Informatics Specialist in Bioinformatics
Contact Information
Wilson Dental Library & Learning Center
Herman Ostrow School of Dentistry of USC
925 W. 34th Street, DEN 21
Los Angeles, CA 90089-0641


Yong-Hwee Eddie Loh

Liaison For


Library Responsibilities

Working with the team to develop an effective and innovative bioinformatics support for the UPC community. Leading the implementation of such strategy and carrying out the routine operation on UPC, including such tasks as user consultation, training, collaborative data analysis, as well as grant application support.

Leading the efforts of augmenting our bioinformatics software offering by implementing open-source bioinformatics tools on our own computing resources.  Developing workshops and provide training on such tools for USC users.

Managing users access of our licensed commercial software for UPC users, as well as participating in various daily operational activities of our program.

Maintains a current awareness of newly developed bioinformatics tools and develops innovative approaches to disseminating this information.

Contact me regarding

Bioinformatics workshop content and schedules
Bioinformatics resources relevant to specific research needs
Application of bioinformatics tools in various stages of research
Analysis and interpretation of high-throughput genomics data

Educational Background

PhD, Biology, Georgia Institute of Technology, USA, 2011

MS, Bioinformatics, Bioinformatics Institute, National University of Singapore, 2004

B.Eng, Chemical Engineering, National University of Singapore, 2000

Selected Publications & Presentations

Labonté B, Engmann O, Purushothaman I, Menard C, Wang J, Tan C, Scarpa JR, Moy G, Loh YE, Cahill M, Lorsch ZS, Hamilton PJ, Calipari ES, Hodes GE, Issler O, Kronman H, Pfau M, Obradovic ALJ, Dong Y, Neve RL, Russo S, Kazarskis A, Tamminga C, Mechawar N, Turecki G, Zhang B, Shen L, Nestler EJ. Sex-specific transcriptional signatures in human depression. Nat Med. 2017 Sep;23(9):1102-1111. doi: 10.1038/nm.4386. Epub 2017 Aug 21. PubMed PMID: 28825715.

Jiang Y*, Loh YE*, Rajarajan P, Hirayama T, Liao W, Kassim BS, Javidfar B, Hartley BJ, Kleofas L, Park RB, Labonte B, Ho SM, Chandrasekaran S, Do C, Ramirez BR, Peter CJ, C W JT, Safaie BM, Morishita H, Roussos P, Nestler EJ, Schaefer A, Tycko B, Brennand KJ, Yagi T, Shen L, Akbarian S. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet. 2017 Aug;49(8):1239-1250. doi: 10.1038/ng.3906. Epub 2017 Jul 3. PubMed PMID: 28671686; PubMed Central PMCID: PMC5560095.

Peña CJ, Kronman HG, Walker DM, Cates HM, Bagot RC, Purushothaman I, Issler O, Loh YE, Leong T, Kiraly DD, Goodman E, Neve RL, Shen L, Nestler EJ. Early life stress confers lifelong stress susceptibility in mice via ventral tegmental area OTX2. Science. 2017 Jun 16;356(6343):1185-1188. doi: 10.1126/science.aan4491. PubMed PMID: 28619944; PubMed Central PMCID: PMC5539403.

Engmann O, Labonté B, Mitchell A, Bashtrykov P, Calipari ES, Rosenbluh C, Loh YE, Walker DM, Burek D, Hamilton PJ, Issler O, Neve RL, Turecki G, Hurd Y, Chess A, Shen L, Mansuy I, Jeltsch A, Akbarian S, Nestler EJ. Cocaine-Induced Chromatin Modifications Associate With Increased Expression and Three-Dimensional Looping of Auts2. Biol Psychiatry. 2017 May 5. pii: S0006-3223(17)31517-2. doi: 10.1016/j.biopsych.2017.04.013. [Epub ahead of print] PubMed PMID: 28577753.

Descalzi G, Mitsi V, Purushothaman I, Gaspari S, Avrampou K, Loh YE, Shen L, Zachariou V. Neuropathic pain promotes adaptive changes in gene expression in brain networks involved in stress and depression. Sci Signal. 2017 Mar 21;10(471). pii: eaaj1549. doi: 10.1126/scisignal.aaj1549. PubMed PMID: 28325815; PubMed Central PMCID: PMC5524975.

Wan L, Wen H, Li Y, Lyu J, Xi Y, Hoshii T, Joseph JK, Wang X, Loh YE, Erb MA, Souza AL, Bradner JE, Shen L, Li W, Li H, Allis CD, Armstrong SA, Shi X. ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature. 2017 Mar 9;543(7644):265-269. doi: 10.1038/nature21687. Epub 2017 Mar 1. PubMed PMID: 28241141; PubMed Central PMCID: PMC5372383.

Loh YE, Feng J, Nestler E, Shen L. Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data. Bio Protoc. 2017 Feb 5;7(3). pii: e2123. doi: 10.21769/BioProtoc.2123. PubMed PMID: 28516124; PubMed Central PMCID: PMC5432020.

Loh YE*, Koemeter-Cox A*, Finelli MJ, Shen L, Friedel RH, Zou H. Comprehensive mapping of 5-hydroxymethylcytosine epigenetic dynamics in axon regeneration. Epigenetics. 2017 Feb;12(2):77-92. doi: 10.1080/15592294.2016.1264560. Epub 2016 Dec 5. PubMed PMID: 27918235; PubMed Central PMCID: PMC5330438.

Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YE, Ma Q, Mitchell AC, Pothula V, Stewart AF, Ernst P, Yao WD, Martin G, Shen L, Jakovcevski M, Akbarian S. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology. 2016 Dec;41(13):3103-3113. doi: 10.1038/npp.2016.144. Epub 2016 Aug 3. PubMed PMID: 27485686; PubMed Central PMCID: PMC5101561.

Lepack AE, Bagot RC, Peña CJ, Loh YE, Farrelly LA, Lu Y, Powell SK, Lorsch ZS, Issler O, Cates HM, Tamminga CA, Molina H, Shen L, Nestler EJ, Allis CD, Maze I. Aberrant H3.3 dynamics in NAc promote vulnerability to depressive-like behavior. Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12562-12567. Epub 2016 Oct 18. PubMed PMID: 27791098; PubMed Central PMCID: PMC5098673.

Quach H*, Rotival M*, Pothlichet J*, Loh YE*, Dannemann M, Zidane N, Laval G, Patin E, Harmant C, Lopez M, Deschamps M, Naffakh N, Duffy D, Coen A, Leroux-Roels G, Clément F, Boland A, Deleuze JF, Kelso J, Albert ML, Quintana-Murci L. Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. Cell. 2016 Oct 20;167(3):643-656.e17. doi: 10.1016/j.cell.2016.09.024. PubMed PMID: 27768888; PubMed Central PMCID: PMC5075285.

Loh YH, Shen L. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. Methods Mol Biol. 2016;1415:371-83. doi: 10.1007/978-1-4939-3572-7_18. PubMed PMID: 27115642.

Siddle KJ, Tailleux L, Deschamps M, Loh YH, Deluen C, Gicquel B, Antoniewski C, Barreiro LB, Farinelli L, Quintana-Murci L. bacterial infection drives the expression dynamics of microRNAs and their isomiRs. PLoS Genet. 2015 Mar 20;11(3):e1005064. doi: 10.1371/journal.pgen.1005064. eCollection 2015 Mar. Erratum in: PLoS Genet. 2015 Jun;11(6):e1005321. PubMed PMID: 25793259; PubMed Central PMCID: PMC4368565.

Hulsey CD, Roberts RJ, Loh YH, Rupp MF, Streelman JT. Lake Malawi cichlid evolution along a benthic/limnetic axis. Ecol Evol. 2013 Jul;3(7):2262-72. doi: 10.1002/ece3.633. Epub 2013 Jun 7. PubMed PMID: 23919168; PubMed Central PMCID: PMC3728963.

Loh YH, Bezault E, Muenzel FM, Roberts RB, Swofford R, Barluenga M, Kidd CE, Howe AE, Di Palma F, Lindblad-Toh K, Hey J, Seehausen O, Salzburger W, Kocher TD, Streelman JT. Origins of shared genetic variation in African cichlids. Mol Biol Evol. 2013 Apr;30(4):906-17. doi: 10.1093/molbev/mss326. Epub 2012 Dec 28. PubMed PMID: 23275489; PubMed Central PMCID: PMC3603313.

O’Quin KE, Smith D, Naseer Z, Schulte J, Engel SD, Loh YH, Streelman JT, Boore JL, Carleton KL. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. BMC Evol Biol. 2011 May 9;11:120. doi: 10.1186/1471-2148-11-120. PubMed PMID: 21554730; PubMed Central PMCID: PMC3116502.

Loh YH, Yi SV, Streelman JT. Evolution of microRNAs and the diversification of species. Genome Biol Evol. 2011;3:55-65. doi: 10.1093/gbe/evq085. Epub 2010 Dec 15. PubMed PMID: 21169229; PubMed Central PMCID: PMC3017390.

Sylvester JB, Rich CA, Loh YH, van Staaden MJ, Fraser GJ, Streelman JT. Brain diversity evolves via differences in patterning. Proc Natl Acad Sci U S A. 2010 May 25;107(21):9718-23. doi: 10.1073/pnas.1000395107. Epub 2010 May 3. PubMed PMID: 20439726; PubMed Central PMCID: PMC2906875.

Elango N, Lee J, Peng Z, Loh YH, Yi SV. Evolutionary rate variation in Old World monkeys. Biol Lett. 2009 Jun 23;5(3):405-8. doi: 10.1098/rsbl.2008.0712. Epub 2009 Mar 4. PubMed PMID: 19324652; PubMed Central PMCID: PMC2679907.

Loh YH, Brenner S, Venkatesh B. Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon). Mol Biol Evol. 2008 Mar;25(3):526-35. Epub 2007 Dec 17. Erratum in: Mol Biol Evol. 2008 Aug;25(8):1788. PubMed PMID: 18089580.

Loh YH, Katz LS, Mims MC, Kocher TD, Yi SV, Streelman JT. Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biol. 2008;9(7):R113. doi: 10.1186/gb-2008-9-7-r113. Epub 2008 Jul 10. PubMed PMID: 18616806; PubMed Central PMCID: PMC2530870.

Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S. Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol. 2007 Apr;5(4):e101. PubMed PMID: 17407382; PubMed Central PMCID: PMC1845163.

Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S. Ancient noncoding elements conserved in the human genome. Science. 2006 Dec 22;314(5807):1892. Erratum in: Science. 2007 Feb 9;315(5813):766. PubMed PMID: 17185593.

Loh YH, Christoffels A, Brenner S, Hunziker W, Venkatesh B. Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes. Genome Res. 2004 Jul;14(7):1248-57. Epub 2004 Jun 14. PubMed PMID: 15197168; PubMed Central PMCID: PMC442139.

*Joint first-author.