Lipovich L, Dachet F, Cai J*, Balan K, Bagla S, Jia H*, Loeb JA: Activity-dependent human brain coding / non-coding gene regulatory networks. Genetics doi:10.1534/genetics.112.145128 (e-publication ahead of print), 2012.
Southwood CM, Lipovich L, Gow A: Tissue-Restricted Transcription from a Conserved Intragenic CpG Island in the Klf1 Gene in Mice. Biol Reprod doi:10.1095/biolreprod.112.099879 (e-publication ahead of print), 2012.
Bánfai B#, Jia H*#, Khatun J#, Wood E*, Risk B, Gundling W*, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel PJ, Giddings MC, Brown JB^, Lipovich L^: Long noncoding RNAs are rarely translated in two human cell lines. Genome Research 22: 1646-1657, 2012. #joint first authors, ^ joint last authors
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Gonzalez D, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez J, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard T, Notredame C, Harrow J, Guigó R: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research 22: 1775-1789, 2012.
Michelhaugh SK^, Lipovich L^, Blythe J*, Jia H*, Kapatos G, and Bannon MJ. Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J Neurochem 116: 459-466, 2011. ^ joint first authors
Lipovich L, Johnson R, and Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. (invited review article) Biochimica et Biophysica Acta 1799: 597-615, 2010.
Jia H*, Osak M*, Bogu GK, Stanton LW, Johnson R, and Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16: 1478-1487, 2010.
Sheik Mohamed J*, Gaughwin PM, Lim B, Robson P, and Lipovich L. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16: 324-337, 2010. Selected by Faculty Of 1000 Biology. Page 3 of 12
Mittal P, Romero R, Tarca AL, Gonzalez J, Draghici S, Xu Y, Dong Z, Nhan-Chang CL, Chaiworapongsa T, Lye S, Kusanovic JP, Lipovich L, Mazaki-Tovi S, Hassan SS, Mesiano S, and Kim CJ. Characterization of the myometrial transcriptome and biological pathways of spontaneous human labor at term. J Perinat Med 38: 617-643, 2010.
Tay SK*, Blythe J*, and Lipovich L. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci USA 106: 12019-12024, 2009.
Goodman M, Sterner KN, Islam M, Uddin M, Sherwood CC, Hof PR, Hou ZC, Lipovich L, Jia H*, Grossman LI, and Wildman DE. Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. Proc Natl Acad Sci USA 106: 20824-20829, 2009.
Johnson R*, Teh CHL, Jia H*, Vanisri RR*, Pandey T*, Lu ZH*, Buckley NJ, Stanton LW, and Lipovich L. Regulation of neural macroRNAs by the transcriptional repressor, REST. RNA 15: 85-96, 2009.
Lee TM* and Lipovich L. Structural differences of orthologous genes: insights from humanprimate comparisons. Genomics 92: 134-143, 2008. (Article was represented by an issue Cover Illustration, requested by the Editors and provided by the Authors.)
Kunarso G*, Wong KY, Stanton LW, and Lipovich L. Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency. BMC Genomics 9(1):155 (e-publication), 2008. *Designated as a “Highly Accessed article” by BioMed Central.*
Johnson R*, Teh CH, Kunarso G*, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM, Karuturi RK, Wei CL, Buckley NJ, and Stanton LW. REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biology 6(10):e256(e-publication), 2008.
Lim CY, Tam WL*, Zhang J, Ang HS, Jia H*, Lipovich L, Ng HH, Wei CL, Sung WK, Robson P, Yang H, and Lim B. Sall4 Regulates Distinct Transcription Circuitries in Different Blastocyst-Derived Stem Cell Lineages. Cell Stem Cell 3: 543-554, 2008.
Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y, and Chin KC. Genome-wide mapping of RELA (p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Molecular Cell 27: 622-635, 2007.
Orlov Y^^, Zhou JT, Lipovich L, Shahab A, and Kuznetsov VA. Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis. In Silico Biology 7:3 241-260 (e-publication), 2007.
Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, and Liu ET. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genetics 3(6):e87 (e-publication), 2007.
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G*, Ng E*, Batalov S, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, and Lipovich L. Complex loci in mammalian genomes. PLoS Genetics 2(4):e47 (e-publication), 2006. Page 4 of 12
Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, and Hayashizaki Y. Mice and men: their promoter properties. PLoS Genetics 2(4):e54 (e-publication), 2006.
Loh YH, Wu Q, Chew JL, Vega VB, Zhang WW, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, and Ng HH. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics 38: 431-440, 2006.
Lipovich L, Vanisri RR*, Kong SL, Lin CY, and Liu ET. Primate-specific endogenous cisantisense transcription in the human 5q31 protocadherin gene cluster. Journal of Molecular Evolution 62: 73-88, 2006. (Article was represented by an issue Cover Illustration, requested by the Editors and provided by the Authors.)
Lipovich L and King MC. Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Research 16: 45-54, 2006.
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566, 2005.
Carninci P, FANTOM Consortium member list (including Lipovich L), Hayashizaki Y; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563, 2005.
Ng WP, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Wong CH, Ridwan A, Liu ET, and Ruan Y. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2: 105-111, 2005.
Wei CL, Ng WP, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, and Ruan Y. 5’ Long Serial Analysis of Gene Expression (LongSAGE) and 3’ LongSAGE for transcriptome characterization and genome annotation. Proceedings of the National Academy of Sciences (USA) 101: 11701-11706, 2004.
Lipovich L, Abkowitz J, King MC, Hughes A, and Quigley JG. Ancient conserved gene clusters, functional diversification of paralogous genes, and de novo gene generation in duplicons of the human FLVCR locus. Gene 286: 203-213, 2002.
Lipovich L, Lynch ED, Lee MK, and King MC. A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31. Genome Biology 2: 0011(e-publication), 2001.
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, and McCouch SR. Computational and experimental analysis of microsatellites in rice (Oryza sativa L): frequency, length variation, and utility as genetic markers. Genome Research 11: 1441-1552, 2001. Page 5 of 12
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park W, Ayres N, and Cartinhour S. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) Theoretical and Applied Genetics 100: 713-722, 2000.
Temnykh S, Park W, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, and McCouch SR. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.) Theoretical and Applied Genetics 100: 697-712, 2000.
* Asterisks denote present or past Lipovich Lab members