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A

Aggarwal A, S. Kosaraju R, Pop M.. 1998. Drawing of Two-Dimensional Irregular Meshes. Graph DrawingGraph Drawing. 1547

Alemu E.Y, Carl J.W, H. Bravo C, Hannenhalli S.. 2014. Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.

Auslander N, Wagner A, Oberhardt M, Ruppin E. 2016. Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PLOS Computational Biology. 12(9):e1005125.

B

Boca SM, Bravo HCorrada, Caffo B, Leek JT, Parmigiani G. 2013. A decision-theory approach to interpretable set analysis for high-dimensional data. BiometricsBiometrics. 69

C

Chokesajjawatee N, Zo Y-G, Colwell RR. 2008. Determination of Clonality and Relatedness of Vibrio Cholerae Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 74

D

Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY. 2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.

Davison M, Treangen T, Koren S, Pop M, Bhaya D. 2016. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.. PLoS One. 11(9):e0160574.

Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al.. 2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.

E

Everett L, San Wang L-, Hannenhalli S. 2006. Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 22

F

Fernandes MCecilia, Dillon LAL, Belew ATrey, Bravo HCorrada, Mosser DM, El-Sayed NM. 2016. Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures. mBio. 7(3):e00027-16.

G

Ghedin E., Wang S., Spiro D., Caler E., Zhao Q., Crabtree J., Allen J.E, Delcher A.L, Guiliano D.B, Miranda-Saavedra D. et al.. 2007. Draft genome of the filarial nematode parasite Brugia malayi. ScienceScience. 317

Ghodsi M, Liu B, Pop M.. 2011. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC BioinformaticsBMC Bioinformatics. 12

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.. 2013. De novo likelihood-based measures for comparing genome assemblies. BMC research notes. 6

Grim CJ, Jaiani E, Whitehouse CA, Janelidze N, Kokashvili T, Tediashvili M, Colwell RR, Huq A. 2009. Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2

H

Hannenhalli S, Perumalla K., Chandrasekharan N., Sridhar R.. 1993. A distributed algorithm for ear decomposition. Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93.

Hill CM, Astrovskaya I, Huang H, Koren S, Memon A, Treangen T, Pop M. 2013. De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Hochheiser H., Baehrecke E.H, Mount SM, Shneiderman B. 2003. Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3

Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B. 2005. Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003). Institute for Systems Research Technical ReportsInstitute for Systems Research Technical Reports.

Huq A, Grim C, Colwell RR, G. Nair B. 2006. Detection, Isolation, and Identification of Vibrio cholerae from the Environment. Current Protocols in MicrobiologyCurrent Protocols in Microbiology.

K

Keeley MB, Wood MA, Isiegas C, Stein J, Hellman K, Hannenhalli S, Abel T. 2006. Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus. Learning & MemoryLearn. Mem.Learning & MemoryLearn. Mem.. 13

Kim R., Kulkarni P., Hannenhalli S. 2013. Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC CancerBMC CancerBMC Cancer. 13:144.

Kirkness E.F, Bafna V., Halpern A.L, Levy S., Remington K., Rusch D.B, Delcher A.L, Pop M., Wang W., Fraser C.M et al.. 2003. The dog genome: survey sequencing and comparative analysis. ScienceScience. 301

Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celià-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y et al.. 2011. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.. Nat Med. 17(9):1101-8.

Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Terrassa Tà-, Mercatali L, Khan Z, Goodarzi H, Hua Y et al.. 2011. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Medicine. 17(9):1101-1108.

S. Kosaraju R, Pop M.. 1998. De-amortization of Algorithms. Computing and CombinatoricsComputing and Combinatorics. 1449

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