| Year |
Citation |
Score |
| 2023 |
Saha E, Fanfani V, Mandros P, Ben-Guebila M, Fischer J, Hoff-Shutta K, Glass K, DeMeo DL, Lopes-Ramos C, Quackenbush J. Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO). Biorxiv : the Preprint Server For Biology. PMID 38014256 DOI: 10.1101/2023.11.16.567119 |
0.318 |
|
| 2023 |
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, ... ... Quackenbush J, et al. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. 24: 45. PMID 36894939 DOI: 10.1186/s13059-023-02877-1 |
0.703 |
|
| 2022 |
Gaynor SM, Fagny M, Lin X, Platig J, Quackenbush J. Connectivity in eQTL networks dictates reproducibility and genomic properties. Cell Reports Methods. 2: 100218. PMID 35637906 DOI: 10.1016/j.crmeth.2022.100218 |
0.301 |
|
| 2022 |
Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush J. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. PMID 35459940 DOI: 10.1038/s41592-022-01479-2 |
0.671 |
|
| 2022 |
Guebila MB, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush J. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. Nar Genomics and Bioinformatics. 4: lqac002. PMID 35156023 DOI: 10.1093/nargab/lqac002 |
0.674 |
|
| 2021 |
Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Constructing gene regulatory networks using epigenetic data. Npj Systems Biology and Applications. 7: 45. PMID 34887443 DOI: 10.1038/s41540-021-00208-3 |
0.309 |
|
| 2021 |
Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J. GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Research. PMID 34508353 DOI: 10.1093/nar/gkab778 |
0.693 |
|
| 2021 |
Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML. Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Research. PMID 34493595 DOI: 10.1158/0008-5472.CAN-21-0730 |
0.684 |
|
| 2021 |
Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene Targeting in Disease Networks. Frontiers in Genetics. 12: 649942. PMID 33968133 DOI: 10.3389/fgene.2021.649942 |
0.322 |
|
| 2020 |
Qiang J, Ding W, Kuijjer M, Quackenbush J, Chen P. Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. Ieee Access : Practical Innovations, Open Solutions. 8: 67775-67789. PMID 36329870 DOI: 10.1109/access.2020.2982569 |
0.655 |
|
| 2020 |
Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics (Oxford, England). PMID 32860050 DOI: 10.1093/Bioinformatics/Btaa571 |
0.665 |
|
| 2020 |
Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports. 31: 107795. PMID 32579922 DOI: 10.1016/J.Celrep.2020.107795 |
0.698 |
|
| 2020 |
Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, ... ... Quackenbush J, et al. Molecular networks in Network Medicine: Development and applications. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1489. PMID 32307915 DOI: 10.1002/Wsbm.1489 |
0.37 |
|
| 2020 |
Lietz CE, Garbutt C, Barry WT, Deshpande V, Chen YL, Lozano-Calderon SA, Wang Y, Lawney B, Ebb D, Cote GM, Duan Z, Hornicek FJ, Choy E, Petur Nielsen G, Haibe-Kains B, ... Quackenbush J, et al. MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma. Scientific Reports. 10: 4409. PMID 32157112 DOI: 10.1038/S41598-020-61236-3 |
0.355 |
|
| 2020 |
Altenbuchinger M, Weihs A, Quackenbush J, Grabe HJ, Zacharias HU. Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 1863: 194418. PMID 31639475 DOI: 10.1016/J.Bbagrm.2019.194418 |
0.419 |
|
| 2020 |
Lopes-Ramos CM, Kuijjer M, Glass K, DeMeo D, Quackenbush J. Abstract 6569: Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation Cancer Research. 80: 6569-6569. DOI: 10.1158/1538-7445.Am2020-6569 |
0.683 |
|
| 2020 |
Qiang J, Ding W, Kuijjer ML, Quackenbush J, Chen P. Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer Ieee Access. 8: 67775-67789. DOI: 10.1109/Access.2020.2982569 |
0.638 |
|
| 2019 |
Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC. The impact of stroma admixture on molecular subtypes and prognostic gene signatures in serous ovarian cancer. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 31871106 DOI: 10.1158/1055-9965.Epi-18-1359 |
0.348 |
|
| 2019 |
Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British Journal of Cancer. PMID 31806877 DOI: 10.1038/S41416-019-0614-3 |
0.651 |
|
| 2019 |
Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. Bmc Cancer. 19: 1003. PMID 31653243 DOI: 10.1186/S12885-019-6235-7 |
0.668 |
|
| 2019 |
Gaynor SM, Sun R, Lin X, Quackenbush J. Identification of differentially expressed gene sets using the Generalized Berk-Jones statistica. Bioinformatics (Oxford, England). PMID 31062858 DOI: 10.1093/Bioinformatics/Btz277 |
0.424 |
|
| 2019 |
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 79: 2084. PMID 30987980 DOI: 10.1158/0008-5472.Can-19-0678 |
0.678 |
|
| 2019 |
Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. Iscience. 14: 226-240. PMID 30981959 DOI: 10.1016/J.Isci.2019.03.021 |
0.691 |
|
| 2018 |
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 78: 5538-5547. PMID 30275053 DOI: 10.1158/0008-5472.Can-18-0454 |
0.695 |
|
| 2018 |
Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J. Histopathological Image QTL Discovery of Immune Infiltration Variants. Iscience. 5: 80-89. PMID 30240647 DOI: 10.1016/J.Isci.2018.07.001 |
0.311 |
|
| 2018 |
Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal of Cancer. PMID 29765148 DOI: 10.1038/S41416-018-0109-7 |
0.65 |
|
| 2018 |
Padi M, Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. Npj Systems Biology and Applications. 4: 16. PMID 29707235 DOI: 10.1038/s41540-018-0052-5 |
0.306 |
|
| 2018 |
Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang J, Xiao N, Greil R, Rinnerthaler G, Gampenrieder SP, Heimberger AB, Berry DA, ... ... Quackenbush J, et al. Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. Nature Communications. 9: 1219. PMID 29572535 DOI: 10.1038/S41467-018-03631-Z |
0.314 |
|
| 2018 |
Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Human Genomics. 12: 1. PMID 29335020 DOI: 10.1186/S40246-018-0132-Z |
0.341 |
|
| 2018 |
Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang R, Xiao N, Greil R, Rinnerthaler G, Gampenrieder S, Heimberger A, Berry D, ... ... Quackenbush J, et al. Abstract P2-09-09: Polyligand profiling differentiates cancer patients according to their benefit of treatment Cancer Research. 78. DOI: 10.1158/1538-7445.Sabcs17-P2-09-09 |
0.305 |
|
| 2017 |
Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. Bmc Systems Biology. 11: 139. PMID 29237467 DOI: 10.1186/S12918-017-0517-Y |
0.366 |
|
| 2017 |
Wang YE, Kutnetsov L, Partensky A, Farid J, Quackenbush J. WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data. Cancer Research. 77: e11-e14. PMID 29092929 DOI: 10.1158/0008-5472.Can-17-0802 |
0.337 |
|
| 2017 |
Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Reports. 21: 1077-1088. PMID 29069589 DOI: 10.1016/J.Celrep.2017.10.001 |
0.691 |
|
| 2017 |
Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. Bmc Bioinformatics. 18: 437. PMID 28974199 DOI: 10.1186/S12859-017-1847-X |
0.657 |
|
| 2017 |
Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. Bmc Genomics. 18: 723. PMID 28899340 DOI: 10.1186/S12864-017-4111-X |
0.661 |
|
| 2017 |
Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851834 DOI: 10.1073/Pnas.1707375114 |
0.685 |
|
| 2017 |
Nishihara R, Glass K, Mima K, Hamada T, Nowak JA, Qian ZR, Kraft P, Giovannucci EL, Fuchs CS, Chan AT, Quackenbush J, Ogino S, Onnela JP. Biomarker correlation network in colorectal carcinoma by tumor anatomic location. Bmc Bioinformatics. 18: 304. PMID 28623901 DOI: 10.1186/S12859-017-1718-5 |
0.348 |
|
| 2017 |
Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, ... ... Quackenbush J, et al. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. Journal of Hematology & Oncology. 10: 107. PMID 28506242 DOI: 10.1186/S13045-017-0465-4 |
0.632 |
|
| 2017 |
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biology. 18: 84. PMID 28482897 DOI: 10.1186/S13059-017-1218-Y |
0.301 |
|
| 2017 |
Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks with pandaR. Bioinformatics (Oxford, England). PMID 28334344 DOI: 10.1093/Bioinformatics/Btx139 |
0.404 |
|
| 2017 |
Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo DL, Cho MH, Qiu W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, ... Quackenbush J, et al. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Scientific Reports. 7: 44232. PMID 28287180 DOI: 10.1038/Srep44232 |
0.411 |
|
| 2017 |
Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. Plos One. 12: e0170181. PMID 28152060 DOI: 10.1371/Journal.Pone.0170181 |
0.388 |
|
| 2017 |
Quackenbush J. Using networks to understand the genotype-phenotype connection F1000research. 6. DOI: 10.7490/F1000Research.1114478.1 |
0.309 |
|
| 2016 |
Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000research. 5: 2333. PMID 28928933 DOI: 10.12688/F1000Research.9611.3 |
0.327 |
|
| 2016 |
Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. Plos Computational Biology. 12: e1005033. PMID 27618581 DOI: 10.1371/Journal.Pcbi.1005033 |
0.344 |
|
| 2016 |
Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin R. Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. Jci Insight. 1. PMID 27617304 DOI: 10.1172/Jci.Insight.87988 |
0.34 |
|
| 2016 |
Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AM, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 0. PMID 27564456 DOI: 10.1080/15592294.2016.1226451 |
0.328 |
|
| 2016 |
Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinformatics (Oxford, England). PMID 27540268 DOI: 10.1093/Bioinformatics/Btw538 |
0.311 |
|
| 2016 |
Vargas AJ, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. PMID 27524493 DOI: 10.1016/J.Ygeno.2016.08.001 |
0.327 |
|
| 2016 |
Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. Assessment of pharmacogenomic agreement. F1000research. 5: 825. PMID 27408686 DOI: 10.12688/F1000Research.8705.1 |
0.318 |
|
| 2016 |
van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics (Oxford, England). PMID 27402905 DOI: 10.1093/Bioinformatics/Btw422 |
0.692 |
|
| 2016 |
Kusko RL, Brothers Ii JF, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, et al. Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying COPD and IPF. American Journal of Respiratory and Critical Care Medicine. PMID 27104832 DOI: 10.1164/Rccm.201510-2026Oc |
0.317 |
|
| 2016 |
Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez-Arias A, Gunawardena J. Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation. Cell Reports. PMID 26832399 DOI: 10.1016/J.Celrep.2015.12.101 |
0.319 |
|
| 2016 |
De Nicolo A, Haibe-Kains B, Taşan M, Cusick ME, Vidal M, Quackenbush J, Joukov V, Livingston DM. Analysis of BRCA1-related functional associations in sporadic triple negative breast cancer: A network-based approach. Journal of Clinical Oncology. 34: 1070-1070. DOI: 10.1200/Jco.2016.34.15_Suppl.1070 |
0.332 |
|
| 2015 |
Padi M, Quackenbush J. Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. Bmc Systems Biology. 9: 80. PMID 26576632 DOI: 10.1186/S12918-015-0228-1 |
0.41 |
|
| 2015 |
De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, Zheng Y, Holman AG, Wang YE, Dal Cin P, Fletcher JA, Rubio R, Croft L, Quackenbush J, Sugarbaker PE, et al. Gender-Specific Molecular and Clinical Features underlie Malignant Pleural Mesothelioma. Cancer Research. PMID 26554828 DOI: 10.1158/0008-5472.Can-15-0751 |
0.311 |
|
| 2015 |
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. Using shRNA experiments to validate gene regulatory networks. Genomics Data. 4: 123-6. PMID 26484195 DOI: 10.1016/J.Gdata.2015.03.011 |
0.419 |
|
| 2015 |
Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. Bmc Bioinformatics. 16: 115. PMID 25888305 DOI: 10.1186/S12859-015-0551-Y |
0.418 |
|
| 2015 |
Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Medicine. 7: 12. PMID 25763110 DOI: 10.1186/S13073-015-0137-3 |
0.344 |
|
| 2015 |
Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, et al. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. Rna (New York, N.Y.). 21: 164-71. PMID 25519487 DOI: 10.1261/Rna.046060.114 |
0.31 |
|
| 2015 |
Castaldi PJ, Cho MH, Zhou X, Qiu W, Mcgeachie M, Celli B, Bakke P, Gulsvik A, Lomas DA, Crapo JD, Beaty TH, Rennard S, Harshfield B, Lange C, Singh D, ... ... Quackenbush J, et al. Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci. Human Molecular Genetics. 24: 1200-10. PMID 25315895 DOI: 10.1093/Hmg/Ddu525 |
0.346 |
|
| 2015 |
Kuijjer ML, Glass K, Quackenbush J. Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-20 |
0.711 |
|
| 2015 |
Scherer D, Toth R, Kelemen L, Risch A, Hazra A, Issa JP, Moreno V, Eeles RA, Quackenbush J, Goode EL, Ogino S, Hung R, Ulrich CM. Abstract 4612: Genetic variants in epigenetic pathways and risk of multiple cancer types in the GAME-ON consortium Cancer Research. 75: 4612-4612. DOI: 10.1158/1538-7445.Am2015-4612 |
0.33 |
|
| 2015 |
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. Using shRNA experiments to validate gene regulatory networks Genomics Data. 4: 123-126. DOI: 10.1016/j.gdata.2015.03.011 |
0.304 |
|
| 2014 |
Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P. The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle (Georgetown, Tex.). 13: 2889-900. PMID 25486477 DOI: 10.4161/15384101.2014.946850 |
0.328 |
|
| 2014 |
Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. Bmc Systems Biology. 8: 118. PMID 25431000 DOI: 10.1186/S12918-014-0118-Y |
0.347 |
|
| 2014 |
Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, et al. Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. American Journal of Respiratory and Critical Care Medicine. 190: 1263-72. PMID 25333685 DOI: 10.1164/Rccm.201408-1452Oc |
0.305 |
|
| 2014 |
Mason EA, Mar JC, Laslett AL, Pera MF, Quackenbush J, Wolvetang E, Wells CA. Gene expression variability as a unifying element of the pluripotency network. Stem Cell Reports. 3: 365-77. PMID 25254348 DOI: 10.1016/J.Stemcr.2014.06.008 |
0.404 |
|
| 2014 |
Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B. Relevance of different prior knowledge sources for inferring gene interaction networks. Frontiers in Genetics. 5: 177. PMID 25009552 DOI: 10.3389/Fgene.2014.00177 |
0.399 |
|
| 2014 |
Chu JH, Hersh CP, Castaldi PJ, Cho MH, Raby BA, Laird N, Bowler R, Rennard S, Loscalzo J, Quackenbush J, Silverman EK. Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. Bmc Systems Biology. 8: 78. PMID 24964944 DOI: 10.1186/1752-0509-8-78 |
0.307 |
|
| 2014 |
Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, ... Quackenbush J, et al. Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nature Communications. 5: 4006. PMID 24892406 DOI: 10.1038/Ncomms5006 |
0.32 |
|
| 2014 |
Ferrari G, Quackenbush J, Strobeck J, Hu L, Johnson CK, Mak A, Shaw RE, Sayles K, Brizzio ME, Zapolanski A, Grau JB. Comparative genome-wide transcriptional analysis of human left and right internal mammary arteries. Genomics. 104: 36-44. PMID 24858532 DOI: 10.1016/J.Ygeno.2014.04.005 |
0.311 |
|
| 2014 |
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J. Inference and validation of predictive gene networks from biomedical literature and gene expression data Genomics. 103: 329-336. PMID 24691108 DOI: 10.1016/J.Ygeno.2014.03.004 |
0.411 |
|
| 2014 |
Lee JW, Norden AD, Ligon KL, Golby AJ, Beroukhim R, Quackenbush J, Wells W, Oelschlager K, Maetzold D, Wen PY. Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study. Epilepsy Research. 108: 843-52. PMID 24690158 DOI: 10.1016/J.Eplepsyres.2014.02.021 |
0.364 |
|
| 2014 |
Adamia S, Bar-Natan M, Haibe-Kains B, Pilarski PM, Bach C, Pevzner S, Calimeri T, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Galinsky I, Mathews S, Dagogo-Jack I, Wadleigh M, ... ... Quackenbush J, et al. NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood. 123: 2816-25. PMID 24574459 DOI: 10.1182/Blood-2013-02-481507 |
0.37 |
|
| 2014 |
Adamia S, Haibe-Kains B, Pilarski PM, Bar-Natan M, Pevzner S, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Burke J, Galinsky I, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, ... ... Quackenbush J, et al. A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 1135-45. PMID 24284058 DOI: 10.1158/1078-0432.Ccr-13-0956 |
0.342 |
|
| 2014 |
Sharron Lin X, Hu L, Sandy K, Correll M, Quackenbush J, Wu CL, Scott McDougal W. Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens. Urologic Oncology. 32: 327-36. PMID 24055427 DOI: 10.1016/J.Urolonc.2013.06.014 |
0.323 |
|
| 2014 |
Quiroz-Zarate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Carey V, Hankinson SE, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Abstract 3269: QTLs in breast tumor and breast normal adjacent FFPE specimens from the Nurses’ Health Study Cancer Research. 74: 3269-3269. DOI: 10.1158/1538-7445.Am2014-3269 |
0.341 |
|
| 2013 |
Fan JB, Quackenbush J, Wacek B. Accelerating genomic data publishing and sharing. Genomics Data. 1: 1. PMID 26484049 DOI: 10.1016/J.Gdata.2013.05.001 |
0.345 |
|
| 2013 |
Merritt MA, Bentink S, Schwede M, Iwanicki MP, Quackenbush J, Woo T, Agoston ES, Reinhardt F, Crum CP, Berkowitz RS, Mok SC, Witt AE, Jones MA, Wang B, Ince TA. Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes. Plos One. 8: e80314. PMID 24303006 DOI: 10.1371/Journal.Pone.0080314 |
0.321 |
|
| 2013 |
Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J. Inconsistency in large pharmacogenomic studies. Nature. 504: 389-93. PMID 24284626 DOI: 10.1038/Nature12831 |
0.357 |
|
| 2013 |
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. Plos One. 8: e64832. PMID 23741402 DOI: 10.1371/Journal.Pone.0064832 |
0.415 |
|
| 2013 |
Schwede M, Spentzos D, Bentink S, Hofmann O, Haibe-Kains B, Harrington D, Quackenbush J, Culhane AC. Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis. Plos One. 8: e57799. PMID 23536770 DOI: 10.1371/Journal.Pone.0057799 |
0.348 |
|
| 2013 |
Zhou X, Qiu W, Sathirapongsasuti JF, Cho MH, Mancini JD, Lao T, Thibault DM, Litonjua AA, Bakke PS, Gulsvik A, Lomas DA, Beaty TH, Hersh CP, Anderson C, Geigenmuller U, ... ... Quackenbush J, et al. Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells. Genomics. 101: 263-72. PMID 23459001 DOI: 10.1016/J.Ygeno.2013.02.010 |
0.405 |
|
| 2013 |
Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B. Significance analysis of prognostic signatures. Plos Computational Biology. 9: e1002875. PMID 23365551 DOI: 10.1371/Journal.Pcbi.1002875 |
0.398 |
|
| 2013 |
Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B. RamiGO: an R/Bioconductor package providing an AmiGO visualize interface. Bioinformatics (Oxford, England). 29: 666-8. PMID 23297033 DOI: 10.1093/Bioinformatics/Bts708 |
0.328 |
|
| 2013 |
Li W, Han J, Widlund H, Correll M, Wang Y, Quackenbush J, Mihm M, Canales AL, Golub T, Hoshida Y, Hunter D, Murphy G, Kupper T, Qureshi A. Abstract 1347: CXCR4 pathway associated with family history of melanoma. Cancer Research. 73: 1347-1347. DOI: 10.1158/1538-7445.Am2013-1347 |
0.319 |
|
| 2012 |
Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, et al. Expression profiling of archival tumors for long-term health studies. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 6136-46. PMID 23136189 DOI: 10.1158/1078-0432.Ccr-12-1915 |
0.322 |
|
| 2012 |
Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, ... ... Quackenbush J, et al. Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 5806-15. PMID 22912389 DOI: 10.1158/1078-0432.Ccr-12-0857 |
0.308 |
|
| 2012 |
Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, ... ... Quackenbush J, et al. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 487: 491-5. PMID 22810586 DOI: 10.1038/Nature11288 |
0.402 |
|
| 2012 |
Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: Iterative binary bi-clustering of gene sets Bioinformatics. 28: 2484-2492. PMID 22789589 DOI: 10.1093/Bioinformatics/Bts438 |
0.41 |
|
| 2012 |
Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, ... ... Quackenbush J, et al. Viral perturbations of host networks reflect disease etiology. Plos Computational Biology. 8: e1002531. PMID 22761553 DOI: 10.1371/Journal.Pcbi.1002531 |
0.311 |
|
| 2012 |
Skiadas CC, Duan S, Correll M, Rubio R, Karaca N, Ginsburg ES, Quackenbush J, Racowsky C. Ovarian reserve status in young women is associated with altered gene expression in membrana granulosa cells. Molecular Human Reproduction. 18: 362-71. PMID 22355044 DOI: 10.1093/Molehr/Gas008 |
0.36 |
|
| 2012 |
Bentink S, Haibe-Kains B, Risch T, Fan JB, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Culhane A, Drapkin R, Quackenbush J, Matulonis UA. Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. Plos One. 7: e30269. PMID 22348002 DOI: 10.1371/Journal.Pone.0030269 |
0.377 |
|
| 2012 |
Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. A three-gene model to robustly identify breast cancer molecular subtypes. Journal of the National Cancer Institute. 104: 311-25. PMID 22262870 DOI: 10.1093/Jnci/Djr545 |
0.379 |
|
| 2012 |
Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C. nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinformatics (Oxford, England). 28: 726-8. PMID 22247278 DOI: 10.1093/Bioinformatics/Bts011 |
0.413 |
|
| 2012 |
Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, ... Quackenbush J, et al. GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Research. 40: D1060-6. PMID 22110038 DOI: 10.1093/Nar/Gkr901 |
0.413 |
|
| 2012 |
Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J. Predictive networks: A flexible, open source, web application for integration and analysis of human gene networks Nucleic Acids Research. 40: D866-D875. PMID 22096235 DOI: 10.1093/Nar/Gkr1050 |
0.437 |
|
| 2012 |
Brothers J, Kusko R, Liu G, Luo L, Guardela BJ, Tedrow J, Alekesyev Y, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Sebastiani P, Lenburg M, Kaminski N, et al. Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-P4 |
0.341 |
|
| 2012 |
Kusko RL, Brothers J, Liu G, Luo L, Guardela BJ, Tedrow J, Aleksyev Y, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Lenburg M, Schwartz DA, Beane J, et al. Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-P21 |
0.342 |
|
| 2012 |
Quackenbush J. Abstract IA11: Extracting predictive networks from high-dimensional data. Cancer Epidemiology and Prevention Biomarkers. 21. DOI: 10.1158/1055-9965.Gwas-Ia11 |
0.397 |
|
| 2011 |
Mar JC, Matigian NA, Quackenbush J, Wells CA. attract: A method for identifying core pathways that define cellular phenotypes. Plos One. 6: e25445. PMID 22022396 DOI: 10.1371/Journal.Pone.0025445 |
0.385 |
|
| 2011 |
Howe EA, Sinha R, Schlauch D, Quackenbush J. RNA-Seq analysis in MeV Bioinformatics. 27: 3209-3210. PMID 21976420 DOI: 10.1093/Bioinformatics/Btr490 |
0.339 |
|
| 2011 |
Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, Silburn PA, McGrath JJ, Quackenbush J, Wells CA. Variance of gene expression identifies altered network constraints in neurological disease. Plos Genetics. 7: e1002207. PMID 21852951 DOI: 10.1371/Journal.Pgen.1002207 |
0.413 |
|
| 2011 |
Marko NF, Quackenbush J, Weil RJ. Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. Plos One. 6: e20826. PMID 21829433 DOI: 10.1371/Journal.Pone.0020826 |
0.367 |
|
| 2011 |
Gewurz BE, Mar JC, Padi M, Zhao B, Shinners NP, Takasaki K, Bedoya E, Zou JY, Cahir-McFarland E, Quackenbush J, Kieff E. Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. Journal of Virology. 85: 6764-73. PMID 21543491 DOI: 10.1128/Jvi.00422-11 |
0.306 |
|
| 2011 |
Konstantinopoulos PA, Cannistra SA, Fountzilas H, Culhane A, Pillay K, Rueda B, Cramer D, Seiden M, Birrer M, Coukos G, Zhang L, Quackenbush J, Spentzos D. Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. Plos One. 6: e18202. PMID 21479231 DOI: 10.1371/Journal.Pone.0018202 |
0.328 |
|
| 2011 |
Mar JC, Wells CA, Quackenbush J. Defining an informativeness metric for clustering gene expression data. Bioinformatics (Oxford, England). 27: 1094-100. PMID 21330289 DOI: 10.1093/Bioinformatics/Btr074 |
0.345 |
|
| 2011 |
Liu F, White JA, Antonescu C, Gusenleitner D, Quackenbush J. GCOD - GeneChip Oncology Database. Bmc Bioinformatics. 12: 46. PMID 21291543 DOI: 10.1186/1471-2105-12-46 |
0.348 |
|
| 2011 |
Zhao B, Mar JC, Maruo S, Lee S, Gewurz BE, Johannsen E, Holton K, Rubio R, Takada K, Quackenbush J, Kieff E. Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines. Proceedings of the National Academy of Sciences of the United States of America. 108: 337-42. PMID 21173222 DOI: 10.1073/Pnas.1017419108 |
0.383 |
|
| 2011 |
Adamia S, Bar-Natan M, Haibe-Kains B, Avet-Loiseau H, Lode L, Pevzner S, Verselis S, Fox E, Galinsky I, Quackenbush J, Stone RM, Griffin JD. Genome-Wide Aberrant Splicing in Patients with Acute Myeloid Leukemia (AML) Indetifies Potential Novel Targets Blood. 118: 761-761. DOI: 10.1182/Blood.V118.21.761.761 |
0.359 |
|
| 2010 |
Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, ... ... Quackenbush J, et al. Therapeutic implications of GIPC1 silencing in cancer. Plos One. 5: e15581. PMID 21209904 DOI: 10.1371/Journal.Pone.0015581 |
0.339 |
|
| 2010 |
Tseveleki V, Rubio R, Vamvakas S, White J, Taoufik E, Petit E, Quackenbush J, Probert L. Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes. Genomics. 96: 82-91. PMID 20435134 DOI: 10.1016/J.Ygeno.2010.04.004 |
0.358 |
|
| 2010 |
Antonescu C, Antonescu V, Sultana R, Quackenbush J. Using the DFCI gene index databases for biological discovery Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 20205187 DOI: 10.1002/0471250953.Bi0106S29 |
0.368 |
|
| 2010 |
Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J. GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Research. 38: D716-25. PMID 19934259 DOI: 10.1093/Nar/Gkp1015 |
0.398 |
|
| 2010 |
Chen DT, Nasir A, Culhane A, Venkataramu C, Fulp W, Rubio R, Wang T, Agrawal D, McCarthy SM, Gruidl M, Bloom G, Anderson T, White J, Quackenbush J, Yeatman T. Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Research and Treatment. 119: 335-46. PMID 19266279 DOI: 10.1007/S10549-009-0344-Y |
0.338 |
|
| 2010 |
Marko NF, Quackenbush J, Weil RJ. Abstract B8: Why is there no consensus on GBM subgroups? Understanding the nature of biological and statistical variability in The Cancer Genome Atlas GBM data and the implications for molecular tumor classification Clinical Cancer Research. 16. DOI: 10.1158/1078-0432.Tcme10-B8 |
0.36 |
|
| 2009 |
Mar JC, Quackenbush J. Decomposition of gene expression state space trajectories Plos Computational Biology. 5. PMID 20041215 DOI: 10.1371/Journal.Pcbi.1000626 |
0.367 |
|
| 2009 |
Aryee MJ, Gutiérrez-Pabello JA, Kramnik I, Maiti T, Quackenbush J. An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation) Bmc Bioinformatics. 10: 409-409. PMID 20003283 DOI: 10.1186/1471-2105-10-409 |
0.376 |
|
| 2009 |
April C, Klotzle B, Royce T, Wickham-Garcia E, Boyaniwsky T, Izzo J, Cox D, Jones W, Rubio R, Holton K, Matulonis U, Quackenbush J, Fan JB. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. Plos One. 4: e8162. PMID 19997620 DOI: 10.1371/Journal.Pone.0008162 |
0.392 |
|
| 2009 |
Quackenbush J. Data reporting standards: making the things we use better Genome Medicine. 1: 111-111. PMID 19939294 DOI: 10.1186/Gm111 |
0.301 |
|
| 2009 |
Santagata S, Maire CL, Idbaih A, Geffers L, Correll M, Holton K, Quackenbush J, Ligon KL. CRX is a diagnostic marker of retinal and pineal lineage tumors. Plos One. 4: e7932. PMID 19936203 DOI: 10.1371/Journal.Pone.0007932 |
0.344 |
|
| 2009 |
Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Chang J, Brown P. Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 15: 6327-40. PMID 19808870 DOI: 10.1158/1078-0432.Ccr-09-1107 |
0.322 |
|
| 2009 |
Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Research. 69: 7480-5. PMID 19723662 DOI: 10.1158/0008-5472.Can-08-3350 |
0.326 |
|
| 2009 |
Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, ... ... Quackenbush J, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41: 553-62. PMID 19377474 DOI: 10.1038/Ng.375 |
0.366 |
|
| 2009 |
Mar JC, Kimura Y, Schroder K, Irvine KM, Hayashizaki Y, Suzuki H, Hume D, Quackenbush J. Data-driven normalization strategies for high-throughput quantitative RT-PCR. Bmc Bioinformatics. 10: 110. PMID 19374774 DOI: 10.1186/1471-2105-10-110 |
0.393 |
|
| 2009 |
Colak D, Kaya N, Al-Zahrani J, Al Bakheet A, Muiya P, Andres E, Quackenbush J, Dzimiri N. Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy. Genomics. 94: 20-31. PMID 19332114 DOI: 10.1016/J.Ygeno.2009.03.003 |
0.381 |
|
| 2009 |
Fedorov VB, Goropashnaya AV, Tøien O, Stewart NC, Gracey AY, Chang C, Qin S, Pertea G, Quackenbush J, Showe LC, Showe MK, Boyer BB, Barnes BM. Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). Physiological Genomics. 37: 108-18. PMID 19240299 DOI: 10.1152/Physiolgenomics.90398.2008 |
0.349 |
|
| 2009 |
Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics. 25: 701-702. DOI: 10.1093/Bioinformatics/Btp038 |
0.36 |
|
| 2008 |
Kahvejian A, Quackenbush J, Thompson JF. What would you do if you could sequence everything? Nature Biotechnology. 26: 1125-33. PMID 18846086 DOI: 10.1038/Nbt1494 |
0.329 |
|
| 2008 |
Djebbari A, Quackenbush J. Seeded Bayesian Networks: Constructing genetic networks from microarray data Bmc Systems Biology. 2: 57-57. PMID 18601736 DOI: 10.1186/1752-0509-2-57 |
0.426 |
|
| 2008 |
Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, et al. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. Bmc Genomics. 9: 285. PMID 18549499 DOI: 10.1186/1471-2164-9-285 |
0.371 |
|
| 2008 |
Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J. Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics. 91: 508-11. PMID 18434084 DOI: 10.1016/J.Ygeno.2008.03.002 |
0.348 |
|
| 2007 |
Chan AP, Rabinowicz PD, Quackenbush J, Buell CR, Town CD. Plant database resources at The Institute for Genomic Research. Methods in Molecular Biology (Clifton, N.J.). 406: 113-36. PMID 18287690 DOI: 10.1007/978-1-59745-535-0_5 |
0.346 |
|
| 2007 |
Raj JU, Aliferis C, Caprioli RM, Cowley AW, Davies PF, Duncan MW, Erle DJ, Erzurum SC, Finn PW, Ischiropoulos H, Kaminski N, Kleeberger SR, Leikauf GD, Loyd JE, Martin TR, ... ... Quackenbush J, et al. Genomics and proteomics of lung disease: conference summary. American Journal of Physiology. Lung Cellular and Molecular Physiology. 293: L45-51. PMID 17468134 DOI: 10.1152/Ajplung.00139.2007 |
0.336 |
|
| 2007 |
Danley PD, Mullen SP, Liu F, Nene V, Quackenbush J, Shaw KL. A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution. Bmc Genomics. 8: 109. PMID 17459168 DOI: 10.1186/1471-2164-8-109 |
0.397 |
|
| 2007 |
Quackenbush J. Extracting biology from high-dimensional biological data. The Journal of Experimental Biology. 210: 1507-1517. PMID 17449816 DOI: 10.1242/Jeb.004432 |
0.356 |
|
| 2006 |
Mar JC, Rubio R, Quackenbush J. Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples Genome Biology. 7: 1-12. PMID 17169148 DOI: 10.1186/Gb-2006-7-12-R119 |
0.365 |
|
| 2006 |
Maher EA, Brennan C, Wen PY, Durso L, Ligon KL, Richardson A, Khatry D, Feng B, Sinha R, Louis DN, Quackenbush J, Black PM, Chin L, DePinho RA. Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities. Cancer Research. 66: 11502-13. PMID 17114236 DOI: 10.1158/0008-5472.Can-06-2072 |
0.353 |
|
| 2006 |
Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite. Methods in Enzymology. 411: 134-93. PMID 16939790 DOI: 10.1016/S0076-6879(06)11009-5 |
0.326 |
|
| 2006 |
Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, ... ... Quackenbush J, et al. Uneven chromosome contraction and expansion in the maize genome. Genome Research. 16: 1241-51. PMID 16902087 DOI: 10.1101/Gr.5338906 |
0.326 |
|
| 2006 |
Quackenbush J. From 'omes to biology. Animal Genetics. 37: 48-56. PMID 16887002 DOI: 10.1111/J.1365-2052.2006.01476.X |
0.331 |
|
| 2006 |
Quackenbush J. Microarray analysis and tumor classification. The New England Journal of Medicine. 354: 2463-2472. PMID 16760446 DOI: 10.1056/Nejmra042342 |
0.387 |
|
| 2006 |
Quackenbush J. Standardizing the standards. Molecular Systems Biology. 2. PMID 16738556 DOI: 10.1038/Msb4100052 |
0.33 |
|
| 2006 |
Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, ... ... Quackenbush J, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. Plos Genetics. 2: e62. PMID 16683036 DOI: 10.1371/Journal.Pgen.0020062 |
0.357 |
|
| 2006 |
Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD. The TIGR Maize Database Nucleic Acids Research.. 34: D771-776. PMID 16381977 DOI: 10.1093/Nar/Gkj072 |
0.336 |
|
| 2005 |
Hackl H, Burkard TR, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, Trajanoski Z. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biology. 6: R108. PMID 16420668 DOI: 10.1186/Gb-2005-6-13-R108 |
0.416 |
|
| 2005 |
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, ... ... Quackenbush J, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014 |
0.333 |
|
| 2005 |
Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JM. Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Molecular and Biochemical Parasitology. 144: 1-9. PMID 16085323 DOI: 10.1016/J.Molbiopara.2005.05.016 |
0.372 |
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| 2005 |
Quackenbush J. Extracting meaning from functional genomics experiments. Toxicology and Applied Pharmacology. 207: 195-199. PMID 16002114 DOI: 10.1016/J.Taap.2005.04.029 |
0.411 |
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| 2005 |
Kwong KY, Bloom GC, Yang I, Boulware D, Coppola D, Haseman J, Chen E, McGrath A, Makusky AJ, Taylor J, Steiner S, Zhou J, Yeatman TJ, Quackenbush J. Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics. 86: 142-58. PMID 15951154 DOI: 10.1016/J.Ygeno.2005.03.012 |
0.387 |
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| 2005 |
Djebbari A, Karamycheva S, Howe E, Quackenbush J. MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms Bioinformatics. 21: 3324-3326. PMID 15919728 DOI: 10.1093/Bioinformatics/Bti503 |
0.373 |
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| 2005 |
Margolin AA, Greshock J, Naylor TL, Mosse Y, Maris JM, Bignell G, Saeed AI, Quackenbush J, Weber BL. CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics (Oxford, England). 21: 3308-11. PMID 15905276 DOI: 10.1093/Bioinformatics/Bti500 |
0.349 |
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| 2005 |
Guerrero FD, Miller RJ, Rousseau M-, Sunkara S, Quackenbush J, Lee Y, Nene V. BmiGI: a database of cDNAs expressed in Boophilus microplus, the tropical/southern cattle tick. Insect Biochemistry and Molecular Biology. 35: 585-595. PMID 15857764 DOI: 10.1016/J.Ibmb.2005.01.020 |
0.339 |
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| 2005 |
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, ... ... Quackenbush J, et al. Multiple-laboratory comparison of microarray platforms. Nature Methods. 2: 345-50. PMID 15846361 DOI: 10.1038/Nmeth756 |
0.355 |
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| 2005 |
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J. Independence and reproducibility across microarray platforms. Nature Methods. 2: 337-44. PMID 15846360 DOI: 10.1038/Nmeth757 |
0.402 |
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| 2005 |
Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiology. 137: 1115-29. PMID 15734912 DOI: 10.1104/Pp.104.055475 |
0.368 |
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| 2005 |
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JGN, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, ... ... Quackenbush J, et al. Erratum: Corrigendum: Multiple-laboratory comparison of microarray platforms Nature Methods. 2: 477-477. DOI: 10.1038/Nmeth0605-477B |
0.301 |
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| 2004 |
Kim HS, Yu Y, Snesrud EC, Moy LP, Linford LD, Haas BJ, Nierman WC, Quackenbush J. Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome. Plant Journal. 41: 212-220. PMID 15634198 DOI: 10.1111/J.1365-313X.2004.02295.X |
0.377 |
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| 2004 |
Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan AP, Cheung F, Quackenbush J. The TIGR gene indices : clustering and assembling EST and known genes and integration with eukaryotic genomes Nucleic Acids Research. 33: 71-74. PMID 15608288 DOI: 10.1093/Nar/Gki064 |
0.412 |
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| 2004 |
Nene V, Lee D, Kang’a S, Skilton R, Shah T, Villiers Ed, Mwaura S, Taylor D, Quackenbush J, Bishop R. Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva Insect Biochemistry and Molecular Biology. 34: 1117-1128. PMID 15475305 DOI: 10.1016/J.Ibmb.2004.07.002 |
0.383 |
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| 2004 |
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Standards for microarray data: an open letter. Environmental Health Perspectives. 112: A666-7. PMID 15345376 DOI: 10.1289/Ehp.112-1277123 |
0.358 |
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| 2004 |
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Submission of microarray data to public repositories. Plos Biology. 2: E317. PMID 15340489 DOI: 10.1371/Journal.Pbio.0020317 |
0.322 |
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| 2004 |
Cook DN, Wang S, Wang Y, Howles GP, Whitehead GS, Berman KG, Church TD, Frank BC, Gaspard RM, Yu Y, Quackenbush J, Schwartz DA. Genetic regulation of endotoxin-induced airway disease. Genomics. 83: 961-969. PMID 15177550 DOI: 10.1016/J.Ygeno.2003.12.008 |
0.345 |
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| 2004 |
Cronin M, Ghosh K, Sistare F, Quackenbush J, Vilker V, O'Connell C. Universal RNA reference materials for gene expression. Clinical Chemistry. 50: 1464-71. PMID 15155546 DOI: 10.1373/Clinchem.2004.035675 |
0.331 |
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| 2004 |
Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JG. Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biology. 5: R34. PMID 15128448 DOI: 10.1186/Gb-2004-5-5-R34 |
0.366 |
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| 2004 |
Larkin JE, Frank BC, Gaspard RM, Duka I, Gavras H, Quackenbush J. Cardiac transcriptional response to acute and chronic angiotensin II treatments. Physiological Genomics. 18: 152-66. PMID 15126644 DOI: 10.1152/Physiolgenomics.00057.2004 |
0.302 |
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| 2004 |
Sharov V, Kwong KY, Frank B, Chen E, Hasseman J, Gaspard R, Yu Y, Yang I, Quackenbush J. The limits of log-ratios. Bmc Biotechnology. 4: 3. PMID 15113428 DOI: 10.1186/1472-6750-4-3 |
0.343 |
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| 2004 |
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, ... ... Quackenbush J, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. Plos Biology. 2: e162. PMID 15103394 DOI: 10.1371/Journal.Pbio.0020162 |
0.389 |
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| 2004 |
Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. Multi-platform, multi-site, microarray-based human tumor classification. The American Journal of Pathology. 164: 9-16. PMID 14695313 DOI: 10.1016/S0002-9440(10)63090-8 |
0.309 |
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| 2004 |
Stoeckert CJ, Quackenbush J, Brazma A, Ball CA. Minimum information about a functional genomics experiment: The state of microarray standards and their extension to other technologies Drug Discovery Today: Targets. 3: 159-164. DOI: 10.1016/S1741-8372(04)02435-1 |
0.349 |
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| 2003 |
Lee Y, Quackenbush J. UNIT 1.6 Using the TIGR Gene Index Databases for Biological Discovery Current Protocols in Human Genetics. Unit 1.6. PMID 18428690 DOI: 10.1002/0471250953.Bi0106S03 |
0.376 |
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| 2003 |
Rexroad CE, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenetic and Genome Research. 102: 347-54. PMID 14970727 DOI: 10.1159/000075773 |
0.346 |
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| 2003 |
Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ. Osteopontin identified as colon cancer tumor progression marker. Comptes Rendus Biologies. 326: 1041-3. PMID 14744111 DOI: 10.1016/J.Crvi.2003.09.007 |
0.322 |
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| 2003 |
Klapa MI, Quackenbush J. The quest for the mechanisms of life. Biotechnology and Bioengineering. 84: 739-42. PMID 14708113 DOI: 10.1002/Bit.10858 |
0.404 |
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| 2003 |
Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, ... ... Quackenbush J, et al. Enrichment of gene-coding sequences in maize by genome filtration. Science (New York, N.Y.). 302: 2118-20. PMID 14684821 DOI: 10.1126/Science.1090047 |
0.333 |
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| 2003 |
Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA, Dias Neto E, Grivet M, Gruber A, Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, ... ... Quackenbush J, et al. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proceedings of the National Academy of Sciences of the United States of America. 100: 13418-23. PMID 14593198 DOI: 10.1073/Pnas.1233632100 |
0.331 |
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| 2003 |
Quackenbush J. Microarrays--Guilt by Association Science. 302: 240-241. PMID 14551426 DOI: 10.1126/Science.1090887 |
0.405 |
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| 2003 |
Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J. Development and evaluation of an automated annotation pipeline and cDNA annotation system Genome Research. 13: 1542-1551. PMID 12819153 DOI: 10.1101/Gr.992803 |
0.345 |
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| 2003 |
Wells CA, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Research. 13: 1360-5. PMID 12819134 DOI: 10.1101/Gr.1056103 |
0.373 |
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| 2003 |
Merrick JM, Osman A, Tsai J, Quackenbush J, LoVerde PT, Lee NH. The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences. The Journal of Parasitology. 89: 261-9. PMID 12760639 DOI: 10.1645/0022-3395(2003)089[0261:Tsmgig]2.0.Co;2 |
0.387 |
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| 2003 |
Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. Biotechniques. 45-51. PMID 12664684 DOI: 10.2144/Mar03Dudoit |
0.317 |
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| 2003 |
Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ, Quackenbush J, Richardson J, Bult CJ. Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database. Genome Biology. 4: R16. PMID 12620126 DOI: 10.1186/Gb-2003-4-2-R16 |
0.396 |
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| 2003 |
Kim H, Snesrud EC, Haas B, Cheung F, Town CD, Quackenbush J. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Research. 13: 327-340. PMID 12618363 DOI: 10.1101/Gr.552003 |
0.373 |
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| 2003 |
Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, ... Quackenbush J, et al. Comparative analyses of potato expressed sequence tag libraries. Plant Physiology. 131: 419-29. PMID 12586867 DOI: 10.1104/Pp.013581 |
0.346 |
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| 2003 |
Wang HY, Malek RL, Kwitek AE, Greene AS, Luu TV, Behbahani B, Frank B, Quackenbush J, Lee NH. Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biology. 4: R5. PMID 12540297 DOI: 10.1186/Gb-2003-4-1-R5 |
0.354 |
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| 2003 |
Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Research. 31: 229-33. PMID 12519988 DOI: 10.1093/Nar/Gkg059 |
0.324 |
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| 2002 |
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, ... ... Quackenbush J, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 420: 563-73. PMID 12466851 DOI: 10.1038/Nature01266 |
0.33 |
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| 2002 |
Quackenbush J. Microarray data normalization and transformation Nature Genetics. 32: 496-501. PMID 12454644 DOI: 10.1038/Ng1032 |
0.357 |
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| 2002 |
Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biology. 3: research0062. PMID 12429061 DOI: 10.1186/Gb-2002-3-11-Research0062 |
0.38 |
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| 2002 |
Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. Biotechniques. 33: 924-930. PMID 12398202 DOI: 10.2144/02334Mt06 |
0.326 |
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| 2002 |
Nene V, Lee D, Quackenbush J, Skilton R, Mwaura S, Gardner MJ, Bishop R. AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum International Journal For Parasitology. 32: 1447-1456. PMID 12392910 DOI: 10.1016/S0020-7519(02)00159-5 |
0.35 |
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| 2002 |
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, ... ... Quackenbush J, et al. Standards for microarray data. Science (New York, N.Y.). 298: 539. PMID 12387284 DOI: 10.1126/Science.298.5593.539B |
0.321 |
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| 2002 |
Malek RL, Irby RB, Guo QM, Lee K, Wong S, He M, Tsai J, Frank B, Liu ET, Quackenbush J, Jove R, Yeatman TJ, Lee NH. Identification of Src transformation fingerprint in human colon cancer. Oncogene. 21: 7256-65. PMID 12370817 DOI: 10.1038/Sj.Onc.1205900 |
0.385 |
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| 2002 |
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, ... ... Quackenbush J, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/Nature01099 |
0.31 |
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| 2002 |
Fahrenkrug SC, Smith TP, Freking BA, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, Quackenbush J, Keele JW. Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 13: 475-8. PMID 12226715 DOI: 10.1007/S00335-001-2072-4 |
0.382 |
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| 2002 |
Sonstegard TS, Capuco AV, White J, Van Tassell CP, Connor EE, Cho J, Sultana R, Shade L, Wray JE, Wells KD, Quackenbush J. Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 13: 373-9. PMID 12140684 DOI: 10.1007/S00335-001-2145-4 |
0.391 |
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| 2002 |
Andersson T, Unneberg P, Nilsson P, Odeberg J, Quackenbush J, Lundeberg J. Monitoring of representational difference analysis subtraction procedures by global microarrays. Biotechniques. 32: 1348-1358. PMID 12074166 DOI: 10.2144/02326Mt06 |
0.365 |
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| 2002 |
Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ. Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling. Journal of the National Cancer Institute. 94: 513-21. PMID 11929952 DOI: 10.1093/Jnci/94.7.513 |
0.337 |
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| 2002 |
Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J. Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Research. 12: 493-502. PMID 11875039 DOI: 10.1101/Gr.212002 |
0.376 |
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| 2002 |
Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics (Oxford, England). 18: 207-8. PMID 11836235 DOI: 10.1093/Bioinformatics/18.1.207 |
0.348 |
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| 2001 |
Flores-Morales A, Sta Hlberg N, Tollet-Egnell P, Lundeberg J, Malek RL, Quackenbush J, Lee NH, Norstedt G. Microarray Analysis of the in Vivo Effects of Hypophysectomy and Growth Hormone Treatment on Gene Expression in the Rat. Endocrinology. 142: 3163-3176. PMID 28201349 DOI: 10.1210/Endo.142.7.8235 |
0.371 |
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| 2001 |
Tsai J, Sultana R, Lee Y, Pertea GM, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J. RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biology. 2: 1-4. PMID 16173164 DOI: 10.1186/Gb-2001-2-11-Software0002 |
0.413 |
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| 2001 |
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 29: 365-71. PMID 11726920 DOI: 10.1038/Ng1201-365 |
0.379 |
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| 2001 |
Quackenbush J. The power of public access: the human genome project and the scientific process. Nature Genetics. 29: 4-6. PMID 11528377 DOI: 10.1038/Ng0901-4 |
0.301 |
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| 2001 |
Kappe SH, Gardner MJ, Brown SM, Ross J, Matuschewski K, Ribeiro JM, Adams JH, Quackenbush J, Cho J, Carucci DJ, Hoffman SL, Nussenzweig V. Exploring the transcriptome of the malaria sporozoite stage. Proceedings of the National Academy of Sciences of the United States of America. 98: 9895-900. PMID 11493695 DOI: 10.1073/Pnas.171185198 |
0.343 |
|
| 2001 |
Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T. Effects of ischemia on gene expression Journal of Surgical Research. 99: 222-227. PMID 11469890 DOI: 10.1006/Jsre.2001.6195 |
0.378 |
|
| 2001 |
Quackenbush J. Computational Analysis Of Microarray Data Nature Reviews Genetics. 2: 418-427. PMID 11389458 DOI: 10.1038/35076576 |
0.347 |
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| 2001 |
Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, ... ... Quackenbush J, et al. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Research. 11: 626-30. PMID 11282978 DOI: 10.1101/Gr.170101 |
0.347 |
|
| 2001 |
Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR. Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species Plant Physiology. 125: 1166-1174. PMID 11244096 DOI: 10.1104/Pp.125.3.1166 |
0.342 |
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| 2001 |
Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, ... ... Quackenbush J, et al. Functional annotation of a full-length mouse cDNA collection. Nature. 409: 685-90. PMID 11217851 DOI: 10.1038/35055500 |
0.373 |
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| 2001 |
Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Research. 29: 159-64. PMID 11125077 DOI: 10.1093/Nar/29.1.159 |
0.395 |
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| 2001 |
Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques. 29: 548-50, 552-4, 556 . PMID 10997270 DOI: 10.2144/00293Bi01 |
0.354 |
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| 2000 |
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. An optimized protocol for analysis of EST sequences. Nucleic Acids Research. 28: 3657-65. PMID 10982889 DOI: 10.1093/Nar/28.18.3657 |
0.363 |
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| 2000 |
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. Gene index analysis of the human genome estimates approximately 120,000 genes. Nature Genetics. 25: 239-40. PMID 10835646 DOI: 10.1038/76126 |
0.393 |
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| 2000 |
El-Sayed NM, Hegde P, Quackenbush J, Melville SE, Donelson JE. The African trypanosome genome. International Journal For Parasitology. 30: 329-45. PMID 10731558 DOI: 10.1016/S0020-7519(00)00015-1 |
0.335 |
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| 2000 |
Quackenbush J, Liang F, Holt I, Pertea G, Upton J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Research. 28: 141-5. PMID 10592205 DOI: 10.1093/Nar/28.1.141 |
0.4 |
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| 1999 |
Malek RL, Guo Q, Ruffy M, Liu ET, Holt I, Chandra I, Liang F, Upton J, Quackenbush J, Jove R, Yeatman TJ, Lee NH. Use of the Rat Gene Index to examine gene expression patterns from Src-transformed rat fibroblasts that exhibit broad differences in metastatic potential Nature Genetics. 23: 61-61. DOI: 10.1038/14362 |
0.308 |
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| 1999 |
Hegde P, Earle-Hughes J, Abernathy K, Dharap S, Saeed AI, Sharov V, Lee NH, Yeatman T, Quackenbush J. Identification of genes involved in colon cancer metastasis using cDNA microarrays Nature Genetics. 23: 50-50. DOI: 10.1038/14322 |
0.368 |
|
| 1997 |
Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, ... ... Quackenbush J, et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390: 580-6. PMID 9403685 DOI: 10.1038/37551 |
0.374 |
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| 1997 |
Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, ... Quackenbush J, et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390: 364-70. PMID 9389475 DOI: 10.1038/37052 |
0.337 |
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| 1996 |
Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, ... ... Quackenbush J, et al. A gene map of the human genome. Science (New York, N.Y.). 274: 540-6. PMID 8849440 DOI: 10.1126/Science.274.5287.540 |
0.352 |
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