Student publications

2016 Student Publications

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species
Phung TN, Huber CD, Lohmueller KE.
PLOS Genetics. August 2016.

PReFerSim: fast simulation of demography and selection under the Poisson Random Field model
Ortega-Del Vecchyo D, Mardsen CD,  Lohmueller KE.
Bioinformatics. July 2016.

SURVIV for survival analysis of mRNA isoform variation
Shen S, Wang Y, Wang C, Wu YN, Xing Y.
Nature Communications. June 2016.

Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets.
Cass A, Bahn JH, Lee JH, Creer C, Kim Y, Hsiao YE, Xiao X.
Nucleic Acids Research. 2016.

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.
Brown R, Lee H, Eskin A, Kichaev G, Lohmueller KE, et al.
European journal of human genetics: EJHG. January 2016.

Genomic flatlining in the endangered island fox.
Robinson, JA, Ortega-Del Vecchyo D, Fan Z, Kim BY, vonHoldt BM, Marsden CD, Lohmueller KE*, Wayne RK*.
Current Biology. 2016.


2015 Student Publications

Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies.
Kichaev G, Pasaniuc B.
American Journal of Human Genetics. 2015; 97(2):260-71.

Identification of causal genes for complex traits.
Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E.
Bioinformatics (Oxford, England). 2015; 31(12):i206-13.

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.
Brown R, Lee H, Eskin A, Kichaev G, Lohmueller KE, Reversade B, Nelson SF, Pasaniuc, B.
European Journal of Human Genetics. 2015.

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, et al.
PLoS Genetics. 2014; 10(10):e1004722.

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen, P-Y, and Pellegrini, M.
BMC Genomics. 2013; 14(1):774.

Dual Roles of RNF2 in Melanoma Progression
Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, KEung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar A, Ernst J, Chin L.
Cancer Discovery. 2015; CD-15.

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.
Brown R., et al.
European Journal of Human Genetics. 2015.

Leveraging local ancestry to detect gene-gene interactions in genome-wide data.
Aschard H., Gusev A, Brown R, and Pasaniuc B.
BMC Genetics. 2015; 16(1):124.

Natural selection reduces linked neutral divergence between distantly related species.
Phung T., Huber C., and Lohmueller K.
bioRxiv. 2015.

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates.
Aakre CD, Herrou J, Phung TN, Perchu, BS, Crosson S, and Laub,MT.
Cell. 2015; 163(3):594-606.

Genetic and environmental control of host-gut microbiota interaction.
Org E, Parks B, Joo JW, Mehrabian M, Blum Y, Kang EY, Emert B, Knight R, Drake T, Eskin E, Lusis AJ.
Genome Research. 2015.

Efficient and accurate multiple-phenotype regression method for high dimensional data considering population structure.
Joo JW, Kang EY, Org E, Furlotte N, Parks B, Lusis AJ, Eskin E.
Research in Computational Molecular Biology. 2015; 136-153.

Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth. frontiers in plant science.
Maymon M., Martinez-Hidalgo P, Tran S, Ice T, Craemer K, Anbarchian T, et al.
Frontiers in Plant Science. 2015.

A Simple Strategy for Reducing False Negatives in Calling Variants from Single-Cell Sequencing Data.
Cong J, Miao Z, He X.
PLoS ONE. 2015; 10(4).

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers.
Sidore C, Busonero F, Maschio A, Porcu E, Naitza S, Zoledziewska M, Mulas A, Pistis G, Steri M, Danjou F, Kwong A, Ortega Del Vecchyo D, Chiang CWK, Bragg-Gresham J, et al.
Nature Genetics. 2015.

Height-reducing variants and selection for short stature in Sardinia.
Zoledziewska M, Sidore C, Chiang CWK, Sanna S, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A, Ortega Del Vecchyo D, Floris M, et al.
Nature Genetics. 2015.

The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice.
Li Z, Yu J, Hosohama L, Nee K, Gkountela S, Chaudhari S, Cass AA, Xiao X, Clark AT.
The EMBO Journal. 2015; 34: 748-758.

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility.
Wang Y, Cheng H, Pan Z, Ren J, Liu Z, Xue Y.
Journal of Molecular Cell Biology. 2015.

dbPSP: a curated database for protein phosphorylation sites in prokaryotes.
Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z, Xue Y.
Database. 2015.

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse.
Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobson SE, Pellegrini M.
eLife 4. 2015; e06205.

Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.
Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB.
Nature Communications. 2015.

Anti-inflammatory therapies of amyotrophic lateral sclerosis guided by immune pathways.
Lam L, Halder RC, Montoya DJ, Rubbi L, Rinaldi A, Sagong B, Weitzman S, Rubattino R, Singh RR, Pellegrini M, Fiala M.
Am J Neurodegener Dis. 2015; 4(2):28-39.

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.
Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.
BMC Genomics. 2015; 16 Suppl 12:S11.


2014 Student Publications

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, et al.
PLoS genetics. 2014; 10(10):e1004722.

Human germline and pan-cancer variomes and their distinct functional profiles.
Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R.
Nucleic Acids Research. 2014; gku772.

Census-based rapid and accurate metagenome taxonomic profiling.
Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R.
BCM genomics. 2014; 15(1):918.

Amerindian-specific regions under positive selection harbour new lipid variants in Latinos.
Ko A, Cantor RM, Weissglas-Volkov D, Nikkola E, Linga Reddy PMV, Sinsheimer JS, Pasaniuc B, Brown R, Alvarez M, Rodriguez A, et al.
Nature communications. 2014; 5(3983).

Enhanced methods for local ancestry assignment in sequenced admixed individuals.
Brown R, Pasaniuc B.
PLoS Comput Biol. 2014; 10(4).

Privacy Preserving Protocol for Detecting Genetic Relatives Using Rare Variants.
Hormozdiari F, Joo JW, Guan F, Ostrosky R, Sahai A, Eskin E.
Bioinformatics. 2014; 30(12): i204-i211.

Identifying Genetic Relatives without Compromising Privacy.
He D, Furlaotte NA, Hormozdiari F, Joo JW, Ostrovsky R, Sahai A, Eskin E.
Genome Res. 2014; 24(4): 664-72.

Genome-Wide Association Study for Age-Related Hearing Loss (AHL) in the Mouse: A Meta-Analysis.
Ohmen F, Kang EU, Li X, Joo JW, Hormozdiari F, Zheng QY, Davis R, Lusis AJ, Eskin E, Friedman R.
Journal of the Association for Research in Otolaryngology. 2014; 15(3):335-352.

Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies
Joo JW, Sul JH, Han B, Ye C, Eskin E.
Genome biology. 2014; 15(4): r61.

Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins.
Yourshaw M, Taylor SP, Rao AR, Martin MG, Nelson SF.
Briefings in bioinformatics. 2014; bbu008.

Genome sequencing highlights the dynamic early history of dogs.
Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, et al.
PLoS genetics. 2014; 10(1):e1004016

PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.
Wang J, Lin X, Wang S, Wang C, Wang Q, Duan X, Lu P, Wang Q, Wang C, Liu XS, Huang J.
Scientific Reports. 2014; 4.

Comparative analysis of metazoan chromatin architecture.
Ho JWK, Liu T, Jung YL, Alver BH, Lee S, Wang C, et al.
Nature. 2014; 512(7515):449-52.

COX-2 inhibition prevents the appearance of cutaneous squamous cell carcinomas accelerated by BRAF inhibitors.
Escuin-Ordinas H, Atefi M, Fu Y, Cass A, Ng C, Huang RR, Yashar S, Comin-Anduix B, Avramis E, Cochran AJ, Marais R, Lo RS, Graeber TG, Herschman HR, Ribas A.
Molecular oncology. 2014; 8(2):250-260.

Canonical nucleosome organization at promoters forms during genome activation.
Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS.
Genome Research. 2014; 24(2):260-266.

Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues.
Pan Z, Liu Z, Cheng H, Wang Y, Gao T, Ullah S, Ren J, Xue Y.
Scientific Reports. 2014; 4:7331.

MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle.
Huang Z, Ma Lili, Wang Y, Pan Z, Ren J, Liu Z, Xue Y.
Nucleic Acids Research. 2014; 43:D328-D334.

CPLM: a database of protein lysine modifications.
Liu Z, Wang Y, Gao T, Pan Z, Cheng H, Yang Q, Cheng Z, Guo A, Ren J, Xue Y.
Nucleic Acids Research. 2014; 42:D531-D536.


2013 Student Publications

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen, P-Y, and Pellegrini, M.
BMC Genomics. 2013; 14(1):774.

ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing.
Massie M, Nothaft F, Hartl C, Kozanitis C, Schumacher A, Joseph AD, Patterson DA.
EECS Department, University of California, Berkeley, Tech. Rep. 2013.

From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline.
Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy‐Moonshine A, et al.
Current Protocols in Bioinformatics. 2013.

SMaSH: a benchmarking toolkit for human genome variant calling.
Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis, K, et al.
Bioinformatics. 2013; 30(19):2787-2795.

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.
Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE.
Journal of the American Medical Informatics Association. 2013; 21(1):31-36.

A Bacterial Toxin Inhibits DNA Replication Elongation through a Direct Interaction with the β Sliding Clamp.
Aakre CD, Phung TN, Huang D, Laub MT.
Molecular cell. 2013; 52(5):617-628.

CASZ1 inhibits cell cycle progression in neuroblastoma by restoring pRb activity.
Liu Z, Rader J, He S, Phung T, and Thiele CJ.
Cell Cycle. 2013; 12(14):2210-2218.

Enhanced Delivery and Potency of Self-Amplifying mRNA Vaccines by Electroporation in Situ.
Cu Y, Broderick KE, Banerjee K, Hickman J, Otten G, Barnett S, Kichaev G, et al.
Vaccines. 2013; 1(3):367-383.

Elucidating the Kinetics of Expression and Immune Cell Infiltration Resulting from Plasmid Gene Delivery Enhanced by Surface Dermal Electroporation.
Mendoza JM, Amante DH, Kichaev G, Knott CL, Kiosses WB, et al.
Vaccines. 2013; 1(3):384-397.

Electroporation mediated DNA vaccination directly to a mucosal surface results in improved immune responses.
Kichaev G, Mendoza JM, Amante D, Smith TR, McCoy JR, et al.
Human vaccines & immunotherapeutics. 2013; 9(10):2041-2048.

Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,323 mouse samples.
Kang EY, Han B, Furlotte N, Joo JW, Shih D, Davis R, Lusis J, Eskin E.
PLoS Genetics. 2014; 10(1):e1004022.

Rare genomic variants link bipolar disorder with anxiety disorders to CREB-regulated intracellular signaling pathways.
Kerner B, Rao AR, Christensen B, Dandekar S, Yourshaw M, Nelson SF.
Frontiers in psychiatry. 2013.

Genetic, morphological, geographical and ecological approaches reveal phylogenetic relationships in complex groups, an example of recently diverged pinyon pine species (Subsection Cembroides).
Flores-Rentería L, Wegier A, Ortega Del Vecchyo D, Ortíz-Medrano A, Piñero D, Whipple A V., Molina-Freaner F, Domínguez CA.
Molecular phylogenetics and evolution. 2013; 69(3):940-949.

Genotype imputation via matrix completion Genotype Imputation via Matrix Completion.
Chi EC, Zhou H, Chen GK, Chi EC, Ortega Del Vecchyo D, Lange K.
Genome research. 2013; 23(3):509-518.

Classify hyperdiploidy status of multiple myeloma patients using gene expression profiles.
Li Y, Wang X, Zheng H, Wang C, Minvielle S, Magrangeas F, Avet-Loiseau H, Shah PK, Zhang Y, Munshi NC, Li C.
PLoS ONE. 2013; 8(3):e58809.

Doxycycline alters metabolism and proliferation of human cell lines.
Ahler E, Sullivan WJ, Cass A, Braas D, York AG, Bensinger SJ, Graeber TG, Christofk HR.
PLoS ONE. 2013; 8(5):e64561.

Host immunity contributes to the anti-melanoma activity of BRAF inhibitors.
Knight DA, Ngiow SF, Li M, Parmenter T, Mok S, Cass A, Haynes NM, Kinross K, Yagita H, Koya RC, Graeber TG, Ribas A, McArthur GA, Smyth MJ.
The Journal of clinical investigation. 2013; 123(3):1371.


2012 Student Publications

The functional spectrum of low-frequency coding variation.
Marth G, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zhen-Bradley X, Hartl C, Tyler-Smith C, et al.
Genome biology. 2012; 12(9):R84.

Combination use of ultrasound irradiation and ionic liquid in enzymatic isomerization of glucose to fructose.
Wang Y, Pan Y, Zhang Z, Sun R, Fang X, Yu D.
Process Biochemistry. 2012; 47(6):976-982.

Weakening of negative relative to positive associations with cocaine-paired cues contributes to cue-induced responding after drug removal.
Su ZI, Kichaev G, Wenzel J, Ben-Shahar O, Ettenberg A.
Pharmacology Biochemistry and Behavior. 2012; 100(3):458-463.

Optimization of electroporation-enhanced intradermal delivery of DNA vaccine using a minimally invasive surface device.
Lin F, Shen X, Kichaev G, Mendoza JM, Yang M, et al.
Human Gene Therapy, Part B: Methods. 2012; 23(3): 157-168.

Optimized in vivo transfer of small interfering RNA targeting dermal tissue using in vivo surface electroporation.
Broderick KE, Chan A, Lin F, Shen X, Kichaev G, et al.
Molecular Therapy-Nucleic Acids. 2012; 1(2):e11.

Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits.
Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC.
Mammalian genome. 2012; 23(9-10):680-692.

New genes in traditional seed systems: diffusion, detectability and persistence of transgenes in a maize metapopulation.
van Heerwaarden J, Ortega Del Vecchyo D, Alvarez-Buylla ER, Bellon MR.
PLoS ONE. 2012; 7(10):e46123.

Computational inference of mRNA stability from histone modification and transcriptome profiles.
Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS.
Nucleic Acids Research. 2012; 40(14):6414-23.

DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
Fu K, Tang Q, Feng J, Liu XS, Zhang Y.
Bioinformatics. 2012; 28(15):1965-1971.


2011 Student Publications

Variation in genome-wide mutation rates within and between families.
Conrad DF, Keebler JEM, DePristo MA, Lindsay SH, Zhang Y, Casals F, Idaghdour Y, Hartl C, Torroja C, et al.
Nature. 2011; 201(1).

A comparative analysis of DNA methylation across human embryonic stem cell lines.
Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M.
Genome Biology. 2011; 12(7):R62.