Leonard Lipovich, PhD

Leonard Lipovich, PhD

Leonard Lipovich, PhD

Narrative Bio

Leonard Lipovich, a graduate of Stuyvesant High School, New York City, earned his B.A. (cum laude) in Genetics and Development from Cornell University (Ithaca, N.Y.) in 1998, and his Ph.D. in Genome Sciences from the University of Washington, Seattle, where Mary-Claire King was his dissertation advisor, in 2003. He completed his postdoctoral training at the Genome Institute of Singapore, where he discovered the first mammalian long non-coding RNA (lncRNA) directly functional in mammalian stem cell pluripotency, and pioneered the concept of lncRNA evolutionary non-conservation, highlighting the abundance of primate-specific lncRNAs in humans. Subsequently, Dr. Lipovich joined Wayne State University in Detroit, Michigan in 2007 as an assistant professor, and was promoted to associate professor with tenure in 2013. The Lipovich Lab was the first group in the world to empirically examine long non-coding RNA (lncRNA) translation in human cells using mass spectrometry, finding that most lncRNAs are not translated, a result validated independently later by other investigators with Ribo-seq approaches. In 2014, Dr. Lipovich received the U.S. National Institutes of Health (NIH) Director's New Innovator Award (a USD $2,300,000 grant) for his work on how primate-specific long non- coding RNAs regulate cell growth and cell death in human breast cancer. Current research in the Lipovich laboratory interrogates the contribution of long non-coding RNA genes to human cancer and metabolic disorders, using integrated computational and experimental approaches: high-throughput reverse genetics, non-coding RNA proteogenomics, and targeted functional validation of direct disease causal lncRNA exonic variants from Genome-Wide Association Studies and Whole-Genome Sequencing of large population cohorts. Dr. Lipovich chaired the Keystone Symposium and the Royal Society International Scientific Meeting on lncRNAs in 2015. He serves on the NIH Accelerating Medicines Partnership (AMP) Coordination Committee. Dr. Lipovich, a funded CHARGE Consortium co-investigator, participated in the ENCODE (Encyclopedia of DNA Elements) and FANTOM (Functional Annotation of Mammalian cDNA) consortia. His long-term goal is to improve human health through personalized, lncRNA-targeted post-genomic therapeutics.

Office Address

540 E Canfield, 3208 Scott Hall, Detroit, MI 48201

Awards & Honors

2018 - The Charles H. Gershenson Distinguished Faculty Fellowship, Wayne State University

2018 – Invited speaker, organizing committee member, and session chair, BGRS/SB'18 (Bioinformatics of Genome Regulation and Structure / Systems Biology ) biannual international conference, Novosibirsk, Russia.

2018,2017,2016,2013 - Invited speaker and session chair, Bio-IT World, Boston (4 times)

2018 and 2016 – Assigned reviewer, NIH (NCI) F99/K00 study section

2013, 2017: Research Excellence Award, School of Medicine, Wayne State University

2017: Speaker, 38th annual Lorne Genome Conference, Australia

2016: Speaker, American Diabetes Association: 76th Scientific Sessions

2016: Invited guest instructor (“The Non-Coding Genome”), VIB (Belgium)

2016: Golden Tiger Award (category: Exceptional Contributions), CHARGE Consortium

2016: Invited Speaker, EMBO Workshop: Systems Biology of Non-Coding RNAs

2015: Assigned Reviewer, NIH, CSR MGB (Molecular Genetics B) & NCI-I Study Sections

2015: Lead organizer, The Royal Society Scientific Meeting on LncRNA

2015: Chair, Keystone Symposium: Long Non-Coding RNA

2014: NIH Director’s New Innovator Award

2014: Invited speaker, Non-Coding RNAs in Cancer (Heidelberg)

2014: Invited speaker, American Society of Gene and Cell Therapy

2014: Invited speaker and session chair, Molecular Medicine Tri-Conference

2014: Invited speaker, King Abdullah University of Science and Technology, Saudi Arabia

2014: Speaker and travel fellowship winner, The RNA Society annual meeting

2013: Research Excellence Award, School of Medicine, Wayne State University

2013: Visiting faculty fellowship, University of New South Wales (Sydney)

2013: Invited speaker, Functional Non-Coding RNA (Baeza, Spain) (chair: John Rinn)

2012: College Teaching Award, School of Medicine, Wayne State University

2012: Speaker and invited workshop chair, Keystone Symposium: Non-Coding RNAs

2012: Invited speaker, AACR Conference: Non-Coding RNAs (organizer: Phil Sharp)

2011: Invited session co-chair, ASHG / International Congress of Human Genetics

2011, 2004: Invited speaker, FANTOM Consortium (4 invited talks given, total)

2010: Speaker, conference award, HHMI, “From the RNA World to the Clinic”

2003: Travel scholarship winner, Cold Spring Harbor Symposia

2001: Travel scholarship winner, Keystone Symposium: Human Genetics / Genomics

2001, 2000: Travel Scholarship winner, The Institute for Genomic Research ( 2 awards)

1998-1994: Dean’s List, Cornell University (7 of 8 quarters)

1992: Regional winner, NASA/NSTA Student Space Involvement Program

1991: Semifinalist, National Merit Scholarship (PSAT score: top 5% New York State)

Undergraduate

Cornell University; Ithaca, New York; B.A. cum laude, Biological Sciences, 1998

Graduate

University of Washington, Seattle, Ph.D. (Molecular Biotechnology), 2003

Position Title

Associate Professor of Molecular Medicine and Genetics, and of Neurology

Prior Appointments

Research Scientist, Genome Institute of Singapore, 2003-2006

Senior Research Scientist (faculty), Genome Institute of Singapore, 2006-2007

Adjunct Assistant Professor, Nanyang Technological University, Singapore, 2006-2007.

Interests

Human genomics, long noncoding RNA, and primate evolution.

Publications

(selected):

Research Summary

Long non-¬coding RNA (lncRNA) genes in human disease and primate phenotypic uniqueness. Identification of disease-¬causing lncRNAs by Genome-¬Wide Association Studies, reverse genetics, and laboratory-¬based validation experiments. Targeting lncRNAs for personalized therapeutics.

1. Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, and Forrest AR. An atlas of human long non-coding RNAs with accurate 5' ends. Nature 543: 199-204, 2017.doi: 10.1038/nature21374.

2: Barry G, Briggs JA , Hwang DW, Nayler SP, Fortuna PR, Jonkhout N, Dachet F, Maag JL, Mestdagh P, Singh EM, Avesson L, Kaczorowski DC, Ozturk E, Jones NC, Vetter I, Arriola-Martinez L, Hu J, Franco GR, Warn VM, Gong A, Dinger ME, Rigo F, Lipovich L, Morris MJ, O'Brien TJ, Lee DS, Loeb JA, Blackshaw S, Mattick JS, Wolvetang EJ. The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states. Sci Rep. 2017 Jan 5;7:40127. doi: 10.1038/srep40127. PubMed PMID: 28054653; PubMed Central PMCID: PMC5214838.

3: Li M, Li Y, Weeks O, Mijatovic V, Teumer A, Huffman JE, Tromp G, Fuchsberger C, Gorski M, Lyytikäinen LP, Nutile T, Sedaghat S, Sorice R, Tin A, Yang Q, Ahluwalia TS, Arking DE, Bihlmeyer NA, Böger CA, Carroll RJ, Chasman DI, Cornelis MC, Dehghan A, Faul JD, Feitosa MF, Gambaro G, Gasparini P, Giulianini F, Heid I, Huang J, Imboden M, Jackson AU, Jeff J, Jhun MA, Katz R, Kifley A, Kilpeläinen TO, Kumar A, Laakso M, Li-Gao R, Lohman K, Lu Y, Mägi R, Malerba G, Mihailov E, Mohlke KL, Mook-Kanamori DO, Robino A, Ruderfer D, Salvi E, Schick UM, Schulz CA, Smith AV, Smith JA, Traglia M, Yerges-Armstrong LM, Zhao W, Goodarzi MO, Kraja AT, Liu C, Wessel J; CHARGE Glycemic-T2D Working Group,.; CHARGE Blood Pressure Working Group,., Boerwinkle E, Borecki IB, Bork-Jensen J, Bottinger EP, Braga D, Brandslund I, Brody JA, Campbell A, Carey DJ, Christensen C, Coresh J, Crook E, Curhan GC, Cusi D, de Boer IH, de Vries AP, Denny JC, Devuyst O, Dreisbach AW, Endlich K, Esko T, Franco OH, Fulop T, Gerhard GS, Glümer C, Gottesman O, Grarup N, Gudnason V, Harris TB, Hayward C, Hocking L, Hofman A, Hu FB, Husemoen LL, Jackson RD, Jørgensen T, Jørgensen ME, Kähönen M, Kardia SL, König W, Kooperberg C, Kriebel J, Launer LJ, Lauritzen T, Lehtimäki T, Levy D, Linksted P, Linneberg A, Liu Y, Loos RJ, Lupo A, Meisinger C, Melander O, Metspalu A, Mitchell P, Nauck M, Nürnberg P, Orho-Melander M, Parsa A, Pedersen O, Peters A, Peters U, Polasek O, Porteous D, Probst-Hensch NM, Psaty BM, Qi L, Raitakari OT, Reiner AP, Rettig R, Ridker PM, Rivadeneira F, Rossouw JE, Schmidt F, Siscovick D, Soranzo N, Strauch K, Toniolo D, Turner ST, Uitterlinden AG, Ulivi S, Velayutham D, Völker U, Völzke H, Waldenberger M, Wang JJ, Weir DR, Witte D, Kuivaniemi H, Fox CS, Franceschini N, Goessling W, Köttgen A, Chu AY. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function. J Am Soc Nephrol. 2017 Mar;28(3):981-994. doi:10.1681/ASN.2016020131. Epub 2016 Dec 5.ASN.2016020131. PubMed PMID: 27920155..

4. Mohamed Yusoff A, Tan TK, Hari R, Koepfli KP, Wee WY, Antunes A, Sitam FT, Rovie-Ryan JJ, Karuppannan KV, Wong GJ, Lipovich L, Warren WC, O'Brien SJ, Choo SW. De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. Sci Rep. 2016 Sep 13;6:28199. doi: 10.1038/srep28199. PubMed PMID: 27618997; PubMed Central PMCID: PMC5020319.

5. Willems SM, Cornes BK, Brody JA, Morrison AC, Lipovich L, Dauriz M, Chen Y, Liu CT, RybinDV, Gibbs RA, Muzny D, Pankow JS, Psaty BM, Boerwinkle E, Rotter JI, Siscovick DS, Vasan RS, Kaplan RC, Isaacs A, Dupuis J, van Duijn CM, and Meigs JB. Association of the IGF1 gene with fasting insulin levels. Eur J Hum Genet. 24: 1337-1343, 2016.

6. Liu CT, Raghavan S, Maruthur N, Kabagambe EK, Hong J, Ng MC, Hivert MF, Lu Y, An P, Bentley AR, Drolet AM*, Gaulton KJ, Guo X, Armstrong LL, Irvin MR, Li M, Lipovich L, Rybin DV, Taylor KD, CHARGE Consortium Member List, AAAG Consortium, CARe Consortium, COGENT-­BP Consortium, eMERGE Consortium, MEDIA Consortium, MAGIC Consortium, Province MA, Kao WH, Siscovick DS, Psaty BM, Wilson JG, Loos RJ, Dupuis J, Rich SS, Florez JC, Rotter JI, Morris AP, and Meigs JB. Trans-ethnic meta-analysis and functional annotation Illuminates the genetic architecture of fasting glucose and insulin. Am J Hum Genet. 99: 56-75, 2016. PMID:27321945 PMCID: PMC5005440 DOI:10.1016/j.ajhg.2016.05.006

7. Milligan MJ, Harvey E, Yu A, Morgan AL, Smith DL, Zhang E, Berengut J, Sivananthan J, Subramaniam R, Skoric A, Collins S, Damski C, Morris KV, Lipovich L. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome. Front Genet. 2016 Mar 24;7:26. doi: 10.3389/fgene.2016.00026. PubMed PMID: 27047535; PubMed Central PMCID: PMC4805607.

8. Lipovich L, Hou Z, Jia H*, Sinkler C, McGowen M, Sterner K, Weckle A, Sugalski A*, Pipes L, Gatti D, Mason C, Sherwood C, Hof P, Kuzawa C, Grossman L, Goodman M, and Wildman D. High- throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. J Comp Neurol. 524: 288-308, 2016. PMID:26132897 PMCID: PMC4685035 DOI:10.1002/cne.23843.

9. Bannon MJ, Savonen CL, Jia H*, Dachet F, Halter SD, Schmidt CJ, Lipovich L, Kapatos G. Identification of long noncoding RNAs dysregulated in the midbrain of human cocaine abusers. J Neurochem. 135: 50-59, 2015.PMID:26222413PMCID:PMC4830632 DOI:10.1111/jnc.13255.

10.Milligan MJ, Lipovich L. Pseudogene-derived lncRNAs: emerging regulators of gene expression. Front Genet. 2015 Feb 4;5:476. doi: 10.3389/fgene.2014.00476.PubMed PMID: 25699073; PubMed Central PMCID: PMC4316772.

11. Wessel J, Chu AY, Willems SM, Wang S, Yaghootkar H, Brody JA, Dauriz M, Hivert MF, Raghavan S, Lipovich L, Hidalgo B, Fox K, Huffman JE, An P, Lu Y, Rasmussen-Torvik LJ, Grarup N, Ehm MG, Li L, Baldridge AS, Stančáková A, Abrol R, Besse C, Boland A, Bork-Jensen J, Fornage M, Freitag DF, Garcia ME, Guo X, Hara K, Isaacs A, Jakobsdottir J, Lange LA, Layton JC, Li M, Hua Zhao J, Meidtner K, Morrison AC, Nalls MA, Peters MJ, Sabater-Lleal M, Schurmann C, Silveira A, Smith AV, Southam L, Stoiber MH, Strawbridge RJ, Taylor KD, Varga TV, Allin KH, Amin N, Aponte JL, Aung T, Barbieri C, Bihlmeyer NA, Boehnke M, ombieri C, Bowden DW, Burns SM, Chen Y, Chen YD, Cheng CY, Correa A, Czajkowski J, Dehghan A, Ehret GB, Eiriksdottir G, Escher SA, Farmaki AE, Frånberg M, Gambaro G, iulianini F, Goddard WA 3rd, Goel A, Gottesman O, Grove ML, Gustafsson S, Hai Y, Hallmans G, Heo J, Hoffmann P, Ikram MK, Jensen RA, Jørgensen ME, Jørgensen T, Karaleftheri M, Khor CC, Kirkpatrick A, Kraja AT, Kuusisto J, Lange EM, Lee IT, Lee WJ, Leong A, Liao J, Liu C, Liu Y, Lindgren CM, Linneberg A, Malerba G, Mamakou V, Marouli E, Maruthur NM, Matchan A, McKean-Cowdin R, McLeod O, Metcalf GA, Mohlke KL, Muzny DM, Ntalla I, Palmer ND, Pasko D, Peter A, Rayner NW, Renström F, Rice K, Sala CF, Sennblad B, Serafetinidis I, Smith JA, Soranzo N, Speliotes EK, Stahl EA, Stirrups K, Tentolouris N, Thanopoulou A, Torres M, Traglia M, Tsafantakis E, Javad S, Yanek LR, Zengini E, Becker DM, Bis JC, Brown JB, Cupples LA, Hansen T, ngelsson E, Karter AJ, Lorenzo C, Mathias RA, Norris JM, Peloso GM, Sheu WH, Toniolo D, Vaidya D, Varma R, Wagenknecht LE, Boeing H, Bottinger EP, Dedoussis G, Deloukas P, Ferrannini E, Franco OH, Franks PW, Gibbs RA, Gudnason V, Hamsten A, Harris TB, Hattersley AT, Hayward C, Hofman A, Jansson JH, Langenberg C, Launer LJ, Levy D, Oostra BA, O'Donnell CJ, O'Rahilly S, Padmanabhan S, Pankow JS, Polasek O, Province MA, Rich SS, Ridker PM, Rudan I, Schulze MB, Smith BH, Uitterlinden AG, Walker M, Watkins H, Wong TY, Zeggini E; EPIC-InterAct Consortium., Laakso M, Borecki IB, Chasman DI, Pedersen O, Psaty BM, Tai ES, van Duijn CM, Wareham NJ, Waterworth DM, Boerwinkle E, Kao WH, Florez JC, Loos RJ, Wilson JG, Frayling TM, Siscovick DS, Dupuis J, Rotter JI, Meigs JB, Scott RA, Goodarzi MO. Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility. Nat Commun. 2015 Jan 29;6:5897. doi: 10.1038/ncomms6897. PubMed PMID: 25631608; PubMed Central PMCID: PMC4311266.18. Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, Saxena A; FANTOM Consortium. CAGE­defined promoter regions of the genes implicated in Rett Syndrome. BMC Genomics. 15: 1177, 2014. doi: 10.1186/1471-2164­15­1177.

12. Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, and Bajic VB. Promoter analysis reveals globally differential regulation of human long non­coding RNA and protein-coding genes. PLoS One. 9(10): e109443, 2014. doi: 10.1371/journal.pone.0109443.^ joint last authors

13. Kuzawa CW, Chugani HT, Grossman LI, Lipovich L, Muzik O, Hof PR, Wildman DE, Sherwood CC, Leonard WR, and Lange N. Metabolic costs and evolutionary implications of human brain development. Proc Natl Acad Sci U S A. 111: 13010­13015, 2014

14. Forrest AR, FANTOM Consortium member list (including Jia H*, Lipovich L, Wood EJ*), Hayashizaki Y; RIKEN PMI and CLST (DGT); FANTOM Consortium. A promoter­level mammalian expression atlas. Nature 507: 462­470, 2014.

15. Lipovich L, Tarca AL, Cai J*, Jia H*, Chugani HT, Sterner KN, Grossman LI, Uddin M, Hof PR, Sherwood CC, Kuzawa CW, Goodman M, Wildman DE: Developmental Changes in the Transcriptome of Human Cerebral Cortex Tissue: Long Noncoding RNA Transcripts. Cerebral Cortex 2014. doi: 10.1093/cercor/bhs414

16. Wood EJ, Chin-Inmanu K, Jia H, Lipovich L. Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. Front Genet. 2013 Sep 26;4:183. doi: 10.3389/fgene.2013.00183. e-publication.

17. Bianchi S, Stimpson CD, Duka T, Larsen MD, Janssen WG, Collins Z, Bauernfeind AL, Schapiro SJ, Baze WB, McArthur MJ, Hopkins WD, Wildman DE, Lipovich L, Kuzawa CW, Jacobs B, Hof PR, and Sherwood CC. Synaptogenesis and development of pyramidal neuron dendritic morphology in the chimpanzee neocortex resembles humans.
Proc Natl Acad Sci USA 110 Suppl 2: 1 10395-10401, 2013.

18. Sterner KN, McGowen MR, Chugani HT, Tarca AL, Sherwood CC, Hof PR, Kuzawa CW, Boddy AM, Raaum RL, Weckle A, Lipovich L, Grossman LI, Uddin M, Goodman M, and Wildman DE. Characterization of human cortical gene expression in relation to glucose utilization. Am J Hum Biol 25: 418-430, 2013.

19. Kraus P, Sivakamasundari V, Lan Lim S, Xing X, Lipovich L, Lufkin T: Making sense of Dlx1 antisense RNA. Developmental Biology 376: 224-235, 2013.

20. 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 192: 1133-1148, 2012.

21. 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

22. 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.

23. Wood E*, Lipovich L: MicroRNAs in opioid addiction: elucidating evolution. Frontiers Genet 3: 241, 2012.

24. Miller DJ, Duka T, Stimpson CD, Schapiro SJ, Baze WB, McArthur MJ, Fobbs AJ, Sousa AM, Sestan N, Wildman DE, Lipovich L, Kuzawa CW, Hof PR, Sherwood CC: Prolonged myelination in human neocortical evolution. Proc Natl Acad Sci USA 109: 16480-16485, 2012.

25. Sterner KN, Weckle A, Chugani HT, Tarca AL, Sherwood CC, Hof PR, Kuzawa CW, Boddy AM, Abbas A, Raaum RL, Grégoire L, Lipovich L, Grossman LI, Uddin M, Goodman M, Wildman DE: Dynamic gene expression in the human cerebral cortex distinguishes children from adults. PLoS One 7: e37714, 2012.

26. Michelhaugh SK#, Lipovich L#, Blythe J*, Jia H*, Kapatos G, 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

27. Jia H*, Osak M*, Bogu GK, Stanton LW, Johnson R, Lipovich L: Genome-wide computational identification and manual annotation of human long noncoding RNA genes.
RNA 16: 1478-1487, 2010.

28. Sheik Mohamed J*, Gaughwin PM, Lim B, Robson P, Lipovich L: Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16: 324-337, 2010.

29. Tay SK*, Blythe J*, Lipovich L: Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci USA 106: 12019-12024, 2009.

30. Goodman M, Sterner KN, Islam M, Uddin M, Sherwood CC, Hof PR, Hou ZC, Lipovich L, Jia H*, Grossman LI, Wildman DE: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. Proc Natl Acad Sci USA 106: 20824-20829, 2009.

31. Johnson R, Teh CHL, Jia H*, Vanisri RR*, Pandey T*, Lu ZH*, Buckley NJ, Stanton LW, Lipovich L: Regulation of neural macroRNAs by the transcriptional repressor, REST.
RNA 15: 85-96, 2009.

32. Lee TM*, Lipovich L: Structural differences of orthologous genes: insights from human-primate comparisons. Genomics 92: 134-143, 2008.

33. Kunarso G*, Wong KY, Stanton LW, 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.

34. 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, Stanton LW: REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biology 6(10):e256(e-publication), 2008.

35. Lim CY, Tam WL, Zhang J, Ang HS, Jia H*, Lipovich L, Ng HH, Wei CL, Sung WK, Robson P, Yang H, Lim B: Sall4 Regulates Distinct Transcription Circuitries in Different Blastocyst-Derived Stem Cell Lineages. Cell Stem Cell 3: 543-554, 2008.

36. Orlov Y, Zhou JT, Lipovich L, Shahab A, 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.

37. 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, Liu ET: Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genetics 3(6):e87 (e-publication), 2007.

38. Engström 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^, Lipovich L^: Complex loci in mammalian genomes. PLoS Genetics 2(4):e47 (e-publication), 2006.^ joint last authors.

39. 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, Hayashizaki Y: Mice and men: their promoter properties. PLoS Genetics 2(4):e54 (e-publication), 2006.

40. 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, Ng HH: The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics 38: 431-440, 2006.

41. Lipovich L, Vanisri RR*, Kong SL, Lin CY, Liu ET: Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. Journal of Molecular Evolution 62: 73-88, 2006.

42. Lipovich L, King MC: Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Research 16: 45-54, 2006.

43. 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.

44. Carninci P, FANTOM Consortium full membership list (more than 200 authors, 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.

45. Ng WP, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Wong CH, Ridwan A, Liu ET, Ruan Y: Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2: 105-111, 2005.

46. Wei CL, Ng WP, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y: 5’ Long Serial Analysis of Gene Expression (LongSAGE) and 3’ LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci USA 101: 11701-11706, 2004.

47. Lipovich L, Abkowitz J, King MC, Hughes A, 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.

48. Lipovich L, Lynch ED, Lee MK, King MC: A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31. Genome Biology 2:0011(e-publication), 2001.
II. Review Articles:

49. Lipovich L, Johnson R, 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.

50. Johnsson P, Lipovich L, Grandér D, Morris KV. Evolutionary conservation of long noncoding RNAs; sequence, structure, function. Biochim Biophys Acta. 2014. doi:pii: S0304-4165(13)00475-3. 10.1016/j.bbagen.2013.10.035. [Epub ahead of print]
 

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