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[transmemb-oxy-content]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: -
e-print: -
footnote: -
grant: -
ignore: -
labcite: R Sasidharan, A Smith and MB Gerstein (in press) PLoS One
labid: transmemb-oxy-content
labtitle: Transmembrane protein oxygen content and compartmentalization of cells.
preprint: -
sortval: -
subject: -
target: -
website: -
website2: -
[chip-seq-simu]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: -
e-print: -
footnote: -
grant: -
ignore: -
labcite: ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (In press) PLoS Computational Biology
labid: chip-seq-simu
labtitle: Modeling ChIP sequencing in silico with applications
preprint: -
sortval: -
subject: -
target: -
website: -
website2: -
[sirnapgene]
Authors: R Sasidharan, M Gerstein
Journal: Nature
PMID: 18528383
Pages: 729-31
Volume: 453
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/sirnapgene/
footnote: -
grant: -
ignore: -
labcite: Sasidharan R, Gerstein M (2008) Nature
labid: sirnapgene
labtitle: Genomics: protein fossils live on as RNA.
preprint: http://papers.gersteinlab.org/e-print/sirnapgene/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[cosbcnv]
Authors: JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein
Journal: Curr Opin Struct Biol
PMID: 18511261
Pages: 366-74
Volume: 18
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/cosbcnv/
footnote: -
grant: -
ignore: -
labcite: JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008) Curr Opin Struct Biol
labid: cosbcnv
labtitle: The current excitement about copy-number variation: how it relates to gene duplications and protein families.
preprint: http://papers.gersteinlab.org/e-print/cosbcnv/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[hcpin]
Authors: YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione
Journal: Mol Cell Proteomics
PMID: 18487680
Pages: -
Volume: -
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/hcpin/
footnote: -
grant: nesg
ignore: -
labcite: Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, Montelione GT (2008) Mol Cell Proteomics
labid: hcpin
labtitle: Targeting the human cancer pathway protein interaction network by structural genomics.
preprint: http://papers.gersteinlab.org/e-print/hcpin/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[3prime]
Authors: Z Lian, A Karpikov, J Lian, MC Mahajan, S Hartman, M Gerstein, M Snyder, SM Weissman
Journal: Genome Res
PMID: 18487515
Pages: -
Volume: -
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/3prime/
footnote: -
grant: -
ignore: -
labcite: Z Lian, A Karpikov, J Lian, MC Mahajan, S Hartman, M Gerstein, M Snyder, SM Weissman (2008) Genome Res
labid: 3prime
labtitle: A Genomics Analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
preprint: http://papers.gersteinlab.org/e-print/3prime/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[rubincancer]
Authors: KD Mertz, F Demichelis, A Sboner, MS Hirsch, PD Cin, K Struckmann, M Storz, S Scherrer, DM Schmid, RT Strebel, NM Probst-Hensch, M Gerstein, H Moch, MA Rubin
Journal: Int J Cancer
PMID: 18478571
Pages: 569-76
Volume: 123
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/rubincancer/
footnote: -
grant: -
ignore: -
labcite: KD Mertz, F Demichelis, A Sboner, MS Hirsch, PD Cin, K Struckmann, M Storz, S Scherrer, DM Schmid, RT Strebel, NM Probst-Hensch, M Gerstein, H Moch, MA Rubin (2008) Int J Cancer 123: 569-76.
labid: rubincancer
labtitle: Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer.
preprint: http://papers.gersteinlab.org/e-print/rubincancer/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[rnaseq]
Authors: U Nagalakshmi, Z Wang, K Waern, C Shou, D Raha, M Gerstein, M Snyder
Journal: Science
PMID: 18451266
Pages: 1344-9
Volume: 320
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/rnaseq/
footnote: -
grant: -
ignore: -
labcite: U Nagalakshmi, Z Wang, K Waern, C Shou, D Raha, M Gerstein, M Snyder (2008) Science 320: 1344-9.
labid: rnaseq
labtitle: The transcriptional landscape of the yeast genome defined by RNA sequencing.
preprint: http://papers.gersteinlab.org/e-print/rnaseq/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[hingemaster]
Authors: SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein
Journal: Proteins
PMID: 18433058
Pages: -
Volume: -
Year: 2008
e-print: -
footnote: -
grant: -
ignore: -
labcite: SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein (2008) Proteins
labid: hingemaster
labtitle: HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors.
preprint: -
sortval: -
subject: -
target: -
website: http://molmovdb.org/cgi-bin/submit-flexoracle.cgi
website2: -
[CD4]
Authors: ZD Zhang, G Weinstock, M Gerstein
Journal: J Mol Evol
PMID: 18414925
Pages: 446-56
Volume: 66
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/CD4/
footnote: -
grant: cegs
ignore: -
labcite: ZD Zhang, G Weinstock, M Gerstein (In press) Journal of Molecular Evolution
labid: CD4
labtitle: Rapid evolution by positive darwinian selection in T-cell antigen CD4 in primates.
preprint: http://papers.gersteinlab.org/e-print/CD4/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[killapp]
Authors: PE Bourne, JL Fink, M Gerstein
Journal: PLoS Comput Biol
PMID: 18369428
Pages: e1000037
Volume: 4
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/killapp/
footnote: -
grant: keck
ignore: -
labcite: PE Bourne, JL Fink, M Gerstein (2008) PLoS Comput Biol 4: e1000037.
labid: killapp
labtitle: Open access: taking full advantage of the content.
preprint: http://papers.gersteinlab.org/e-print/killapp/preprint.pdf
sortval: -
subject: epublishing
target: -
website: -
website2: -
[netdisorder]
Authors: PM Kim, A Sboner, Y Xia, M Gerstein
Journal: Mol Syst Biol
PMID: 18364713
Pages: 179
Volume: 4
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/netdisorder/
footnote: -
grant: proteomicsctr
ignore: -
labcite: PM Kim, A Sboner, Y Xia, M Gerstein (2008) Mol Syst Biol 4: 179.
labid: netdisorder
labtitle: The role of disorder in interaction networks: a structural analysis.
preprint: http://papers.gersteinlab.org/e-print/netdisorder/preprint.pdf
sortval: -
subject: interactions
target: -
website: -
website2: -
[sdafollowup]
Authors: M Seringhaus, M Gerstein
Journal: FEBS Lett
PMID: 18328823
Pages: 1170
Volume: 582
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/sdafollowup/
footnote: -
grant: keck
ignore: -
labcite: M Seringhaus, M Gerstein (2008) FEBS Lett 582: 1170.
labid: sdafollowup
labtitle: Manually structured digital abstracts: a scaffold for automatic text mining.
preprint: http://papers.gersteinlab.org/e-print/sdafollowup/preprint.pdf
sortval: -
subject: epublishing
target: -
website: -
website2: -
[encodespikein]
Authors: DS Johnson, W Li, DB Gordon, A Bhattacharjee, B Curry, J Ghosh, L Brizuela, JS Carroll, M Brown, P Flicek, CM Koch, I Dunham, M Bieda, X Xu, PJ Farnham, P Kapranov, DA Nix, TR Gingeras, X Zhang, H Holster, N Jiang, RD Green, JS Song, SA McCuine, E Anton, L Nguyen, ND Trinklein, Z Ye, K Ching, D Hawkins, B Ren, PC Scacheri, J Rozowsky, A Karpikov, G Euskirchen, S Weissman, M Gerstein, M Snyder, A Yang, Z Moqtaderi, H Hirsch, HP Shulha, Y Fu, Z Weng, K Struhl, RM Myers, JD Lieb, XS Liu
Journal: Genome Res
PMID: 18258921
Pages: 393-403
Volume: 18
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/encodespikein/
footnote: -
grant: encode
ignore: -
labcite: DS Johnson, W Li, DB Gordon, A Bhattacharjee, B Curry, J Ghosh, L Brizuela, JS Carroll, M Brown, P Flicek, CM Koch, I Dunham, M Bieda, X Xu, PJ Farnham, P Kapranov, DA Nix, TR Gingeras, X Zhang, H Holster, N Jiang, R Green, JS Song, SA McCuine, E Anton, L Nguyen, ND Trinklein, Z Ye, K Ching, D Hawkins, B Ren, PC Scacheri, J Rozowsky, A Karpikov, G Euskirchen, S Weissman, M Gerstein, M Snyder, A Yang, Z Moqtaderi, H Hirsch, HP Shulha, Y Fu, Z Weng, K Struhl, RM Myers, JD Lieb, XS Liu (2008) Genome Res
labid: encodespikein
labtitle: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
preprint: http://papers.gersteinlab.org/e-print/encodespikein/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[funnygene]
Authors: MR Seringhaus, PD Cayting, MB Gerstein
Journal: Genome Biol
PMID: 18254929
Pages: 401
Volume: 9
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/funnygene/
footnote: -
grant: keck
ignore: -
labcite: MR Seringhaus, PD Cayting, MB Gerstein (2008) Genome Biol 9: 401.
labid: funnygene
labtitle: Uncovering trends in gene naming.
preprint: http://papers.gersteinlab.org/e-print/funnygene/preprint.pdf
sortval: -
subject: epublishing
target: -
website: http://www.gersteinlab.org/proj/funnygene/
website2: -
[encoderaceseq]
Authors: JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder
Journal: Genome Biol
PMID: 18173853
Pages: R3
Volume: 9
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/encoderaceseq/
footnote: -
grant: encode
ignore: -
labcite: JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder (2008) Genome Biol 9: R3
labid: encoderaceseq
labtitle: Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
preprint: http://papers.gersteinlab.org/e-print/encoderaceseq/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[nr-pseudogenes]
Authors: ZD Zhang, P Cayting, G Weinstock, M Gerstein
Journal: Mol Biol Evol
PMID: 18065488
Pages: 131-43
Volume: 25
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/nr-pseudogenes/
footnote: -
grant: -
ignore: -
labcite: ZD Zhang, P Cayting, G Weinstock, M Gerstein (In press) Molecular Biology and Evolution
labid: nr-pseudogenes
labtitle: Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.
preprint: http://papers.gersteinlab.org/e-print/nr-pseudogenes/preprint.pdf
sortval: -
subject: pseudogenes
target: -
website: http://pseudogene.org/nr/
website2: -
[coevolution]
Authors: KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein
Journal: Bioinformatics
PMID: 18056067
Pages: 290-2
Volume: 24
Year: 2008
e-print: http://papers.gersteinlab.org/e-print/coevolution/
footnote: -
grant: cegs,hpc
ignore: -
labcite: KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, MB Gerstein (2007) Bioinformatics
labid: coevolution
labtitle: An integrated system for studying residue coevolution in proteins.
preprint: http://papers.gersteinlab.org/e-print/coevolution/preprint.pdf
sortval: -
subject: interactions,tools
target: -
website: http://coevolution.gersteinlab.org/coevolution/
website2: -
[semweb-dbinteg]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/semweb-dbinteg/
footnote: -
grant: keck
ignore: -
labcite: KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007) in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30
labid: semweb-dbinteg
labtitle: Semantic Web Approach to Database Integration in the Life Sciences
preprint: http://papers.gersteinlab.org/e-print/semweb-dbinteg/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: http://www.cs.concordia.ca/~baker/SW-RKDLS-May-2006.htm
website2: -
[webantitrust]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/webantitrust/
footnote: -
grant: keck
ignore: -
labcite: D Greenbaum, M Gerstein (2007) in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 413-433
labid: webantitrust
labtitle: Semantic Web Standards: Legal and Social Issues and Implications
preprint: http://papers.gersteinlab.org/e-print/webantitrust/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: http://www.cs.concordia.ca/~baker/SW-RKDLS-May-2006.htm
website2: -
[netpossel]
Authors: PM Kim, JO Korbel, MB Gerstein
Journal: Proc Natl Acad Sci U S A
PMID: 18077332
Pages: 20274-9
Volume: 104
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/netpossel/
footnote: -
grant: cegs
ignore: -
labcite: PM Kim, JO Korbel, MB Gerstein (2007) Proc Natl Acad Sci U S A.
labid: netpossel
labtitle: Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
preprint: http://papers.gersteinlab.org/e-print/netpossel/preprint.pdf
sortval: -
subject: 2007-summary,interactions
target: -
website: http://www.gersteinlab.org/proj/netpossel/
website2: -
[cancerdysreg]
Authors: SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin
Journal: Cancer Res
PMID: 17974971
Pages: 10296-303
Volume: 67
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/cancerdysreg/
footnote: -
grant: -
ignore: -
labcite: SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007) Cancer Res 67: 10296-303.
labid: cancerdysreg
labtitle: Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
preprint: http://papers.gersteinlab.org/e-print/cancerdysreg/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[semweb-ir]
Authors: A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein
Journal: Bioinformatics
PMID: 17923450
Pages: 3073-9
Volume: 23
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/semweb-ir/
footnote: -
grant: nesg
ignore: -
labcite: A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007) Bioinformatics
labid: semweb-ir
labtitle: Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
preprint: http://papers.gersteinlab.org/e-print/semweb-ir/preprint.pdf
sortval: -
subject: 2007-summary,epublishing,tools
target: -
website: http://hub.gersteinlab.org/ir-supp
website2: -
[hsp90]
Authors: AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman
Journal: Cell
PMID: 17923092
Pages: 121-35
Volume: 131
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/hsp90/
footnote: -
grant: keck
ignore: -
labcite: AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman (2007) Cell 131: 121-35.
labid: hsp90
labtitle: Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.
preprint: http://papers.gersteinlab.org/e-print/hsp90/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[sv]
Authors: 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
Journal: Science
PMID: 17901297
Pages: 420-6
Volume: 318
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/sv/
footnote: -
grant: cegs,hpc
ignore: -
labcite: 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
labid: sv
labtitle: Paired-end mapping reveals extensive structural variation in the human genome.
preprint: http://papers.gersteinlab.org/e-print/sv/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://sv.gersteinlab.org
website2: -
[pare]
Authors: EZ Yu, AE Burba, M Gerstein
Journal: BMC Bioinformatics
PMID: 17718915
Pages: 309
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/pare/
footnote: -
grant: proteomicsctr
ignore: -
labcite: -
labid: pare
labtitle: PARE: a tool for comparing protein abundance and mRNA expression data.
preprint: http://papers.gersteinlab.org/e-print/pare/preprint.pdf
sortval: -
subject: 2007-summary,interrelate,tools
target: -
website: http://proteomics.gersteinlab.org
website2: -
[regnetdiverge]
Authors: AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder
Journal: Science
PMID: 17690298
Pages: 815-9
Volume: 317
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/regnetdiverge/
footnote: -
grant: -
ignore: -
labcite: -
labid: regnetdiverge
labtitle: Divergence of transcription factor binding sites across related yeast species.
preprint: http://papers.gersteinlab.org/e-print/regnetdiverge/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://www.gersteinlab.org/proj/regnetdiverge
website2: -
[mimix]
Authors: S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob
Journal: Nat Biotechnol
PMID: 17687370
Pages: 894-8
Volume: 25
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/mimix/
footnote: -
grant: -
ignore: -
labcite: S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007) Nat Biotechnol 25: 894-8.
labid: mimix
labtitle: The minimum information required for reporting a molecular interaction experiment (MIMIx).
preprint: http://papers.gersteinlab.org/e-print/mimix/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[universalarray]
Authors: TE Royce, JS Rozowsky, MB Gerstein
Journal: Nucleic Acids Res
PMID: 17686789
Pages: e99
Volume: 35
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/universalarray/
footnote: -
grant: cegs,hpc
ignore: -
labcite: TE Royce, JS Rozowsky, MB Gerstein (2007) Nucleic Acids Res 35: e99.
labid: universalarray
labtitle: Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
preprint: http://papers.gersteinlab.org/e-print/universalarray/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[YEASTPLATCMP]
Authors: AR Borneman, ZD Zhang, J Rozowsky, MR Seringhaus, M Gerstein, M Snyder
Journal: Funct Integr Genomics
PMID: 17638031
Pages: 335-45
Volume: 7
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/YEASTPLATCMP/
footnote: -
grant: -
ignore: -
labcite: AR Borneman, ZD Zhang, J Rozowsky, MR Seringhaus, M Gerstein, M Snyder (2007) Funct Integr Genomics
labid: YEASTPLATCMP
labtitle: Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
preprint: http://papers.gersteinlab.org/e-print/YEASTPLATCMP/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[flexoracle]
Authors: SC Flores, MB Gerstein
Journal: BMC Bioinformatics
PMID: 17587456
Pages: 215
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/flexoracle/
footnote: -
grant: hpc
ignore: -
labcite: SC Flores, MB Gerstein (2007) BMC Bioinformatics 8: 215.
labid: flexoracle
labtitle: FlexOracle: predicting flexible hinges by identification of stable domains.
preprint: http://papers.gersteinlab.org/e-print/flexoracle/preprint.pdf
sortval: -
subject: 2007-summary,motions
target: -
website: http://molmovdb.org
website2: -
[edgeontology]
Authors: LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein
Journal: Trends Biochem Sci
PMID: 17583513
Pages: 320-31
Volume: 32
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/edgeontology/
footnote: -
grant: nesg
ignore: -
labcite: LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein (2007) Trends Biochem Sci 32: 310-321.
labid: edgeontology
labtitle: Comparing classical pathways and modern networks: towards the development of an edge ontology.
preprint: http://papers.gersteinlab.org/e-print/edgeontology/preprint.pdf
sortval: -
subject: 2007-summary,interactions
target: -
website: -
website2: -
[encode-pilot]
Authors: ENCODE Project Consortium, E Birney, JA Stamatoyannopoulos, A Dutta, R Guigó, TR Gingeras, EH Margulies, Z Weng, M Snyder, ET Dermitzakis, RE Thurman, MS Kuehn, CM Taylor, S Neph, CM Koch, S Asthana, A Malhotra, I Adzhubei, JA Greenbaum, RM Andrews, P Flicek, PJ Boyle, H Cao, NP Carter, GK Clelland, S Davis, N Day, P Dhami, SC Dillon, MO Dorschner, H Fiegler, PG Giresi, J Goldy, M Hawrylycz, A Haydock, R Humbert, KD James, BE Johnson, EM Johnson, TT Frum, ER Rosenzweig, N Karnani, K Lee, GC Lefebvre, PA Navas, F Neri, SC Parker, PJ Sabo, R Sandstrom, A Shafer, D Vetrie, M Weaver, S Wilcox, M Yu, FS Collins, J Dekker, JD Lieb, TD Tullius, GE Crawford, S Sunyaev, WS Noble, I Dunham, F Denoeud, A Reymond, P Kapranov, J Rozowsky, D Zheng, R Castelo, A Frankish, J Harrow, S Ghosh, A Sandelin, IL Hofacker, R Baertsch, D Keefe, S Dike, J Cheng, HA Hirsch, EA Sekinger, J Lagarde, JF Abril, A Shahab, C Flamm, C Fried, J Hackermuller, J Hertel, M Lindemeyer, K Missal, A Tanzer, S Washietl, J Korbel, O Emanuelsson, JS Pedersen, N Holroyd, R Taylor, D Swarbreck, N Matthews, MC Dickson, DJ Thomas, MT Weirauch, J Gilbert, J Drenkow, I Bell, X Zhao, KG Srinivasan, WK Sung, HS Ooi, KP Chiu, S Foissac, T Alioto, M Brent, L Pachter, ML Tress, A Valencia, SW Choo, CY Choo, C Ucla, C Manzano, C Wyss, E Cheung, TG Clark, JB Brown, M Ganesh, S Patel, H Tammana, J Chrast, CN Henrichsen, C Kai, J Kawai, U Nagalakshmi, J Wu, Z Lian, J Lian, P Newburger, X Zhang, P Bickel, JS Mattick, P Carninci, Y Hayashizaki, S Weissman, T Hubbard, RM Myers, J Rogers, PF Stadler, TM Lowe, CL Wei, Y Ruan, K Struhl, M Gerstein, SE Antonarakis, Y Fu, ED Green, U Karaoz, A Siepel, J Taylor, LA Liefer, KA Wetterstrand, PJ Good, EA Feingold, MS Guyer, GM Cooper, G Asimenos, CN Dewey, M Hou, S Nikolaev, JI Montoya-Burgos, A Loytynoja, S Whelan, F Pardi, T Massingham, H Huang, NR Zhang, I Holmes, JC Mullikin, A Ureta-Vidal, B Paten, M Seringhaus, D Church, K Rosenbloom, WJ Kent, EA Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, S Batzoglou, N Goldman, RC Hardison, D Haussler, W Miller, A Sidow, ND Trinklein, ZD Zhang, L Barrera, R Stuart, DC King, A Ameur, S Enroth, MC Bieda, J Kim, AA Bhinge, N Jiang, J Liu, F Yao, VB Vega, CW Lee, P Ng, A Shahab, A Yang, Z Moqtaderi, Z Zhu, X Xu, S Squazzo, MJ Oberley, D Inman, MA Singer, TA Richmond, KJ Munn, A Rada-Iglesias, O Wallerman, J Komorowski, JC Fowler, P Couttet, AW Bruce, OM Dovey, PD Ellis, CF Langford, DA Nix, G Euskirchen, S Hartman, AE Urban, P Kraus, S Van Calcar, N Heintzman, TH Kim, K Wang, C Qu, G Hon, R Luna, CK Glass, MG Rosenfeld, SF Aldred, SJ Cooper, A Halees, JM Lin, HP Shulha, X Zhang, M Xu, JN Haidar, Y Yu, Y Ruan, VR Iyer, RD Green, C Wadelius, PJ Farnham, B Ren, RA Harte, AS Hinrichs, H Trumbower, H Clawson, J Hillman-Jackson, AS Zweig, K Smith, A Thakkapallayil, G Barber, RM Kuhn, D Karolchik, L Armengol, CP Bird, PI de Bakker, AD Kern, N Lopez-Bigas, JD Martin, BE Stranger, A Woodroffe, E Davydov, A Dimas, E Eyras, IB Hallgrimsdóttir, J Huppert, MC Zody, GR Abecasis, X Estivill, GG Bouffard, X Guan, NF Hansen, JR Idol, VV Maduro, B Maskeri, JC McDowell, M Park, PJ Thomas, AC Young, RW Blakesley, DM Muzny, E Sodergren, DA Wheeler, KC Worley, H Jiang, GM Weinstock, RA Gibbs, T Graves, R Fulton, ER Mardis, RK Wilson, M Clamp, J Cuff, S Gnerre, DB Jaffe, JL Chang, K Lindblad-Toh, ES Lander, M Koriabine, M Nefedov, K Osoegawa, Y Yoshinaga, B Zhu, PJ de Jong
Journal: Nature
PMID: 17571346
Pages: 799-816
Volume: 447
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/encode-pilot/
footnote: -
grant: encode
ignore: -
labcite: ENCODE Project Consortium, E Birney, JA Stamatoyannopoulos, A Dutta, R Guig�, TR Gingeras, EH Margulies, Z Weng, M Snyder, ET Dermitzakis, RE Thurman, MS Kuehn, CM Taylor, S Neph, CM Koch, S Asthana, A Malhotra, I Adzhubei, JA Greenbaum, RM Andrews, P Flicek, PJ Boyle, H Cao, NP Carter, GK Clelland, S Davis, N Day, P Dhami, SC Dillon, MO Dorschner, H Fiegler, PG Giresi, J Goldy, M Hawrylycz, A Haydock, R Humbert, KD James, BE Johnson, EM Johnson, TT Frum, ER Rosenzweig, N Karnani, K Lee, GC Lefebvre, PA Navas, F Neri, SC Parker, PJ Sabo, R Sandstrom, A Shafer, D Vetrie, M Weaver, S Wilcox, M Yu, FS Collins, J Dekker, JD Lieb, TD Tullius, GE Crawford, S Sunyaev, WS Noble, I Dunham, F Denoeud, A Reymond, P Kapranov, J Rozowsky, D Zheng, R Castelo, A Frankish, J Harrow, S Ghosh, A Sandelin, IL Hofacker, R Baertsch, D Keefe, S Dike, J Cheng, HA Hirsch, EA Sekinger, J Lagarde, JF Abril, A Shahab, C Flamm, C Fried, J Hackermuller, J Hertel, M Lindemeyer, K Missal, A Tanzer, S Washietl, J Korbel, O Emanuelsson, JS Pedersen, N Holroyd, R Taylor, D Swarbreck, N Matthews, MC Dickson, DJ Thomas, MT Weirauch, J Gilbert, J Drenkow, I Bell, X Zhao, KG Srinivasan, WK Sung, HS Ooi, KP Chiu, S Foissac, T Alioto, M Brent, L Pachter, ML Tress, A Valencia, SW Choo, CY Choo, C Ucla, C Manzano, C Wyss, E Cheung, TG Clark, JB Brown, M Ganesh, S Patel, H Tammana, J Chrast, CN Henrichsen, C Kai, J Kawai, U Nagalakshmi, J Wu, Z Lian, J Lian, P Newburger, X Zhang, P Bickel, JS Mattick, P Carninci, Y Hayashizaki, S Weissman, T Hubbard, RM Myers, J Rogers, PF Stadler, TM Lowe, CL Wei, Y Ruan, K Struhl, M Gerstein, SE Antonarakis, Y Fu, ED Green, U Karaoz, A Siepel, J Taylor, LA Liefer, KA Wetterstrand, PJ Good, EA Feingold, MS Guyer, GM Cooper, G Asimenos, CN Dewey, M Hou, S Nikolaev, JI Montoya-Burgos, A Loytynoja, S Whelan, F Pardi, T Massingham, H Huang, NR Zhang, I Holmes, JC Mullikin, A Ureta-Vidal, B Paten, M Seringhaus, D Church, K Rosenbloom, WJ Kent, EA Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, S Batzoglou, N Goldman, RC Hardison, D Haussler, W Miller, A Sidow, ND Trinklein, ZD Zhang, L Barrera, R Stuart, DC King, A Ameur, S Enroth, MC Bieda, J Kim, AA Bhinge, N Jiang, J Liu, F Yao, VB Vega, CW Lee, P Ng, A Shahab, A Yang, Z Moqtaderi, Z Zhu, X Xu, S Squazzo, MJ Oberley, D Inman, MA Singer, TA Richmond, KJ Munn, A Rada-Iglesias, O Wallerman, J Komorowski, JC Fowler, P Couttet, AW Bruce, OM Dovey, PD Ellis, CF Langford, DA Nix, G Euskirchen, S Hartman, AE Urban, P Kraus, S Van Calcar, N Heintzman, TH Kim, K Wang, C Qu, G Hon, R Luna, CK Glass, MG Rosenfeld, SF Aldred, SJ Cooper, A Halees, JM Lin, HP Shulha, X Zhang, M Xu, JN Haidar, Y Yu, Y Ruan, VR Iyer, RD Green, C Wadelius, PJ Farnham, B Ren, RA Harte, AS Hinrichs, H Trumbower, H Clawson, J Hillman-Jackson, AS Zweig, K Smith, A Thakkapallayil, G Barber, RM Kuhn, D Karolchik, L Armengol, CP Bird, PI de Bakker, AD Kern, N Lopez-Bigas, JD Martin, BE Stranger, A Woodroffe, E Davydov, A Dimas, E Eyras, IB Hallgrimsd�ttir, J Huppert, MC Zody, GR Abecasis, X Estivill, GG Bouffard, X Guan, NF Hansen, JR Idol, VV Maduro, B Maskeri, JC McDowell, M Park, PJ Thomas, AC Young, RW Blakesley, DM Muzny, E Sodergren, DA Wheeler, KC Worley, H Jiang, GM Weinstock, RA Gibbs, T Graves, R Fulton, ER Mardis, RK Wilson, M Clamp, J Cuff, S Gnerre, DB Jaffe, JL Chang, K Lindblad-Toh, ES Lander, M Koriabine, M Nefedov, K Osoegawa, Y Yoshinaga, B Zhu, PJ de Jong (2007) Nature 447: 799-816.
labid: encode-pilot
labtitle: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
preprint: http://papers.gersteinlab.org/e-print/encode-pilot/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://encode.gersteinlab.org
website2: -
[chipchipcmp]
Authors: GM Euskirchen, JS Rozowsky, CL Wei, WH Lee, ZD Zhang, S Hartman, O Emanuelsson, V Stolc, S Weissman, MB Gerstein, Y Ruan, M Snyder
Journal: Genome Res
PMID: 17568005
Pages: 898-909
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/chipchipcmp/
footnote: -
grant: encode
ignore: -
labcite: GM Euskirchen , J Rozowsky, CL Wei, WH Lee, ZD Zhang, S Hartman, O Emanuelsson, V Stolc, S Weissman, MB Gerstein, Y Ruan, M Snyder (in press) Genome Research
labid: chipchipcmp
labtitle: Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
preprint: http://papers.gersteinlab.org/e-print/chipchipcmp/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[encoderna]
Authors: S Washietl, JS Pedersen, JO Korbel, C Stocsits, AR Gruber, J Hackermuller, J Hertel, M Lindemeyer, K Reiche, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, R Guigó, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler
Journal: Genome Res
PMID: 17568003
Pages: 852-64
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/encoderna/
footnote: -
grant: encode
ignore: -
labcite: S Washietl, JS Pedersen, JO Korbel, AR Gruber, J Hackermuller, J Hertel, M Lindemeyer, K Reiche, C Stocsits, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler (in press) Genome Research
labid: encoderna
labtitle: Structured RNAs in the ENCODE selected regions of the human genome.
preprint: http://papers.gersteinlab.org/e-print/encoderna/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[encodepgenes]
Authors: D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigó, J Harrow, MB Gerstein
Journal: Genome Res
PMID: 17568002
Pages: 839-51
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/encodepgenes/
footnote: -
grant: encode
ignore: -
labcite: D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigo, J Harrow, MB Gerstein (in press) Genome Research
labid: encodepgenes
labtitle: Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
preprint: http://papers.gersteinlab.org/e-print/encodepgenes/preprint.pdf
sortval: -
subject: 2007-summary,best,pseudogenes
target: -
website: http://pseudogene.org/ENCODE
website2: -
[tredist]
Authors: ZD Zhang, A Paccanaro, Y Fu, S Weissman, Z Weng, J Chang, M Snyder, MB Gerstein
Journal: Genome Res
PMID: 17567997
Pages: 787-97
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/tredist/
footnote: -
grant: encode
ignore: -
labcite: ZD Zhang, A Paccanaro, Y Fu, S Weissman, Z Weng, J Chang, M Snyder, MB Gerstein (in press) Genome Research
labid: tredist
labtitle: Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
preprint: http://papers.gersteinlab.org/e-print/tredist/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://dart.gersteinlab.org/ENCODE/TR/
website2: -
[dart]
Authors: JS Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel, U Nagalakshmi, J Yang, D Zheng, R Guigó, TR Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein
Journal: Genome Res
PMID: 17567993
Pages: 732-45
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/dart/
footnote: -
grant: encode,hpc
ignore: -
labcite: J Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel1, U Nagalakshmi, J Yang, D Zheng, R Guigo, T Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein (in press) Genome Research
labid: dart
labtitle: The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
preprint: http://papers.gersteinlab.org/e-print/dart/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://DART.gersteinlab.org
website2: -
[encodepromoters]
Authors: ND Trinklein, U Karaoz, J Wu, A Halees, S Force Aldred, PJ Collins, D Zheng, ZD Zhang, MB Gerstein, M Snyder, RM Myers, Z Weng
Journal: Genome Res
PMID: 17567992
Pages: 720-31
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/encodepromoters/
footnote: -
grant: encode
ignore: -
labcite: ND Trinklein, U Karaoz, J Wu, A Halees, SF Aldred1, PJ Collins1, D Zheng, Z Zhang, MB Gerstein, M Snyder, RM Myers1, Z Weng (in press) Genome Research
labid: encodepromoters
labtitle: Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
preprint: http://papers.gersteinlab.org/e-print/encodepromoters/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[grgenerev]
Authors: MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder
Journal: Genome Res
PMID: 17567988
Pages: 669-81
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/grgenerev/
footnote: -
grant: encode
ignore: -
labcite: MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder (2007) Genome Res 17: 669-81.
labid: grgenerev
labtitle: What is a gene, post-ENCODE? History and updated definition.
preprint: http://papers.gersteinlab.org/e-print/grgenerev/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://wiki.gersteinlab.org/pubinfo/What_is_a_gene
website2: -
[pseudomedian]
Authors: TE Royce, NJ Carriero, MB Gerstein
Journal: BMC Bioinformatics
PMID: 17555595
Pages: 186
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/pseudomedian/
footnote: -
grant: cegs,forgetppg,hpc,ycemh
ignore: -
labcite: TE Royce, JS Rozowsky, MB Gerstein (2007) BMC Bioinformatics
labid: pseudomedian
labtitle: An efficient pseudomedian filter for tiling microrrays.
preprint: http://papers.gersteinlab.org/e-print/pseudomedian/preprint.pdf
sortval: -
subject: 2007-summary,expression
target: -
website: http://tiling.gersteinlab.org/pseudomedian/
website2: -
[breakptr]
Authors: JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein
Journal: Proc Natl Acad Sci U S A
PMID: 17551006
Pages: 10110-5
Volume: 104
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/breakptr/
footnote: -
grant: cegs
ignore: -
labcite: JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007) Proc Natl Acad Sci USA
labid: breakptr
labtitle: Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
preprint: http://papers.gersteinlab.org/e-print/breakptr/preprint.pdf
sortval: -
subject: 2007-summary,expression
target: -
website: http://breakptr.gersteinlab.org
website2: -
[funcism]
Authors: H Yu, R Jansen, G Stolovitzky, M Gerstein
Journal: Bioinformatics
PMID: 17540677
Pages: 2163-73
Volume: 23
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/funcism/
footnote: -
grant: cegs,nih-tn
ignore: -
labcite: H Yu, R Jansen, M Gerstein (2007) Bioinformatics
labid: funcism
labtitle: Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
preprint: http://papers.gersteinlab.org/e-print/funcism/preprint.pdf
sortval: -
subject: 2007-summary,interactions
target: -
website: http://www.gersteinlab.org/proj/funcsim/
website2: -
[proteomicsurvey]
Authors: L Wu, SI Hwang, K Rezaul, LJ Lu, V Mayya, M Gerstein, JK Eng, DH Lundgren, DK Han
Journal: Mol Cell Proteomics
PMID: 17519225
Pages: 1343-53
Volume: 6
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/proteomicsurvey/
footnote: -
grant: -
ignore: -
labcite: L Wu, SI Hwang, K Rezaul, LJ Lu, V Mayya, M Gerstein, JK Eng, DH Lundgren, DK Han (2007) Mol Cell Proteomics
labid: proteomicsurvey
labtitle: Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.
preprint: http://papers.gersteinlab.org/e-print/proteomicsurvey/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[HingeAtlas]
Authors: SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein
Journal: BMC Bioinformatics
PMID: 17519025
Pages: 167
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/HingeAtlas/
footnote: -
grant: hpc,keck
ignore: -
labcite: SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007) BMC Bioinformatics 8: 167.
labid: HingeAtlas
labtitle: Hinge Atlas: relating protein sequence to sites of structural flexibility.
preprint: http://papers.gersteinlab.org/e-print/HingeAtlas/preprint.pdf
sortval: -
subject: 2007-summary,motions
target: -
website: http://molmovdb.org/HAG/
website2: -
[tilescope]
Authors: ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein
Journal: Genome Biol
PMID: 17501994
Pages: R81
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/tilescope/
footnote: -
grant: encode,hpc,ycemh
ignore: -
labcite: ZD Zhang, J Rozowsky, H Lam, J Du, M Snyder, MB Gerstein (in press) Genome Biology
labid: tilescope
labtitle: Tilescope: online analysis pipeline for high-density tiling microarray data.
preprint: http://papers.gersteinlab.org/e-print/tilescope/preprint.pdf
sortval: -
subject: 2007-summary,expression,tools
target: -
website: http://tilescope.gersteinlab.org
website2: -
[SDA]
Authors: M Gerstein, M Seringhaus, S Fields
Journal: Nature
PMID: 17495904
Pages: 142
Volume: 447
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/SDA/
footnote: -
grant: -
ignore: -
labcite: M Gerstein, M Seringhaus, S Fields (2007) Nature 447: 142.
labid: SDA
labtitle: Structured digital abstract makes text mining easy.
preprint: http://papers.gersteinlab.org/e-print/SDA/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: -
website2: -
[linkhub]
Authors: AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein
Journal: BMC Bioinformatics
PMID: 17493288
Pages: S5
Volume: 8 Suppl 3
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/linkhub/
footnote: -
grant: nesg
ignore: -
labcite: AK Smith, KH Cheung, KY Yip, M Schultz, MB Gerstein (2007) BMC Bioinformatics
labid: linkhub
labtitle: LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
preprint: http://papers.gersteinlab.org/e-print/linkhub/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://hub.gersteinlab.org/
website2: -
[gettingconnected]
Authors: X Zhu, M Gerstein, M Snyder
Journal: Genes Dev
PMID: 17473168
Pages: 1010-24
Volume: 21
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/gettingconnected/
footnote: -
grant: -
ignore: -
labcite: X Zhu, M Gerstein, M Snyder (2007) Genes Dev 21: 1010-24.
labid: gettingconnected
labtitle: Getting connected: analysis and principles of biological networks.
preprint: http://papers.gersteinlab.org/e-print/gettingconnected/preprint.pdf
sortval: -
subject: 2007-summary,interactions
target: -
website: -
website2: -
[rnai]
Authors: M Gerstein, SM Douglas
Journal: PLoS Comput Biol
PMID: 17465677
Pages: e80
Volume: 3
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/rnai/
footnote: -
grant: -
ignore: -
labcite: M Gerstein, SM Douglas (2007) PLoS Comput Biol 3: e80.
labid: rnai
labtitle: RNAi development.
preprint: http://papers.gersteinlab.org/e-print/rnai/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: http://pubnet.gersteinlab.org/rnai/
website2: -
[bottleneck]
Authors: H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein
Journal: PLoS Comput Biol
PMID: 17447836
Pages: e59
Volume: 3
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/bottleneck/
footnote: -
grant: nih-tn
ignore: -
labcite: H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein (2007) PLoS Comput Biol 3: e59.
labid: bottleneck
labtitle: The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
preprint: http://papers.gersteinlab.org/e-print/bottleneck/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://www.gersteinlab.org/proj/bottleneck/
website2: -
[bioinformatics_sequence_effects]
Authors: TE Royce, JS Rozowsky, MB Gerstein
Journal: Bioinformatics
PMID: 17387113
Pages: 988-97
Volume: 23
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/bioinformatics_sequence_effects/
footnote: -
grant: cegs,ycemh
ignore: -
labcite: -
labid: bioinformatics_sequence_effects
labtitle: Assessing the need for sequence-based normalization in tiling microarray experiments.
preprint: http://papers.gersteinlab.org/e-print/bioinformatics_sequence_effects/preprint.pdf
sortval: -
subject: 2007-summary,microarray
target: -
website: http://tiling.gersteinlab.org/sequence_effects/
website2: -
[pgene-classify]
Authors: D Zheng, MB Gerstein
Journal: Trends Genet
PMID: 17382428
Pages: 219-24
Volume: 23
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/pgene-classify/
footnote: -
grant: cegs,encode
ignore: -
labcite: D Zheng, M Gerstein (2007). Trends Genet 23(5):219-24
labid: pgene-classify
labtitle: The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
preprint: http://papers.gersteinlab.org/e-print/pgene-classify/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://www.pseudogene.org
website2: -
[ricearray]
Authors: L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, X Wang Deng
Journal: PLoS ONE
PMID: 17372628
Pages: e294
Volume: 2
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/ricearray/
footnote: -
grant: ricearray
ignore: -
labcite: L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, X Wang Deng (2007) PLoS ONE 2: e294.
labid: ricearray
labtitle: Global identification and characterization of transcriptionally active regions in the rice genome.
preprint: http://papers.gersteinlab.org/e-print/ricearray/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://dart.gersteinlab.org/rice/
website2: -
[atprotchip]
Authors: SC Popescu, GV Popescu, S Bachan, Z Zhang, M Seay, M Gerstein, M Snyder, SP Dinesh-Kumar
Journal: Proc Natl Acad Sci U S A
PMID: 17360592
Pages: 4730-5
Volume: 104
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/atprotchip/
footnote: -
grant: -
ignore: -
labcite: SC Popescu, GV Popescu, S Bachan, Z Zhang, M Seay, M Gerstein, M Snyder, SP Dinesh-Kumar (2007) Proc Natl Acad Sci U S A 104: 4730-5.
labid: atprotchip
labtitle: Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
preprint: http://papers.gersteinlab.org/e-print/atprotchip/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://plants.gersteinlab.org/
website2: -
[baumannii]
Authors: MG Smith, TA Gianoulis, S Pukatzki, JJ Mekalanos, LN Ornston, M Gerstein, M Snyder
Journal: Genes Dev
PMID: 17344419
Pages: 601-14
Volume: 21
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/baumannii/
footnote: -
grant: cegs,hpc
ignore: -
labcite: Michael G. Smith, Tara A. Gianoulis, Stefan Pukatzki, John J. Mekalanos, L. Nicholas Ornston, Mark Gerstein, and Michael Snyder. Genes and Development (in press)
labid: baumannii
labtitle: New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
preprint: http://papers.gersteinlab.org/e-print/baumannii/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[novelprimaternas]
Authors: Z Zhang, AW Pang, M Gerstein
Journal: BMC Evol Biol
PMID: 17288572
Pages: S14
Volume: 7 Suppl 1
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/novelprimaternas/
footnote: -
grant: -
ignore: -
labcite: Z Zhang, AW Pang, M Gerstein (2007) BMC Evol Biol 7 Suppl 1: S14.
labid: novelprimaternas
labtitle: Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
preprint: http://papers.gersteinlab.org/e-print/novelprimaternas/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[infoarch]
Authors: MR Seringhaus, MB Gerstein
Journal: BMC Bioinformatics
PMID: 17239245
Pages: 17
Volume: 8
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/infoarch/
footnote: -
grant: keck
ignore: -
labcite: -
labid: infoarch
labtitle: Publishing perishing? Towards tomorrow's information architecture.
preprint: http://papers.gersteinlab.org/e-print/infoarch/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: -
website2: -
[chemnobel]
Authors: M Seringhaus, M Gerstein
Journal: Science
PMID: 17204626
Pages: 40-1
Volume: 315
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/chemnobel/
footnote: -
grant: keck
ignore: -
labcite: -
labid: chemnobel
labtitle: Chemistry Nobel rich in structure.
preprint: http://papers.gersteinlab.org/e-print/chemnobel/preprint.pdf
sortval: -
subject: 2007-summary,epublishing
target: -
website: -
website2: -
[cop]
Authors: H Yu, K Nguyen, T Royce, J Qian, K Nelson, M Snyder, M Gerstein
Journal: Nucleic Acids Res
PMID: 17158151
Pages: e8
Volume: 35
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/cop/
footnote: -
grant: -
ignore: -
labcite: H Yu, K Nguyen, T Royce, J Qian, K Nelson, M Snyder, M Gerstein (2007) Nucleic Acids Res 35: e8.
labid: cop
labtitle: Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
preprint: http://papers.gersteinlab.org/e-print/cop/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: http://bioinfo.mbb.yale.edu/ExpressYourself/
website2: -
[platformcmp]
Authors: O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein
Journal: Genome Res
PMID: 17119069
Pages: 886-97
Volume: 17
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/platformcmp/
footnote: -
grant: encode,hpc
ignore: -
labcite: O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, M Gerstein (2006) Genome Research
labid: platformcmp
labtitle: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
preprint: http://papers.gersteinlab.org/e-print/platformcmp/preprint.pdf
sortval: -
subject: 2006-summary,2007-summary,expression
target: -
website: http://tiling.gersteinlab.org/platformcmp/
website2: -
[pgenedb]
Authors: JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein
Journal: Nucleic Acids Res
PMID: 17099229
Pages: D55-60
Volume: 35
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/pgenedb/
footnote: -
grant: cegs,hpc
ignore: -
labcite: J Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Harrrison, M Gerstein (in press) Nucleic Acids Research
labid: pgenedb
labtitle: Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
preprint: http://papers.gersteinlab.org/e-print/pgenedb/preprint.pdf
sortval: -
subject: 2007-summary,pseudogenes,tools
target: -
website: http://pseudogene.org
website2: -
[cbb-prog]
Authors: M Gerstein, D Greenbaum, K Cheung, PL Miller
Journal: J Biomed Inform
PMID: 16650809
Pages: 73-9
Volume: 40
Year: 2007
e-print: http://papers.gersteinlab.org/e-print/cbb-prog/
footnote: -
grant: keck
ignore: -
labcite: M Gerstein, D Greenbaum, K Cheung, PL Miller. J. Biomed. Inform. (in press)
labid: cbb-prog
labtitle: An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
preprint: http://papers.gersteinlab.org/e-print/cbb-prog/preprint.pdf
sortval: -
subject: 2007-summary
target: -
website: -
website2: -
[paperdeath]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/paperdeath/
footnote: -
grant: keck
ignore: -
labcite: Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25
labid: paperdeath
labtitle: The Death of
the Scientific
Paper
preprint: http://papers.gersteinlab.org/e-print/paperdeath/preprint.pdf
sortval: -
subject: 2006-summary,epublishing
target: -
website: http://www.the-scientist.com/2006/9/1/25/1/
website2: -
[powerlaw-analytic]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/powerlaw-analytic/
footnote: -
grant: -
ignore: -
labcite: M Kamal, N Luscombe, J Qian, M Gerstein (2006) in Power Laws, Scale-Free Networks and Genome Biology (edited by EV Koonin, YI Wolf, GP Karev; Springer, New York), pages 165-193
labid: powerlaw-analytic
labtitle: Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure
preprint: http://papers.gersteinlab.org/e-print/powerlaw-analytic/reprint.pdf
sortval: -
subject: 2006-summary
target: -
website: -
website2: -
[quantbiosymp]
Authors: J Rozowsky, J Wu, Z Lian, U Nagalakshmi, JO Korbel, P Kapranov, D Zheng, S Dyke, P Newburger, P Miller, TR Gingeras, S Weissman, M Gerstein, M Snyder
Journal: Cold Spring Harb Symp Quant Biol
PMID: 17381286
Pages: 111-6
Volume: 71
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/quantbiosymp/
footnote: -
grant: -
ignore: -
labcite: J Rozowsky, J Wu, Z Lian, U Nagalakshmi, JO Korbel, P Kapranov, D Zheng, S Dyke, P Newburger, P Miller, TR Gingeras, S Weissman, M Gerstein, M Snyder (2006) Cold Spring Harb Symp Quant Biol 71: 111-6.
labid: quantbiosymp
labtitle: Novel transcribed regions in the human genome.
preprint: http://papers.gersteinlab.org/e-print/quantbiosymp/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[structint]
Authors: PM Kim, LJ Lu, Y Xia, MB Gerstein
Journal: Science
PMID: 17185604
Pages: 1938-41
Volume: 314
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/structint/
footnote: -
grant: proteomicsctr
ignore: -
labcite: PM Kim, LJ Lu, Y Xia, MB Gerstein (in press) Science
labid: structint
labtitle: Relating three-dimensional structures to protein networks provides evolutionary insights.
preprint: http://papers.gersteinlab.org/e-print/structint/preprint.pdf
sortval: -
subject: 2006-summary,best,interactions
target: -
website: http://sin.gersteinlab.org
website2: -
[webmining-letter]
Authors: A Smith, M Gerstein
Journal: Science
PMID: 17170276
Pages: 1682; author reply 1682
Volume: 314
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/webmining-letter/
footnote: -
grant: -
ignore: -
labcite: -
labid: webmining-letter
labtitle: Data mining on the web.
preprint: http://papers.gersteinlab.org/e-print/webmining-letter/preprint.pdf
sortval: -
subject: 2006-summary,epublishing,mining
target: -
website: -
website2: -
[phenome2]
Authors: Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier
Journal: PLoS Comput Biol
PMID: 17112314
Pages: e159
Volume: 2
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/phenome2/
footnote: -
grant: nbc
ignore: -
labcite: Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier (2006) PLoS Comput Biol 2: e159.
labid: phenome2
labtitle: An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
preprint: http://papers.gersteinlab.org/e-print/phenome2/preprint.pdf
sortval: -
subject: -
target: -
website: http://www.gersteinlab.org/proj/phenome/
website2: -
[procat]
Authors: X Zhu, M Gerstein, M Snyder
Journal: Genome Biol
PMID: 17109749
Pages: R110
Volume: 7
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/procat/
footnote: -
grant: -
ignore: -
labcite: -
labid: procat
labtitle: ProCAT: a data analysis approach for protein microarrays.
preprint: http://papers.gersteinlab.org/e-print/procat/preprint.pdf
sortval: -
subject: 2006-summary,expression,tools
target: -
website: http://purelight.biology.yale.edu:8080/servlets-examples/procat.html
website2: -
[bocatfbs]
Authors: LY Wang, M Snyder, M Gerstein
Journal: Genome Biol
PMID: 17078876
Pages: R102
Volume: 7
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/bocatfbs/
footnote: -
grant: encode
ignore: -
labcite: -
labid: bocatfbs
labtitle: BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments.
preprint: http://papers.gersteinlab.org/e-print/bocatfbs/preprint.pdf
sortval: -
subject: 2006-summary,tools
target: -
website: http://www.gersteinlab.org/proj/BoCaTFBS/
website2: -
[hit]
Authors: AE Burba, U Lehnert, EZ Yu, M Gerstein
Journal: Bioinformatics
PMID: 17060355
Pages: 2735-8
Volume: 22
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/hit/
footnote: -
grant: proteomicsctr
ignore: -
labcite: AE Counterman Burba, U Lehnert, EZ Yu, M Gerstein (in press) Bioinformatics
labid: hit
labtitle: Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
preprint: http://papers.gersteinlab.org/e-print/hit/preprint.pdf
sortval: -
subject: 2006-summary,tools,volumes
target: -
website: http://helix.gersteinlab.org
website2: -
[tilinghmm]
Authors: J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein
Journal: Bioinformatics
PMID: 17038339
Pages: 3016-24
Volume: 22
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/tilinghmm/
footnote: -
grant: encode,hpc
ignore: -
labcite: -
labid: tilinghmm
labtitle: A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
preprint: http://papers.gersteinlab.org/e-print/tilinghmm/preprint.pdf
sortval: -
subject: 2006-summary,expression,intro-to-lab
target: -
website: http://tiling.gersteinlab.org/hmm/
website2: -
[phenome]
Authors: CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein
Journal: BMC Genomics
PMID: 17038185
Pages: 257
Volume: 7
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/phenome/
footnote: -
grant: nbc
ignore: -
labcite: CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein (2006) BMC Genomics 7: 257.
labid: phenome
labtitle: Integration of curated databases to identify genotype-phenotype associations.
preprint: http://papers.gersteinlab.org/e-print/phenome/preprint.pdf
sortval: -
subject: -
target: -
website: http://www.gersteinlab.org/proj/phenome/
website2: -
[tyna]
Authors: KY Yip, H Yu, PM Kim, M Schultz, M Gerstein
Journal: Bioinformatics
PMID: 17021160
Pages: 2968-70
Volume: 22
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/tyna/
footnote: -
grant: -
ignore: -
labcite: Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz and Mark Gerstein. Bioinformatics (in press)
labid: tyna
labtitle: The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
preprint: http://papers.gersteinlab.org/e-print/tyna/reprint.pdf
sortval: -
subject: 2006-summary,best,interactions,intro-to-lab,tools
target: -
website: http://networks.gersteinlab.org/tyna/
website2: -
[nethierarchy]
Authors: H Yu, M Gerstein
Journal: Proc Natl Acad Sci U S A
PMID: 17003135
Pages: 14724-31
Volume: 103
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/nethierarchy/
footnote: -
grant: -
ignore: -
labcite: H Yu, M Gerstein (in press) PNAS
labid: nethierarchy
labtitle: Genomic analysis of the hierarchical structure of regulatory networks.
preprint: http://papers.gersteinlab.org/e-print/nethierarchy/preprint.pdf
sortval: -
subject: 2006-summary,best,interactions,intro-to-lab
target: -
website: http://www.gersteinlab.org/proj/nethierarchy/
website2: -
[tos9]
Authors: T Srikantha, AR Borneman, KJ Daniels, C Pujol, W Wu, MR Seringhaus, M Gerstein, S Yi, M Snyder, DR Soll
Journal: Eukaryot Cell
PMID: 16950924
Pages: 1674-87
Volume: 5
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/tos9/
footnote: -
grant: -
ignore: -
labcite: T Srikantha, AR Borneman, KJ Daniels, C Pujol, W Wu, MR Seringhaus, M Gerstein, S Yi, M Snyder, DR Soll (2006) Eukaryot Cell 5: 1674-87.
labid: tos9
labtitle: TOS9 regulates white-opaque switching in Candida albicans.
preprint: http://papers.gersteinlab.org/e-print/tos9/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[mie.microarray.analysis.review]
Authors: TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein
Journal: Methods Enzymol
PMID: 16939796
Pages: 282-311
Volume: 411
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/mie.microarray.analysis.review/
footnote: -
grant: cegs
ignore: -
labcite: TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, M Gerstein (in press) Methods Enzymol
labid: mie.microarray.analysis.review
labtitle: Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
preprint: http://papers.gersteinlab.org/e-print/mie.microarray.analysis.review/preprint.pdf
sortval: -
subject: 2006-summary,expression
target: -
website: -
website2: -
[454amp]
Authors: R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon
Journal: BMC Genomics
PMID: 16928277
Pages: 216
Volume: 7
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/454amp/
footnote: -
grant: -
ignore: -
labcite: R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon (2006) BMC Genomics 7: 216.
labid: 454amp
labtitle: Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
preprint: http://papers.gersteinlab.org/e-print/454amp/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[pseudopiped]
Authors: D Zheng, MB Gerstein
Journal: Genome Biol
PMID: 16925835
Pages: S13.1-10
Volume: 7 Suppl 1
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/pseudopiped/
footnote: -
grant: encode,hpc
ignore: -
labcite: D Zheng, M Gerstein Genome Biol (2006)
labid: pseudopiped
labtitle: A computational approach for identifying pseudogenes in the ENCODE regions.
preprint: http://papers.gersteinlab.org/e-print/pseudopiped/preprint.pdf
sortval: -
subject: 2006-summary,pseudogenes
target: -
website: http://pseudogene.org/pseudoPipeD/index.html
website2: -
[predess]
Authors: M Seringhaus, A Paccanaro, A Borneman, M Snyder, M Gerstein
Journal: Genome Res
PMID: 16899653
Pages: 1126-35
Volume: 16
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/predess/
footnote: -
grant: cegs
ignore: -
labcite: -
labid: predess
labtitle: Predicting essential genes in fungal genomes.
preprint: http://papers.gersteinlab.org/e-print/predess/preprint.pdf
sortval: -
subject: 2006-summary,interrelate
target: -
website: http://www.gersteinlab.org/proj/predess
website2: -
[sciam2]
Authors: M Gerstein, D Zheng
Journal: Sci Am
PMID: 16866288
Pages: 48-55
Volume: 295
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/sciam2/
footnote: -
grant: cegs
ignore: -
labcite: M Gerstein, D Zheng (2006). Sci. Am. (in press)
labid: sciam2
labtitle: The real life of pseudogenes.
preprint: http://papers.gersteinlab.org/e-print/sciam2/preprint.pdf
sortval: -
subject: 2006-summary,best,pseudogenes
target: -
website: http://papers.gersteinlab.org/e-print/sciam2/
website2: -
[netcmp]
Authors: H Yu, Y Xia, V Trifonov, M Gerstein
Journal: Genome Biol
PMID: 16859507
Pages: R55
Volume: 7
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/netcmp/
footnote: -
grant: -
ignore: -
labcite: H Yu, Y Xia, V Trifonov, M Gerstein (in press) Genome Biology
labid: netcmp
labtitle: Design principles of molecular networks revealed by global comparisons and composite motifs.
preprint: http://papers.gersteinlab.org/e-print/netcmp/preprint.pdf
sortval: -
subject: 2006-summary,interactions
target: -
website: http://networks.gersteinlab.org/network/netcomp/
website2: -
[ribotunnel]
Authors: NR Voss, M Gerstein, TA Steitz, PB Moore
Journal: J Mol Biol
PMID: 16784753
Pages: 893-906
Volume: 360
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/ribotunnel/
footnote: -
grant: keck
ignore: -
labcite: NR Voss, MB Gerstein, TA Steitz, PB Moore (in press) J Mol. Biol.
labid: ribotunnel
labtitle: The geometry of the ribosomal polypeptide exit tunnel.
preprint: http://papers.gersteinlab.org/e-print/ribotunnel/preprint.pdf
sortval: -
subject: 2006-summary,volumes
target: -
website: http://geometry.molmovdb.org/3v/
website2: -
[tndist]
Authors: M Seringhaus, A Kumar, J Hartigan, M Snyder, M Gerstein
Journal: Nucleic Acids Res
PMID: 16648358
Pages: e57
Volume: 34
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/tndist/
footnote: -
grant: -
ignore: -
labcite: -
labid: tndist
labtitle: Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.
preprint: http://papers.gersteinlab.org/e-print/tndist/preprint.pdf
sortval: -
subject: 2006-summary
target: -
website: -
website2: -
[genomebrowser]
Authors: M Gerstein
Journal: Nature
PMID: 16598230
Pages: 740
Volume: 440
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/genomebrowser/
footnote: -
grant: -
ignore: -
labcite: -
labid: genomebrowser
labtitle: Tools needed to navigate landscape of the genome.
preprint: http://papers.gersteinlab.org/e-print/genomebrowser/preprint.pdf
sortval: -
subject: 2006-summary,epublishing
target: -
website: -
website2: -
[pseudopipe]
Authors: Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein
Journal: Bioinformatics
PMID: 16574694
Pages: 1437-9
Volume: 22
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/pseudopipe/
footnote: -
grant: cegs,hpc
ignore: -
labcite: -
labid: pseudopipe
labtitle: PseudoPipe: an automated pseudogene identification pipeline.
preprint: http://papers.gersteinlab.org/e-print/pseudopipe/preprint.pdf
sortval: -
subject: 2006-summary,pseudogenes,tools
target: -
website: http://pseudogene.org
website2: -
[krogan-cplx]
Authors: NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrin-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt
Journal: Nature
PMID: 16554755
Pages: 637-43
Volume: 440
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/krogan-cplx/
footnote: -
grant: -
ignore: -
labcite: -
labid: krogan-cplx
labtitle: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
preprint: http://papers.gersteinlab.org/e-print/krogan-cplx/preprint.pdf
sortval: -
subject: 2006-summary,expt-collab,interactions
target: -
website: -
website2: -
[hracgh]
Authors: AE Urban, JO Korbel, R Selzer, T Richmond, A Hacker, GV Popescu, JF Cubells, R Green, BS Emanuel, MB Gerstein, SM Weissman, M Snyder
Journal: Proc Natl Acad Sci U S A
PMID: 16537408
Pages: 4534-9
Volume: 103
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/hracgh/
footnote: -
grant: cegs
ignore: -
labcite: AE Urban, JO Korbel, R Selzer, T Richmond, A Hacker, GV Popescu, JF Cubells, R Green, BS Emanuel, MB Gerstein, SM Weissman, M Snyder (2006) Proc Natl Acad Sci U S A 103: 4534-9.
labid: hracgh
labtitle: High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.
preprint: http://papers.gersteinlab.org/e-print/hracgh/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[defective-clique]
Authors: H Yu, A Paccanaro, V Trifonov, M Gerstein
Journal: Bioinformatics
PMID: 16455753
Pages: 823-9
Volume: 22
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/defective-clique/
footnote: -
grant: nesg
ignore: -
labcite: H Yu, A Paccanaro, V Trifonov, M Gerstein (in press) Bioinformatcs
labid: defective-clique
labtitle: Predicting interactions in protein networks by completing defective cliques.
preprint: http://papers.gersteinlab.org/e-print/defective-clique/preprint.pdf
sortval: -
subject: 2006-summary,interactions
target: -
website: http://topnet.gersteinlab.org/clique/
website2: -
[targethub]
Authors: AR Borneman, JA Leigh-Bell, H Yu, P Bertone, M Gerstein, M Snyder
Journal: Genes Dev
PMID: 16449570
Pages: 435-48
Volume: 20
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/targethub/
footnote: -
grant: -
ignore: -
labcite: AR Borneman, JA Leigh-Bell, H Yu, P Bertone, M Gerstein, M Snyder (2006) Genes Dev 20: 435-48.
labid: targethub
labtitle: Target hub proteins serve as master regulators of development in yeast.
preprint: http://papers.gersteinlab.org/e-print/targethub/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[memint]
Authors: Y Xia, LJ Lu, M Gerstein
Journal: J Mol Biol
PMID: 16413578
Pages: 339-49
Volume: 357
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/memint/
footnote: -
grant: -
ignore: -
labcite: Y Xia, LJ Lu, M Gerstein (2006). J Mol Biol (in press), 2006 Mar 17;357(1):339-49
labid: memint
labtitle: Integrated prediction of the helical membrane protein interactome in yeast.
preprint: http://papers.gersteinlab.org/e-print/memint/preprint.pdf
sortval: -
subject: 2006-summary,interactions
target: -
website: -
website2: -
[molmovdb-update-nar]
Authors: S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein
Journal: Nucleic Acids Res
PMID: 16381870
Pages: D296-301
Volume: 34
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/molmovdb-update-nar/
footnote: -
grant: hpc,keck
ignore: -
labcite: S Flores, N Echols, D Milburn, B Hespenheide, K
Keating, J Lu, S Wells, E Z Yu, M Thorpe, M
Gerstein
labid: molmovdb-update-nar
labtitle: The Database of Macromolecular Motions: new features added at the decade mark.
preprint: http://papers.gersteinlab.org/e-print/molmovdb-update-nar/preprint.pdf
sortval: -
subject: 2006-summary,best,student
target: -
website: http://molmovdb.org
website2: -
[tilingtools]
Authors: P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein
Journal: Genome Res
PMID: 16365382
Pages: 271-81
Volume: 16
Year: 2006
e-print: http://papers.gersteinlab.org/e-print/tilingtools/
footnote: -
grant: cegs,hpc
ignore: -
labcite: P. Bertone, F. Schubert, V. Trifonov, J. Rozowsky, O. Emanuelsson, J. Karro, M-Y Kao, M. Snyder, M. Gerstein. Genome Research (in press).
labid: tilingtools
labtitle: Design optimization methods for genomic DNA tiling arrays.
preprint: http://papers.gersteinlab.org/e-print/tilingtools/preprint.pdf
sortval: -
subject: 2005-Summary,2006-summary,expression,student
target: -
website: http://tiling.gersteinlab.org
website2: -
[ijcnnn]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/ijcnnn/
footnote: -
grant: -
ignore: -
labcite: A Paccanaro, V Trifonov, H Yu, M Gerstein (2005). International Joint Conference on Neural Networks (IJCNN, Jul. 31-Aug. 4, Montreal, Canada), pages 161 - 166, vol. 1
labid: ijcnnn
labtitle: Inferring Protein-Protein Interactions Using Interaction Network Topologies
preprint: http://papers.gersteinlab.org/e-print/ijcnnn/preprint.pdf
sortval: -
subject: interactions
target: -
website: -
website2: -
[intint-chapter]
Authors: -
Journal: -
PMID: -
Pages: -
Volume: -
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/intint-chapter/
footnote: -
grant: -
ignore: -
labcite: LJ Lu, Y Xia, H Yu, A Rives, H Lu, F Schubert, M Gerstein (2005). Data Analysis and Visualization in Genomics and Proteomics (Wiley, NY)
labid: intint-chapter
labtitle: Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis
preprint: http://papers.gersteinlab.org/e-print/intint-chapter/preprint.pdf
sortval: -
subject: 2005-Summary,interactions,student
target: -
website: http://networks.gersteinlab.org/intint/
website2: -
[movableorf]
Authors: DM Gelperin, MA White, ML Wilkinson, Y Kon, LA Kung, KJ Wise, N Lopez-Hoyo, L Jiang, S Piccirillo, H Yu, M Gerstein, ME Dumont, EM Phizicky, M Snyder, EJ Grayhack
Journal: Genes Dev
PMID: 16322557
Pages: 2816-26
Volume: 19
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/movableorf/
footnote: -
grant: -
ignore: -
labcite: DM Gelperin, MA White, ML Wilkinson, Y Kon, LA Kung, KJ Wise, N Lopez-Hoyo, L Jiang, S Piccirillo, H Yu, M Gerstein, ME Dumont, EM Phizicky, M Snyder, EJ Grayhack (2005) Genes Dev 19: 2816-26.
labid: movableorf
labtitle: Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.
preprint: http://papers.gersteinlab.org/e-print/movableorf/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[phosphorylome]
Authors: J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder
Journal: Nature
PMID: 16319894
Pages: 679-84
Volume: 438
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/phosphorylome/
footnote: -
grant: -
ignore: -
labcite: -
labid: phosphorylome
labtitle: Global analysis of protein phosphorylation in yeast.
preprint: http://papers.gersteinlab.org/e-print/phosphorylome/preprint.pdf
sortval: -
subject: 2005-Summary,expt-collab,interactions,microarray
target: -
website: http://networks.gersteinlab.org/phosphorylome
website2: -
[stat1]
Authors: SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder
Journal: Genes Dev
PMID: 16319195
Pages: 2953-68
Volume: 19
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/stat1/
footnote: -
grant: cegs,hpc
ignore: -
labcite: -
labid: stat1
labtitle: Global changes in STAT target selection and transcription regulation upon interferon treatments.
preprint: http://papers.gersteinlab.org/e-print/stat1/preprint.pdf
sortval: -
subject: 2005-Summary,expt-collab,microarray
target: -
website: http://array.mbb.yale.edu/chr22/STAT/
website2: -
[pilot-rice-tiling]
Authors: V Stolc, L Li, X Wang, X Li, N Su, W Tongprasit, B Han, Y Xue, J Li, M Snyder, M Gerstein, J Wang, XW Deng
Journal: Plant Mol Biol
PMID: 16217608
Pages: 137-49
Volume: 59
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/pilot-rice-tiling/
footnote: -
grant: -
ignore: -
labcite: -
labid: pilot-rice-tiling
labtitle: A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
preprint: http://papers.gersteinlab.org/e-print/pilot-rice-tiling/preprint.pdf
sortval: -
subject: -
target: -
website: -
website2: -
[security_data_archiving]
Authors: A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein
Journal: Genome Biol
PMID: 16168090
Pages: 119
Volume: 6
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/security_data_archiving/
footnote: -
grant: cegs
ignore: -
labcite: A Smith, D Greenbaum, SM Douglas, M Long, and M Gerstein (in press) Genome Biol
labid: security_data_archiving
labtitle: Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
preprint: http://papers.gersteinlab.org/e-print/security_data_archiving/preprint.pdf
sortval: -
subject: 2005-Summary,epublishing,student
target: -
website: -
website2: -
[pubnet]
Authors: SM Douglas, GT Montelione, M Gerstein
Journal: Genome Biol
PMID: 16168087
Pages: R80
Volume: 6
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/pubnet/
footnote: -
grant: nesg
ignore: -
labcite: SM Douglas, GT Montelione, M Gerstein (in press) Genome Biol
labid: pubnet
labtitle: PubNet: a flexible system for visualizing literature derived networks.
preprint: http://papers.gersteinlab.org/e-print/pubnet/preprint.pdf
sortval: -
subject: 2005-Summary,best,best2006,epublishing,interactions,student,tools
target: -
website: http://pubnet.gersteinlab.org/
website2: -
[ASIC1]
Authors: T Coric, D Zheng, M Gerstein, CM Canessa
Journal: J Physiol
PMID: 16002453
Pages: 725-35
Volume: 568
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/ASIC1/
footnote: -
grant: -
ignore: -
labcite: -
labid: ASIC1
labtitle: Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.
preprint: http://papers.gersteinlab.org/e-print/ASIC1/preprint.pdf
sortval: -
subject: 2005-Summary,expt-collab
target: -
website: -
website2: -
[intint2]
Authors: LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein
Journal: Genome Res
PMID: 15998909
Pages: 945-53
Volume: 15
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/intint2/
footnote: -
grant: -
ignore: -
labcite: LJ Lu, Y Xia, A Paccanaro, H Yu and M Gerstein (in press) Genome Research
labid: intint2
labtitle: Assessing the limits of genomic data integration for predicting protein networks.
preprint: http://papers.gersteinlab.org/e-print/intint2/preprint.pdf
sortval: -
subject: 2005-Summary,interactions,intro-to-lab,mining
target: -
website: http://networks.gersteinlab.org/intint/
website2: -
[Tiling-analysis]
Authors: TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein
Journal: Trends Genet
PMID: 15979196
Pages: 466-75
Volume: 21
Year: 2005
e-print: http://papers.gersteinlab.org/e-print/Tiling-analysis/
footnote: -
grant: cegs,hpc
ignore: -
labcite: TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein Trends Genet. 2005 Aug;21(8):466-75.
labid: Tiling-analysis
labtitle: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
preprint: http://papers.gersteinlab.org/e-print/Tiling-analysis/preprint.pdf
sortval: -
subject: 2005-Summary,expr |
