bulst S, Johnsen B, Baillie DL, Lochmüller H, Thirion C, Ségalat L.

Hum Mol Genet. 2009 Nov 1;18(21):4089-101. doi: 10.1093/hmg/ddp358. Epub 2009 Jul 31.


Polymorphic segmental duplication in the nematode Caenorhabditis elegans.

Vergara IA, Mah AK, Huang JC, Tarailo-Graovac M, Johnsen RC, Baillie DL, Chen N.

BMC Genomics. 2009 Jul 21;10:329. doi: 10.1186/1471-2164-10-329.


An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.

Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM 3rd, Baillie DL, Holt RA, Jones SJ, Marra MA, Moerman DG.

PLoS Genet. 2009 Jun;5(6):e1000537. doi: 10.1371/journal.pgen.1000537. Epub 2009 Jun 26.


High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in Caenorhabditis elegans.

Jones MR, Chua SY, O'Neil NJ, Johnsen RC, Rose AM, Baillie DL.

Mol Genet Genomics. 2009 Jul;282(1):37-46. doi: 10.1007/s00438-009-0444-8. Epub 2009 Mar 29.


Sarcomeric actin organization is synergistically promoted by tropomodulin, ADF/cofilin, AIP1 and profilin in C. elegans.

Yamashiro S, Cox EA, Baillie DL, Hardin JD, Ono S.

J Cell Sci. 2008 Dec 1;121(Pt 23):3867-77. doi: 10.1242/jcs.040477. Epub 2008 Nov 4.


Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ.

BMC Biol. 2008 Jul 8;6:30. doi: 10.1186/1741-7007-6-30.


GTPase-mediated regulation of the unfolded protein response in Caenorhabditis elegans is dependent on the AAA+ ATPase CDC-48.

Caruso ME, Jenna S, Bouchecareilh M, Baillie DL, Boismenu D, Halawani D, Latterich M, Chevet E.

Mol Cell Biol. 2008 Jul;28(13):4261-74. doi: 10.1128/MCB.02252-07. Epub 2008 May 5.


Genetic balancers.

Edgley ML, Baillie DL, Riddle DL, Rose AM.

WormBook. 2006 Apr 6:1-32. Review. No abstract available.


Caenorhabditis elegans pgp-5 is involved in resistance to bacterial infection and heavy metal and its regulation requires TIR-1 and a p38 map kinase cascade.

Kurz CL, Shapira M, Chen K, Baillie DL, Tan MW.

Biochem Biophys Res Commun. 2007 Nov 16;363(2):438-43. Epub 2007 Sep 12.


High-throughput in vivo analysis of gene expression in Caenorhabditis elegans.

Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG.

PLoS Biol. 2007 Sep;5(9):e237.


Identification and analysis of internal promoters in Caenorhabditis elegans operons.

Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O'Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ.

Genome Res. 2007 Oct;17(10):1478-85. Epub 2007 Aug 21.


Transcriptional regulation of AQP-8, a Caenorhabditis elegans aquaporin exclusively expressed in the excretory system, by the POU homeobox transcription factor CEH-6.

Mah AK, Armstrong KR, Chew DS, Chu JS, Tu DK, Johnsen RC, Chen N, Chamberlin HM, Baillie DL.

J Biol Chem. 2007 Sep 21;282(38):28074-86. Epub 2007 Jul 27.


Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in caenorhabditis species.

Zhao Z, Thomas JH, Chen N, Sheps JA, Baillie DL.

Genetics. 2007 Mar;175(3):1407-18. Epub 2006 Dec 28.


Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics.

Chen N, Mah A, Blacque OE, Chu J, Phgora K, Bakhoum MW, Newbury CR, Khattra J, Chan S, Go A, Efimenko E, Johnsen R, Phirke P, Swoboda P, Marra M, Moerman DG, Leroux MR, Baillie DL, Stein LD.

Genome Biol. 2006;7(12):R126.


The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine.

McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJ, Moerman DG, Robertson AG.

Dev Biol. 2007 Feb 15;302(2):627-45. Epub 2006 Oct 21.


The WD repeat-containing protein IFTA-1 is required for retrograde intraflagellar transport.

Blacque OE, Li C, Inglis PN, Esmail MA, Ou G, Mah AK, Baillie DL, Scholey JM, Leroux MR.

Mol Biol Cell. 2006 Dec;17(12):5053-62. Epub 2006 Oct 4.


Caenorhabditis elegans dpy-14: an essential collagen gene with unique expression profile and physiological roles in early development.

Gallo M, Mah AK, Johnsen RC, Rose AM, Baillie DL.

Mol Genet Genomics. 2006 Jun;275(6):527-39. Epub 2006 Feb 22.


Caenorhabditis elegans expresses three functional profilins in a tissue-specific manner.

Polet D, Lambrechts A, Ono K, Mah A, Peelman F, Vandekerckhove J, Baillie DL, Ampe C, Ono S.

Cell Motil Cytoskeleton. 2006 Jan;63(1):14-28.


Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans.

Zhao Z, Fang L, Chen N, Johnsen RC, Stein L, Baillie DL.

J Biol Chem. 2005 Nov 18;280(46):38787-94. Epub 2005 Sep 13.


Functional genomics of the cilium, a sensory organelle.

Blacque OE, Perens EA, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJ, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR.

Curr Biol. 2005 May 24;15(10):935-41.

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