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Items: 39

1.

Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill.

DeLeo DM, Herrera S, Lengyel SD, Quattrini AM, Kulathinal RJ, Cordes EE.

Mol Ecol. 2018 Oct;27(20):4066-4077. doi: 10.1111/mec.14847. Epub 2018 Sep 22.

PMID:
30137660
2.

The whole lupus: Articulating biosocial interplay in systemic lupus erythematosus epidemiology and population disparities.

Kinsey D, Paul CP, Taylor D, Caricchio R, Kulathinal RJ, Hayes-Conroy A.

Health Place. 2018 May;51:182-188. doi: 10.1016/j.healthplace.2018.03.007. Epub 2018 Apr 12.

PMID:
29655130
3.

Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards.

Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh ST, Kulathinal RJ, McMillan WO, Menke DB, Pratt SC, Rawls JA, Sanjur O, Wilson-Rawls J, Wilson Sayres MA, Fisher RE, Kusumi K.

Genome Biol Evol. 2018 Feb 1;10(2):489-506. doi: 10.1093/gbe/evy013.

4.

The fluidity of biosocial identity and the effects of place, space, and time.

Wiese D, Rodriguez Escobar J, Hsu Y, Kulathinal RJ, Hayes-Conroy A.

Soc Sci Med. 2018 Feb;198:46-52. doi: 10.1016/j.socscimed.2017.12.023. Epub 2017 Dec 18. Review.

PMID:
29275275
5.

FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila.

Kumar S, Konikoff C, Sanderford M, Liu L, Newfeld S, Ye J, Kulathinal RJ.

G3 (Bethesda). 2017 Aug 7;7(8):2791-2797. doi: 10.1534/g3.117.040345.

6.

Integrative genomic analysis identifies ancestry-related expression quantitative trait loci on DNA polymerase β and supports the association of genetic ancestry with survival disparities in head and neck squamous cell carcinoma.

Ramakodi MP, Devarajan K, Blackman E, Gibbs D, Luce D, Deloumeaux J, Duflo S, Liu JC, Mehra R, Kulathinal RJ, Ragin CC.

Cancer. 2017 Mar 1;123(5):849-860. doi: 10.1002/cncr.30457. Epub 2016 Dec 1.

7.

Neurogenomics and the role of a large mutational target on rapid behavioral change.

Stanley CE Jr, Kulathinal RJ.

Biol Direct. 2016 Nov 8;11(1):60.

8.

Large-Scale Discovery of Disease-Disease and Disease-Gene Associations.

Gligorijevic D, Stojanovic J, Djuric N, Radosavljevic V, Grbovic M, Kulathinal RJ, Obradovic Z.

Sci Rep. 2016 Aug 31;6:32404. doi: 10.1038/srep32404.

9.

flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection.

Stanley CE Jr, Kulathinal RJ.

G3 (Bethesda). 2016 Aug 9;6(8):2355-63. doi: 10.1534/g3.116.031138.

10.

Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster.

Stanley CE Jr, Kulathinal RJ.

BMC Evol Biol. 2016 Jan 5;16:6. doi: 10.1186/s12862-015-0580-1.

11.

Ancestral-derived effects on the mutational landscape of laryngeal cancer.

Ramakodi MP, Kulathinal RJ, Chung Y, Serebriiskii I, Liu JC, Ragin CC.

Genomics. 2016 Mar;107(2-3):76-82. doi: 10.1016/j.ygeno.2015.12.004. Epub 2015 Dec 22.

12.

Designing a broad-spectrum integrative approach for cancer prevention and treatment.

Block KI, Gyllenhaal C, Lowe L, Amedei A, Amin ARMR, Amin A, Aquilano K, Arbiser J, Arreola A, Arzumanyan A, Ashraf SS, Azmi AS, Benencia F, Bhakta D, Bilsland A, Bishayee A, Blain SW, Block PB, Boosani CS, Carey TE, Carnero A, Carotenuto M, Casey SC, Chakrabarti M, Chaturvedi R, Chen GZ, Chen H, Chen S, Chen YC, Choi BK, Ciriolo MR, Coley HM, Collins AR, Connell M, Crawford S, Curran CS, Dabrosin C, Damia G, Dasgupta S, DeBerardinis RJ, Decker WK, Dhawan P, Diehl AME, Dong JT, Dou QP, Drew JE, Elkord E, El-Rayes B, Feitelson MA, Felsher DW, Ferguson LR, Fimognari C, Firestone GL, Frezza C, Fujii H, Fuster MM, Generali D, Georgakilas AG, Gieseler F, Gilbertson M, Green MF, Grue B, Guha G, Halicka D, Helferich WG, Heneberg P, Hentosh P, Hirschey MD, Hofseth LJ, Holcombe RF, Honoki K, Hsu HY, Huang GS, Jensen LD, Jiang WG, Jones LW, Karpowicz PA, Keith WN, Kerkar SP, Khan GN, Khatami M, Ko YH, Kucuk O, Kulathinal RJ, Kumar NB, Kwon BS, Le A, Lea MA, Lee HY, Lichtor T, Lin LT, Locasale JW, Lokeshwar BL, Longo VD, Lyssiotis CA, MacKenzie KL, Malhotra M, Marino M, Martinez-Chantar ML, Matheu A, Maxwell C, McDonnell E, Meeker AK, Mehrmohamadi M, Mehta K, Michelotti GA, Mohammad RM, Mohammed SI, Morre DJ, Muralidhar V, Muqbil I, Murphy MP, Nagaraju GP, Nahta R, Niccolai E, Nowsheen S, Panis C, Pantano F, Parslow VR, Pawelec G, Pedersen PL, Poore B, Poudyal D, Prakash S, Prince M, Raffaghello L, Rathmell JC, Rathmell WK, Ray SK, Reichrath J, Rezazadeh S, Ribatti D, Ricciardiello L, Robey RB, Rodier F, Rupasinghe HPV, Russo GL, Ryan EP, Samadi AK, Sanchez-Garcia I, Sanders AJ, Santini D, Sarkar M, Sasada T, Saxena NK, Shackelford RE, Shantha Kumara HMC, Sharma D, Shin DM, Sidransky D, Siegelin MD, Signori E, Singh N, Sivanand S, Sliva D, Smythe C, Spagnuolo C, Stafforini DM, Stagg J, Subbarayan PR, Sundin T, Talib WH, Thompson SK, Tran PT, Ungefroren H, Vander Heiden MG, Venkateswaran V, Vinay DS, Vlachostergios PJ, Wang Z, Wellen KE, Whelan RL, Yang ES, Yang H, Yang X, Yaswen P, Yedjou C, Yin X, Zhu J, Zollo M.

Semin Cancer Biol. 2015 Dec;35 Suppl:S276-S304. doi: 10.1016/j.semcancer.2015.09.007. Review.

13.

Sustained proliferation in cancer: Mechanisms and novel therapeutic targets.

Feitelson MA, Arzumanyan A, Kulathinal RJ, Blain SW, Holcombe RF, Mahajna J, Marino M, Martinez-Chantar ML, Nawroth R, Sanchez-Garcia I, Sharma D, Saxena NK, Singh N, Vlachostergios PJ, Guo S, Honoki K, Fujii H, Georgakilas AG, Bilsland A, Amedei A, Niccolai E, Amin A, Ashraf SS, Boosani CS, Guha G, Ciriolo MR, Aquilano K, Chen S, Mohammed SI, Azmi AS, Bhakta D, Halicka D, Keith WN, Nowsheen S.

Semin Cancer Biol. 2015 Dec;35 Suppl:S25-S54. doi: 10.1016/j.semcancer.2015.02.006. Epub 2015 Apr 17. Review.

14.

Genetic Architecture of Sexual Dimorphism in Humans.

Rigby N, Kulathinal RJ.

J Cell Physiol. 2015 Oct;230(10):2304-10. doi: 10.1002/jcp.24979. Review.

PMID:
25740260
15.

Hybridization reveals the evolving genomic architecture of speciation.

Kronforst MR, Hansen ME, Crawford NG, Gallant JR, Zhang W, Kulathinal RJ, Kapan DD, Mullen SP.

Cell Rep. 2013 Nov 14;5(3):666-77. doi: 10.1016/j.celrep.2013.09.042. Epub 2013 Oct 31.

16.

Functional genetics in the post-genomics era: building a better roadmap in Drosophila.

Kulathinal RJ.

G3 (Bethesda). 2013 Sep 4;3(9):1451-2. doi: 10.1534/g3.113.007351.

17.

Functional genetics in the post-genomics era: building a better roadmap in Drosophila.

Kulathinal RJ.

Genetics. 2013 Sep;195(1):7-8. doi: 10.1534/genetics.113.156497.

18.

Sex-biased networks and nodes of sexually antagonistic conflict in Drosophila.

Hansen ME, Kulathinal RJ.

Int J Evol Biol. 2013;2013:545392. doi: 10.1155/2013/545392. Epub 2013 Jan 22.

19.

Developing a community-based genetic nomenclature for anole lizards.

Kusumi K, Kulathinal RJ, Abzhanov A, Boissinot S, Crawford NG, Faircloth BC, Glenn TC, Janes DE, Losos JB, Menke DB, Poe S, Sanger TJ, Schneider CJ, Stapley J, Wade J, Wilson-Rawls J.

BMC Genomics. 2011 Nov 11;12:554. doi: 10.1186/1471-2164-12-554.

20.

Elevated Evolutionary Rates among Functionally Diverged Reproductive Genes across Deep Vertebrate Lineages.

Grassa CJ, Kulathinal RJ.

Int J Evol Biol. 2011;2011:274975. doi: 10.4061/2011/274975. Epub 2011 Jul 28.

21.

Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila.

Renn SC, Machado HE, Jones A, Soneji K, Kulathinal RJ, Hofmann HA.

BMC Genomics. 2010 Apr 29;11:271. doi: 10.1186/1471-2164-11-271.

22.

The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing.

Kulathinal RJ, Stevison LS, Noor MA.

PLoS Genet. 2009 Jul;5(7):e1000550. doi: 10.1371/journal.pgen.1000550. Epub 2009 Jul 3.

23.

The B-type lamin is required for somatic repression of testis-specific gene clusters.

Shevelyov YY, Lavrov SA, Mikhaylova LM, Nurminsky ID, Kulathinal RJ, Egorova KS, Rozovsky YM, Nurminsky DI.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3282-7. doi: 10.1073/pnas.0811933106. Epub 2009 Feb 13.

24.
25.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG.

Genome Biol Evol. 2009 Nov 18;1:449-65. doi: 10.1093/gbe/evp048.

26.

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence.

Kulathinal RJ, Bennett SM, Fitzpatrick CL, Noor MA.

Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10051-6. doi: 10.1073/pnas.0801848105. Epub 2008 Jul 11.

27.

Evolution in the fast lane: rapidly evolving sex-related genes in Drosophila.

Haerty W, Jagadeeshan S, Kulathinal RJ, Wong A, Ravi Ram K, Sirot LK, Levesque L, Artieri CG, Wolfner MF, Civetta A, Singh RS.

Genetics. 2007 Nov;177(3):1321-35.

28.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
29.

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.

Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.

Genome Res. 2007 Dec;17(12):1823-36. Epub 2007 Nov 7.

30.

Male sex drive and the masculinization of the genome.

Singh RS, Kulathinal RJ.

Bioessays. 2005 May;27(5):518-25.

PMID:
15832384
31.

The latest buzz in comparative genomics.

Kulathinal RJ, Hartl DL.

Genome Biol. 2005;6(1):201. Epub 2005 Jan 4. Review.

32.

Compensated deleterious mutations in insect genomes.

Kulathinal RJ, Bettencourt BR, Hartl DL.

Science. 2004 Nov 26;306(5701):1553-4. Epub 2004 Oct 21.

33.

The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.

Castillo-Davis CI, Kondrashov FA, Hartl DL, Kulathinal RJ.

Genome Res. 2004 May;14(5):802-11.

34.
35.

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection.

Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL.

J Mol Evol. 2003;57 Suppl 1:S154-64.

PMID:
15008412
36.
37.

Mammalian sperm proteins are rapidly evolving: evidence of positive selection in functionally diverse genes.

Torgerson DG, Kulathinal RJ, Singh RS.

Mol Biol Evol. 2002 Nov;19(11):1973-80.

PMID:
12411606
38.

Sex gene pool evolution and speciation: a new paradigm.

Singh RS, Kulathinal RJ.

Genes Genet Syst. 2000 Jun;75(3):119-30. Review.

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