Leonard Lipovich, Ph.D.
Assistant Professor
3228 Scott Hall
540 East Canfield
Detroit, MI 48201
Voice: 313-577-9683
FAX: 313-577-5218
llipovich@med.wayne.edu
Assistant Professor (also with Neurology); Ph.D., University of Washington, 2003. Genomic complexity; primate comparative genomics; bioinformatics and functional genomics of long noncoding-RNA transcripts; computing the genomic basis of species phenotypic uniqueness.
Research Interests
A formidable conundrum of the post-genomic era is the abundance of eukaryotic transcripts which have limited interspecies conservation, do not encode proteins or small RNAs, and are devoid of known functional roles. My group integrates bioinformatics and experimentation to decode the complexity of mammalian transcriptomes, with an emphasis on primate and human phenotypic uniqueness. First, we are cataloguing primate-specfic and noncoding-RNA genes in the human genome, and enhancing multispecies genomic sequence comparisons with transcript-to-genome alignments aiming to understand gene birth and gene structure evolution in primates. Additionally, we are designing custom expression microarrays for analysis of the noncoding and nonconserved transcriptome. We will test for differential expression of noncoding-RNA and evolutionarily young genes under specific induced cell differentiation conditions in culture, as well as in brains of patients affected by neuropsychiatric disorders. Third, we will perform reverse RNomics by using specific human neuronally expressed long noncoding RNAs as baits to trap their interacting proteins. We are also interested in applying chIP-sequencing and system perturbation approaches for assignment of novel noncoding-RNA genes to regulatory networks downstream of known transcription factors. We are participating in a collaborative effort with King's College London and the Genome Institute of Singapore to functionally characterize the distinctions of the REST (NRSF) target gene repertoires between humans and mice.
Selected Publications
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. Mol 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 Biol 7:0041 (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.
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 cis-antisense
transcription in the human 5q31 protocadherin gene cluster. Journal of Molecular Evolution 62: 73-88, 2006.
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 and King MC. Novel transcriptional units and unconventional gene pairs in the human genome: toward a sequence-level basis for primate-specific phenotypes? Cold Spring Harbor Symposia on Quantitative Biology 68: 461-470, 2003.
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.
Center for Molecular Medicine and Genetics • Wayne State University School of Medicine • 3127 Scott Hall • 540 East Canfield • Detroit, MI 48201
Administrative Office: (313) 577-5323 Fax: (313) 577-5218 • Email: info@genetics.wayne.edu • Webmaster: webmaster@genetics.wayne.edu
