Selected Recent Publications by BIG Students

 

Luis Barrera

Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW 3rd, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, Gamble CE, Iagovitina A, Singhania A, Michelson AM, Bulyk ML. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nature Methods (2013) 10(8):774-780.

 

Gaurav Bhatia

Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. PLoS Comput Biol. 2010

A covering method for detecting genetic associations between rare variants and
common phenotypes.

 

Bhatia G, et.al Am J Hum Genet. 2011
Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.

 

Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte
E, Sipe JC, Murray SS, Deleuze JF, Bafna V, Topol EJ, Frazer KA. Genome
Biol. 2010
Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level.

 

Daniel Day

Anchan RM, Quaas P, Gerami-Naini B, Bartake H, Griffin A, Zhou Y, Day D, Eaton JL, George LL, Naber C, Turbe-Doan A, Park PJ, Hornstein MD, Maas RL. Hum Mol Genet. 2011
Amniocytes can serve a dual function as a source of iPS cells and feeder layers.

 

Day DS, Luquette LJ, Park PJ, Kharchenko PV. Genome Biol. 2010
Estimating enrichment of repetitive elements from high-throughput sequence data.

 

Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. Nat Struct Mol Biol. 2011
An assessment of histone-modification antibody quality.

 

Jesse M. Engreitz

Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. Bioinformatics. 2011
ProfileChaser: searching microarray repositories based on genome-wide patterns of
differential expression.

 

Engreitz JM, Daigle BJ Jr, Marshall JJ, Altman RB. J Biomed Inform. 2010
Independent component analysis: mining microarray data for fundamental human gene expression modules.

 

Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. BMC
Bioinformatics. 2010
Content-based microarray search using differential expression profiles.

 

Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG, Urbach A, Thornton JE, Triboulet R, Gregory RI; DIAGRAM Consortium; MAGIC Investigators, Altshuler D, Daley GQ. Cell. 2011
The Lin28/let-7 axis regulates glucose metabolism.

 

Ally Eran

Eisenberg I, Eran A, Nishino I, Moggio M, Lamperti C, Amato AA, Lidov HG, Kang PB, North KN, Mitrani-Rosenbaum S, Flanigan KM, Neely LA, Whitney D, Beggs AH, Kohane IS, Kunkel LM. Proc Natl Acad Sci U S A. 2007
Distinctive patterns of microRNA expression in primary muscular disorders.

 

Eran A, Graham KR, Vatalaro K, McCarthy J, Collins C, Peters H, Brewster SJ, Hanson E, Hundley R, Rappaport L, Holm IA, Kohane IS, Kunkel LM. J. Clin. Invest. 2009
Comment on “Autistic-like phenotypes in Cadps2-knockout mice and aberrant CADPS2 splicing in autistic patients”

 

Daniel Goodman

Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Science. 2011
Precise manipulation of chromosomes in vivo enables genome-wide codon replacement.

 

Melissa Gymrek

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Nat Methods. 2010
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

 

Gymrek M, Erlich Y. Genome Med. 2011
Using DNA sequencers as stethoscopes.

 

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM. Mol Cell Proteomics. 2010
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

 

Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Genome Res. 2010
Digital transcriptome profiling from attomole-level RNA samples.

 

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M,
Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE. Cell. 2011
Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells.

 

Nathan S. Haseley

Ozlu N, Akten B, Timm W, Haseley N, Steen H, Steen JA. Wiley Interdiscip Rev Syst Biol Med. 2010
Phosphoproteomics.

 

Elena Helman

Helman E, Naxerova K, Kohane IS. Oncogene. 2011
DNA hypermethylation in lung cancer is targeted at differentiation-associated genes.

 

Sindi S, Helman E, Bashir A, Raphael BJ. Bioinformatics. 2009
A geometric approach for classification and comparison of structural variants.

 

Uri Laserson

Fera D, Kim N, Shiffeldrim N, Zorn J, Laserson U, Gan HH, Schlick T. BMC Bioinformatics. 2004
RAG: RNA-As-Graphs web resource.

 

Gan HH, Fera D, Zorn J, Shiffeldrim N, Tang M, Laserson U, Kim N, Schlick T. Bioinformatics. 2004
RAG: RNA-As-Graphs database--concepts, analysis, and features.

 

Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Gakidis MA, Church GM, Kesari S, Leproust EM, Solimini NL, Elledge SJ. Nat Biotechnol. 2011
Autoantigen discovery with a synthetic human peptidome.

 

Laserson U, Gan HH, Schlick T. Nucleic Acids Res. 2005
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs.

 

Arjun K. Manrai

Shin H, Liu T, Manrai AK, Liu XS. Bioinformatics. 2009
CEAS: cis-regulatory element annotation system.

 

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Genome Biol. 2007
Model-based analysis of two-color arrays (MA2C).

 

Michael S. Rooney

Dionisio KL, Rooney MS, Arku RE, Friedman AB, Hughes AF, Vallarino J, Agyei-Mensah S, Spengler JD, Ezzati M. Environ Health Perspect. 2010
Within-neighborhood patterns and sources of particle pollution: mobile monitoring and geographic information system analysis in four communities in Accra, Ghana.

 

James X. Sun

Sun JX, Mullikin JC, Patterson N, Reich DE. Mol Biol Evol. 2009
Microsatellites are molecular clocks that support accurate inferences about history.

 

Sun JX, Reisner AT, Saeed M, Heldt T, Mark RG. Crit Care Med. 2009
The cardiac output from blood pressure algorithms trial.