University of California, Riverside

Genetics, Genomics and Bioinformatics



Students


Steven AhrendtSteven Ahrendt picture

B.S., Biology, Purdue

Member of Stajich Lab

Awards: Dean's Distinguished Fellowship, 2010; Klotz Memorial travel award, 2012. Poster award from the Genetics Society of America for poster presentation at the 27th Fungal Genetics Conference, 2013.

Publications: Khodadad C, Ahrendt S, Parrish M, and Foster J. Microgravity-induced changes in the normal developmental time line of an animal-bacteria symbiosis. Scientific Reports. 2013.  Foster J, Kerney K, Parrish M, Khodadad C, and Ahrendt S. Potential of the Euprymna/Vibrio Symbiosis as a Model to Assess the Impact of Microgravity on Bacteria-Induced Animal Development. Gravitational and Space Biology. 2011.  Foster J, Green S, Ahrendt S, Golubic S, Reid RP, Hetherington K, Bebout L. Molecular and morphological characterization of cyanobacterial diversity in the marine stromatolites of Highborne Cay, Bahamas. ISME J. 2009.  La D, Esquivel-Rodriguez J, Venkatraman V, Li B, Sael L, Ueng S, Ahrendt S, and Kihara D. 3DSURFER: software for high throughput protein surface comparison and analysis. Bioinformatics. 2009.  Timothy Y. James, Adrian Pelin, Linda Bonen, Steven Ahrendt, Divya Sain, Nicolas Corradi, and Jason E Stajich. 2013. "Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia." Current Biology 23 (16).

Mikkal Blick

B.S., Biology, University of Redlands

Rotating

Awards:  Chancellor's Distinguished Fellowship and Summer Diversity Award, 2014.

 

 

Stephen Bolaris

B.S., Molecular and Cellular Biology, University of Arizona

Member of Larsen Lab

Awards:  Dean's Distinguished Fellowship, 2013; Best Poster--Plant Genome Stability and Change Conference, UC Davis, July 17-20, 2014.

 

Ilva CabreraIlva Cabrera

B.S. Molecular Cell Biology, California State University, Long Beach; B.A. Sociology, California State University, Long Beach

Member of Borkovich Lab

Currently I am investigating the role of regulators of G protein signaling (RGS) proteins in heterotrimeric G protein signaling in the model filamentous fungus Neurospora crassa.

Awards: NSF-IGERT Fellowship in Video Bioinformatics; FASEB MARC travel award, 2011; AGEP travel award, 2010; Graduate Division Fellowship, 2009.

Publications: Carla J. Eaton, Ilva E. Cabrera, Jacqueline A. Servin, Sara J. Wright, Murray P. Cox and Katherine A. Borkovich (2012) The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa. PLOS ONE

Thanin Chantarachot

B.S., Biology, Prince of Songkla University, Thailand; M.S., Botany, Chulalongkorn University, Thailand

Member of Bailey-Serres Lab

Awards: Thai Fellowship - The Institute for the Promotion of Teaching Science and Technology.


Stephanie CoffmanStephanie Coffman

B.S., Molecular and Cellular Biology, Cal State Fresno

Member of Ding Lab

Awards: Chancellor's Distinguished Fellowship, 2010.  Video Bioninformatics IGERT Fellowship, 2011.  Honorable Mention, 2012, Best Presentation, 2013 - GGB Graduate Student Research Symposium.

 

Jonathan DeansJonathan Deans

B.S., Bioinfomatics, UC Santa Cruz

Member of Sladek Lab

 

 

Albert DoAlbert Do

B.S., Biological Sciences, Cal State Fullerton; M.S., Biology UCI

Rotating

Awards:  Chancellor's Distinguished Fellowship, 2014.



Arit Ghosh

B.S.,  Biotechnology, West Bengal U.of Tech, India; M.S., University of Nebraska, Microbiology and Molecular Biology

Member of Borkovich Lab

My research revolves around the study of signal transduction pathways in the filamentous fungus – Neurospora crassa. Through my thesis, I would attempt to unravel the roles of different components of the mitogen-activated protein kinases (MAPK) and the G protein-signaling pathway in order to present an interactome level view of the signaling landscapes in Neurospora crassa.

Awards: Dean's Distinguished Fellowship, 2011.  Klotz Memorial Travel Award 2013.

Publications: Arit Ghosh, Jacqueline A. Servin, Gyungsoon Park and Katherine A. Borkovich, Global Analysis of Serine/Threonine and Tyrosine Protein Phosphatase Catalytic Subunit Genes in Neurospora crassa Reveals Interplay Between Phosphatases and the p38 Mitogen-Activated Protein Kinase. G3: Genes, Genomes, Genetics.

Raissa Green

B.S., Genetics, UC Davis

Member of White Lab

Awards: Dean's Distinguished Fellowship, 2011.

Ji Su HaJi Su Ha

B.S., Agriculture, Kyungpook National University, Korea

Member of Raikhel Lab

Awards: Dean's Distinguished Fellowship, 2011.

Publications:  Shiping Liu, Keira J. Lucas, Sourav Roy, Jisu
Ha, and Alexander S. Raikhel, Mosquito-specific microRNA-1174 targets serine hydroxymethyltransferase to control key functions in the gutPNAS 2014 ; published ahead of print September 22, 2014, doi:10.1073/pnas.1416278111.

Amanda HollowellAmanda Hollowell

B.S., Genetics, UC Davis

Member of Sachs lab

Awards: Graduate Division Fellowship, 2009.  2013-14 Graduate Research Mentoring Program Fellowship.

Meenakshi KagdaMeenakshi Kagda picture

B.S., Biotechnology, N.V. Patel College of Sciences, India; M.S., Biotechnology, BRD School of Biosciencesiology, India

Member of Judelson Lab 

Awards: Dean's Distinguished Fellowship, 2010.  Klotz Memorial Award for Travel (2013).  Oomycete Molecular Research Collaboration Network (OMGN) travel award (2013).

Publications:  Sourav Roy, Meenakshi Kagda, Howard S. Judelson (2013) Genome-wide Prediction and Functional Validation of Promoter Motifs Regulating Gene Expression in Spore and Infection Stages of Phytophthora infestans. PLoS Pathog 9(3): e1003182. doi:10.1371/journal.ppat.1003182

Conferences attended and poster presented at: Fungal Genetics Conference (2013) in Asilomar.  Oomycete Molecular Research Collaboration Network (OMGN) in Asilomar.

Lichao Li

B.S., Biotechnology, Beijing University of Chemical Technology

Rotating

Awards:  Dean's Distinguished Fellowship, 2014.

 

Ruidong Li

B.S., Agronomy, Huazhong Agricultural University; M.S., Genetics, Chinese Academy of Sciences.

Member of Gu Lab

Awards:  Dean's Distinguished Fellowship, 2013.

Shaofang LiShaofang Li

B.S., Biology, Northeast Normal University; M.S., Genetics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, China

Member of Chen Lab

Awards: Graduate Division Fellowship, 2009.  2013-14 Dissertation Year Program Fellowship.

Publications: Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S et al. 2014. DNA Topoisomerase 1 alpha Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis. Plos Genet 10(7).  Dinh TT, Luscher E, Li S, Liu X, Won SY, Chen X. 2014. Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors. Methods in molecular biology 1110: 127-156.  Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S et al. 2012. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336(6087): 1445-1448.

Yahui Li

B.S., Pharmaceutical Engineering, China Pharmaceutical University.

Member of Karginov Lab

Awards: Dean's Distinguished Fellowship, 2013.

Zhelin (Jeff) Li

B.S., Biology, Cal State LA

Rotating

Awards:  Chancellor's Distinguished Fellowship, 2014.

Publications: Barrett, C. F., Freudenstein, J. V., Li, J., Mayfield-Jones, D. R., Perez, L., Pires, J. C., and C. Santos. 2014. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution, DOI: 10.1093/molbev/msu252.

Conferences:  Presentation at the 22nd Annual CSULA Symposium on RSCA.

Jui-Yu LiaoJuiYu Liao

B.S. and M.S., Plant Pathology and Microbiology, National Taiwan University

Member of Jin Lab

Awards:  Dean's Distinguished Fellowship, 2014.

 

Yifan LiiYifan Lii

B.S, Biochemistry/Cell Biology, UC San Diego

Member of Jin lab

Awards: NSF-IGERT fellow.

Publications: Forward chemical screening of small RNA pathways. Lii Y, Jin H. Methods Mol Biol. 2014;1056:95-101. doi: 10.1007/978-1-62703-592-7_9.  Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues.
Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H.
Mol Plant. 2013 May;6(3):704-15. doi: 10.1093/mp/sst051. Epub 2013 Mar 15. Review.  Contribution of small RNA pathway components in plant immunity.
Seo JK, Wu J, Lii Y, Li Y, Jin H. Mol Plant Microbe Interact. 2013 Jun;26(6):617-25. doi: 10.1094/MPMI-10-12-0255-IA. Review.  Isolation and profiling of protein-associated small RNAs. Zhao H, Lii Y, Zhu P, Jin H. Methods Mol Biol. 2012;883:165-76. doi: 10.1007/978-1-61779-839-9_13.  Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Zhang X, Xia J, Lii YE, Barrera-Figueroa BE, Zhou X, Gao S, Lu L, Niu D, Chen Z, Leung C, Wong T, Zhang H, Guo J, Li Y, Liu R, Liang W, Zhu JK, Zhang W, Jin H. Genome Biol. 2012;13(3):R20. doi: 10.1186/gb-2012-13-3-r20.

Jinfeng Lujinfeng Lu picture

B.S., Biological Science, Peking University

Member of Ding Lab

Awards: Dean's Distinguished Fellowship, 2010. Honorable Mention - GGB Graduate Student Research Symposium, 2103.  2014-15 Dissertation Year Program Fellowship.

Maggie LuMaggie Lu

B.S., Biotechnology, UC Davis

Member of Le Roch Lab

Awards: Dean's Distinguished Fellowship, 2012.

Keira LucasKeira Lucas

B.S., Molecular Biology, Cal State Fresno

Member of A. Raikhel Lab

My research involves understanding the molecular mechanisms linked to female mosquito blood meal processes and reproductive events. In particular, I am investigating the role of both conserved and mosquito-specific microRNAs during the reproductive life stages of the female mosquito.

Awards: Dean's Distinguished Fellowship, 2010. Earle C. Anthony Travel award and an ESA Entomology 2013 Program Enhancement Fund award, 2013.

Publications:  Lucas, K.J. & Raikhel, A.S. (2013) Insect microRNAs: biogenesis, expression profiling and biological functions. Insect Biochem Mol Biol. 43(1):24-38. DOI: 10.1016/j.ibmb.2012.10.009. Epub 2012 Nov 16.  Lucas, K.J., Myles, K.M., & Raikhel, A.S. (2013) Small RNAs: a new frontier in mosquito biology. Trends Parasitol. 29(6):295-303. Lucas, K.J., Myles, K,M, & Raikhel, A.S. (2013) Small RNAs: a new frontier in mosquito biology. Trends Parasitol. ;29(6):295-303.

Mitchell LucasMitchell Lucas picture

B.S., Molecular, Cellular, Developmental Biology, Cal State Fresno

Member of Close Lab

• Marker-Assisted Selection
• "Bead-assay" SNP Genotyping
• Association Studies
• Comparative Genomics

Awards: Chancellor's Distinguished Fellowship, 2010.  2013 - 2015 USDA AFRI NIFA Fellowship.  2013-14 Dissertation Year Program Fellowship.


Sawyer Masonjones

B.S., Biology, University of Florida

Rotating

Awards:  Dean's Distinguished Fellowship, 2014.

 

 

Michael Matson Miichael Matson

B.S., Biological Sciences, University of Missouri-Columbia

Member of Judelson Lab

Awards: Dean's Distinguished Fellowship, 2012.  Best Poster - GGB Graduate Student Research Symposium, 2013. Plant Pathology Klotz travel grant.

Presentations: IIGB post-doc symposium, June 2104; Genetics, Genomics & Bioinformatics Graduate Student Research symposium.

Symposiums attended: North American Late Blight Symposium in Minneapolis, 2014.

Alexander Michkovaa

B.S., Agrochemistry and Soil Science, Moscow Timiriazev Agricultural Academy; M.S., Agricultural Biotechnology, Moscow Timiriazev Agricultural Academy, Russia

Member of Borkovich Lab

Awards: Dean's Distinguished Fellowship.

 


Sarah PerrySarah Perry

B.A., Biology, Westmont College

Member of Ray Lab

Awards: Dean's Distinguished Fellowship, 2010.




Patrick Schreiner

B.S., Biology and Bioinformatics, Loyola University

Member of Atkinson Lab

My research is regarding the identification of piRNA-mediated gene regulation.

Awards: Dean's Distinguished Fellowship, 2012.


 Jolly Shrivastava

B.S., Life Sciences, Ch. Charan Singh University, India; M.S., Biology, University of North Carolina; M.S., Biology, Cal State Fullerton

Member of Judelson Lab

I am working on Phytophthora infestans, causal agent of late blight potato disease. I am using bioinformatics tools to answer questions pertaining to variation in P. infestans that will help us in understanding the pathogenicity of the organism and develop more resistant potato plants.

Awards: Chancellor's Distinguished Fellowship, 2011. 

Publications: Judelson HS, Shrivastava J, Manson J (2012) Decay of Genes Encoding the Oomycete Flagellar Proteome in the Downy Mildew Hyaloperonospora arabidopsidis.PLoS ONE 7(10): e47624. doi:10.1371/journal.pone.0047624


Caroline SjogrenCaroline Sjogren

B.A., Biology, UC Riverside

Member of Larsen Lab

Awards: Dean's Distinguished Fellowship, 2011; Outstanding Teaching Assistant, 2013; Best Poster--Plant Genome Stability and Change Conference, UC Davis, July 17-20, 2014.  Awarded an NSF Fellowship to attend the conference.

Publications: Nezames CD, Sjogren CA, Barajas JF, Larsen PB. (2012). The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum-depenent root growth inhibition. Plant Cell (2) 608-21.

Eric Smith Eric Smith

B.A., Biology, University of Saint Thomas

Member of White Lab

Awards: Dean's Distinguished Fellowship, 2012.

 

 

Erin Sternburg

B.S.,  Biology, Cal State Long Beach

Member of Karginov Lab

Awards: Chancellor's Distinguished Fellowship, 2013.

 

 

Suhas Sureshchandra

B.S., Biotechnology, Visveswaraiah Technological University; M.S. Bioinformatics, Indiana University

Rotating

Awards: Dean's Distinguished Fellowship, 2014.

Publications: Bilian Jin, Jason Ernst, Rochelle L Tiedemann, Hongyan Xu, Suhas Sureshchandra, Manolis Kellis, Stephen Dalton, Chen Liu, Jeong-Hyeon Choi and Keith Robertson. "Linking DNA Methyltransferases (DNMTs) to epigenetic marks and nucleosome structure genome-wide in human tumor cells" Cell Reports 2(5):1411-1424, 2012. Mark P. Peterson, Danielle J. Whittaker, Shruthi Ambreth, Suhas Sureshchandra, Keithanne Mockatis, Aaron Buechlein, Jeong-Hyeon Choi, Zhao Lai, John Colbourne, Haixu Tang and Ellen Ketterson. "De novo transcriptome sequencing in a songbird, the dark-eyes junco (Junco hyemalis): Genomic tools for an ecological model system" BMC Genomics, 13:305, 2012. Hongseok Tae, DongSung Ryu, Suhas Sureshchandra and Jeong-Hyeon Choi. "ESTClean: A Cleaning Tool for Next-Gen Transcriptome Shotgun sequencing" BMC Bioinformatics, 13:247, 2012.

Poster Presentation: BSpipe – A software package for next-gen bisulfite sequencing data analysis" 2011 IEEE International Conference on Bioinformatics and Biomedicine, Atlanta Georgia.

 

 

Tim TranTim Tran

B.S., Microbiology, UC Davis; M.S., Biomedical Lab Science, San Francisco State

Member of Nugent Lab

Awards: Dean's Distinguished Fellowship, 2012; Summer Diversity Stipend, 2012.

Publications: Am J Transplant. 2012 Oct;12(10):2710-2718. doi: 10.1111/j.1600-6143.2012.04253.x.
A Peripheral Blood Diagnostic Test for Acute Rejection in Renal Transplantation.
Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R,Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM.


More Information 

Footer