Gerstein Lab Publications

Main  •  By Subject  •  Queries  •  Code  •  Other Writings

Below are papers related to high performance computing that have been done using the high-performance computing facilities. Some of these papers pre-dated the new Yale Biomedical supercomputer and used a pilot cluster put together in preparation for the big supercomputer grant. One can see the large impact that high performance computing has had by looking at the number of these papers in relation to the total number of lab papers.


URL: http://info.med.yale.edu/hpc/
Articles funded by this grant:
An integrated system for studying residue coevolution in proteins.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). Bioinformatics 24: 290-2.
website
preprint
medline

Paired-end mapping reveals extensive structural variation in the human genome.
JO Korbel, AE Urban, JP Affourtit, B Godwin, F Grubert, JF Simons, PM Kim, D Palejev, NJ Carriero, L Du, BE Taillon, Z Chen, A Tanzer, AC Saunders, J Chi, F Yang, NP Carter, ME Hurles, SM Weissman, TT Harkins, MB Gerstein, M Egholm, M Snyder (2007). Science 318: 420-6.
website
preprint
medline

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
TE Royce, JS Rozowsky, MB Gerstein (2007). Nucleic Acids Res 35: e99.
 
preprint
medline

FlexOracle: predicting flexible hinges by identification of stable domains.
SC Flores, MB Gerstein (2007). BMC Bioinformatics 8: 215.
website
preprint
medline

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
JS Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel, U Nagalakshmi, J Yang, D Zheng, R Guigo, TR Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein (2007). Genome Res 17: 732-45.
website
preprint
medline

An efficient pseudomedian filter for tiling microrrays.
TE Royce, NJ Carriero, MB Gerstein (2007). BMC Bioinformatics 8: 186.
website
preprint
medline

Hinge Atlas: relating protein sequence to sites of structural flexibility.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). BMC Bioinformatics 8: 167.
website
preprint
medline

Tilescope: online analysis pipeline for high-density tiling microarray data.
ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein (2007). Genome Biol 8: R81.
website
preprint
medline

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
MG Smith, TA Gianoulis, S Pukatzki, JJ Mekalanos, LN Ornston, M Gerstein, M Snyder (2007). Genes Dev 21: 601-14.
 
preprint
medline

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein (2007). Genome Res 17: 886-97.
website
preprint
medline

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007). Nucleic Acids Res 35: D55-60.
website
preprint
medline

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein (2006). Bioinformatics 22: 3016-24.
website
preprint
medline

A computational approach for identifying pseudogenes in the ENCODE regions.
D Zheng, MB Gerstein (2006). Genome Biol 7 Suppl 1: S13.1-10.
website
preprint
medline

PseudoPipe: an automated pseudogene identification pipeline.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006). Bioinformatics 22: 1437-9.
website
preprint
medline

The Database of Macromolecular Motions: new features added at the decade mark.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006). Nucleic Acids Res 34: D296-301.
website
preprint
medline

Design optimization methods for genomic DNA tiling arrays.
P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006). Genome Res 16: 271-81.
website
preprint
medline

Global changes in STAT target selection and transcription regulation upon interferon treatments.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19: 2953-68.
website
preprint
medline

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005). Trends Genet 21: 466-75.
 
preprint
medline

Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005). J Mol Biol 349: 27-45.
website
preprint
medline

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005). Nucleic Acids Res 33: 2374-83.
website
preprint
medline

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005). Nucleic Acids Res 33: 1710-21.
website
preprint
medline

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005). Protein Sci 14: 633-43.
website
preprint
medline

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
N Carriero, MV Osier, KH Cheung, PL Miller, M Gerstein, H Zhao, B Wu, S Rifkin, J Chang, H Zhang, K White, K Williams, M Schultz (2005). J Am Med Inform Assoc 12: 90-8.
 
preprint
medline

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.
EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schubeler (2004). Proc Natl Acad Sci U S A 101: 17771-6.
website
preprint
medline

Global identification of human transcribed sequences with genome tiling arrays.
P Bertone, V Stolc, TE Royce, JS Rozowsky, AE Urban, X Zhu, JL Rinn, W Tongprasit, M Samanta, S Weissman, M Gerstein, M Snyder (2004). Science 306: 2242-6.
website
preprint
medline

Comparative analysis of processed pseudogenes in the mouse and human genomes.
Z Zhang, N Carriero, M Gerstein (2004). Trends Genet 20: 62-7.
website
preprint
medline

A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.
PM Harrison, N Carriero, Y Liu, M Gerstein (2003). J Mol Biol 333: 885-92.
website
preprint
medline

The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.
Z Zhang, M Gerstein (2003). Gene 312: 61-72.
website
preprint
medline

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Z Zhang, M Gerstein (2003). Genomics 81: 468-80.
website
preprint
medline

The transcriptional activity of human Chromosome 22.
JL Rinn, G Euskirchen, P Bertone, R Martone, NM Luscombe, S Hartman, PM Harrison, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Genes Dev 17: 529-40.
website
preprint
medline


Return to front page