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ORCIDJohn Quackenbush
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- affiliation: Dana-Farber Cancer Institute, Boston, USA
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Books and Theses
- 2003
[b1]Helen C. Causton, John Quackenbush, Alvis Brazma:
Microarray gene expression data analysis - a beginner's guide. Blackwell 2003, ISBN 978-1-40510-682-5, pp. I-VIII, 1-160
Journal Articles
- 2022
- [j51]Marouen Ben Guebila
, Camila Miranda Lopes-Ramos, Deborah A. Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush:
GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 50(D1): 610-621 (2022) - [j50]John Quackenbush:
Looking back at the first twenty years of genomics. Quant. Biol. 10(1): 6 (2022) - 2020
- [j49]Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen:
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE Access 8: 67775-67789 (2020) - [j48]Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass:
PUMA: PANDA Using MicroRNA Associations. Bioinform. 36(18): 4765-4773 (2020) - 2019
- [j47]Sheila M. Gaynor, Ryan Sun, Xihong Lin, John Quackenbush:
Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinform. 35(22): 4568-4576 (2019) - 2017
- [j46]Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush:
Estimating gene regulatory networks with pandaR. Bioinform. 33(14): 2232-2234 (2017) - [j45]Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela:
Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinform. 18(1): 304 (2017) - [j44]Joseph N. Paulson, Cho-Yi Chen, Camila Miranda Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush:
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinform. 18(1): 437:1-437:10 (2017) - 2016
- [j43]David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer:
PyPanda: a Python package for gene regulatory network reconstruction. Bioinform. 32(21): 3363-3365 (2016) - [j42]Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson:
BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinform. 32(24): 3836-3838 (2016) - [j41]Zhaleh Safikhani, Nehme Hachem, Petr Smirnov, Mark Freeman, Anna Goldenberg, Nicolai J. Birkbak, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Safikhani et al. reply. Nat. 540(7631): E2-E4 (2016) - [j40]John Platig, Peter J. Castaldi, Dawn L. DeMeo, John Quackenbush:
Bipartite Community Structure of eQTLs. PLoS Comput. Biol. 12(9) (2016) - 2015
- [j39]Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan:
A network model for angiogenesis in ovarian cancer. BMC Bioinform. 16: 115:1-115:17 (2015) - [j38]Megha Padi, John Quackenbush:
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Syst. Biol. 9: 80 (2015) - 2014
- [j37]Jen-hwa Chu, Craig P. Hersh, Peter J. Castaldi, Michael H. Cho, Benjamin A. Raby, Nan M. Laird, Russell Bowler, Stephen I. Rennard, Joseph Loscalzo, John Quackenbush, Edwin K. Silverman:
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. BMC Syst. Biol. 8: 78 (2014) - [j36]Kimberly Glass, John Quackenbush, Edwin K. Silverman, Bartolome Celli, Stephen I. Rennard, Guo-Cheng Yuan, Dawn L. DeMeo:
Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst. Biol. 8: 118 (2014) - 2013
- [j35]Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains:
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinform. 29(5): 666-668 (2013) - [j34]Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. 20(4): 597-602 (2013) - [j33]Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush:
Inconsistency in large pharmacogenomic studies. Nat. 504(7480): 389-393 (2013) - [j32]Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains:
Significance Analysis of Prognostic Signatures. PLoS Comput. Biol. 9(1) (2013) - 2012
- [j31]Thomas W. Chittenden, Eleanor Howe, Jennifer M. Taylor, Jessica Cara Mar, Martin J. Aryee, Harold Gómez, Razvan Sultana, John C. Braisted, Sarita J. Nair, John Quackenbush, Chris Holmes:
nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinform. 28(5): 726-728 (2012) - [j30]Daniel Gusenleitner, Eleanor Howe, Stefan Bentink, John Quackenbush, Aedín C. Culhane:
iBBiG: iterative binary bi-clustering of gene sets. Bioinform. 28(19): 2484-2492 (2012) - [j29]Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush:
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. 40(Database-Issue): 866-875 (2012) - [j28]Aedín C. Culhane, Markus S. Schröder, Razvan Sultana, Shaita C. Picard, Enzo N. Martinelli, Caroline Kelly, Benjamin Haibe-Kains, Misha Kapushesky, Anne-Alyssa St Pierre, William Flahive, Kermshlise C. Picard, Daniel Gusenleitner, Gerald Papenhausen, Niall O'Connor, Mick Correll, John Quackenbush:
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 40(Database-Issue): 1060-1066 (2012) - [j27]Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica Cara Mar, Michael A. Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod A. Marto, Nicholas A. Christakis, Elliott Kieff, Frederick P. Roth, Jennifer Roecklein-Canfield, James A. DeCaprio, Michael E. Cusick, John Quackenbush, David E. Hill, Karl Münger, Marc Vidal, Albert-László Barabási:
Viral Perturbations of Host Networks Reflect Disease Etiology. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j26]Jessica Cara Mar, Christine A. Wells, John Quackenbush:
Defining an informativeness metric for clustering gene expression data. Bioinform. 27(8): 1094-1100 (2011) - [j25]Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson:
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinform. 27(19): 2648-2654 (2011) - [j24]Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains:
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinform. 27(22): 3206-3208 (2011) - [j23]Eleanor Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush:
RNA-Seq analysis in MeV. Bioinform. 27(22): 3209-3210 (2011) - [j22]Fenglong Liu, Joseph White, Corina Antonescu, John Quackenbush:
GCOD - GeneChip Oncology Database. BMC Bioinform. 12: 46 (2011) - [j21]Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush:
Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. 12: 458 (2011) - 2010
- [j20]Aedín C. Culhane, Thomas Schwarzl, Razvan Sultana, Kermshlise C. Picard, Shaita C. Picard, Tim H. Lu, Katherine R. Franklin, Simon J. French, Gerald Papenhausen, Mick Correll, John Quackenbush:
GeneSigDB - a curated database of gene expression signatures. Nucleic Acids Res. 38(Database-Issue): 716-725 (2010) - 2009
- [j19]Alex Bateman, John Quackenbush:
Editorial. Bioinform. 25(4): 429 (2009) - [j18]David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo:
Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. 25(6): 701-702 (2009) - [j17]Martin J. Aryee, José A. Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush:
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinform. 10: 409 (2009) - [j16]Jessica Cara Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush:
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinform. 10 (2009) - [j15]Jessica Cara Mar, John Quackenbush:
Decomposition of Gene Expression State Space Trajectories. PLoS Comput. Biol. 5(12) (2009) - 2008
- [j14]Amira Djebbari, John Quackenbush:
Seeded Bayesian Networks: Constructing genetic networks from microarray data. BMC Syst. Biol. 2: 57 (2008) - 2007
- [j13]Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu:
Microarray blob-defect removal improves array analysis. Bioinform. 23(8): 966-971 (2007) - 2006
- [j12]John Quackenbush, Steven Salzberg:
It is time to end the patenting of software. Bioinform. 22(12): 1416-1417 (2006) - [j11]Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma:
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7: 489 (2006) - [j10]Agnes P. Chan, Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C. Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, Pablo D. Rabinowicz:
The TIGR Maize Database. Nucleic Acids Res. 34(Database-Issue): 771-776 (2006) - 2005
- [j9]Adam A. Margolin, Joel Greshock, Tara L. Naylor, Yael Mosse, John M. Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, Barbara L. Weber:
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinform. 21(15): 3308-3311 (2005) - [j8]Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush:
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinform. 21(15): 3324-3326 (2005) - [j7]Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush:
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33(Database-Issue): 71-74 (2005) - 2003
- [j6]Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush:
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinform. 19(5): 651-652 (2003) - [j5]Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard B. Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell:
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. 31(1): 229-233 (2003) - 2002
- [j4]Alexander Sturn, John Quackenbush, Zlatko Trajanoski:
Genesis: cluster analysis of microarray data. Bioinform. 18(1): 207-208 (2002) - [j3]Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank C. P. Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald C. Taylor, Alvis Brazma, John Quackenbush:
An open letter to the scientific journals. Bioinform. 18(11): 1409 (2002) - 2001
- [j2]John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Joseph White:
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29(1): 159-164 (2001) - 2000
- [j1]John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, Jonathan Upton:
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28(1): 141-145 (2000)
Conference and Workshop Papers
- 2024
- [c14]Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Kimberly Glass, Dawn L. DeMeo, Camila Miranda Lopes-Ramos, John Quackenbush:
BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. RECOMB 2024: 328-331 - [c13]Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger:
SpaCeNet: Spatial Cellular Networks from Omics Data. RECOMB 2024: 344-347 - 2021
- [c12]Rebekka Burkholz, John Quackenbush:
Cascade Size Distributions: Why They Matter and How to Compute Them Efficiently. AAAI 2021: 6840-6849 - [c11]Deborah A. Weighill, Marouen Ben Guebila, Camila Miranda Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig, Rebekka Burkholz:
Gene Regulatory Network Inference as Relaxed Graph Matching. AAAI 2021: 10263-10272 - [c10]Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka:
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. NeurIPS 2021: 14580-14592 - 2020
- [c9]Tianyu Kang, Ping Chen, John Quackenbush, Wei Ding:
A Novel Deep Learning Model by Stacking Conditional Restricted Boltzmann Machine and Deep Neural Network. KDD 2020: 1316-1324 - [c8]Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen:
Catalysis Clustering with GAN by Incorporating Domain Knowledge. KDD 2020: 1344-1352 - 2019
- [c7]Lana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush:
Session introduction. PSB 2019: 332-337 - 2018
- [c6]Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding:
Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping. ICDM 2018: 1079-1084 - 2015
- [c5]Kimberly Glass, John Quackenbush, Jeremy Kepner:
High performance computing of gene regulatory networks using a message-passing model. HPEC 2015: 1-6 - 2009
- [c4]Michael F. Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom:
Session Introduction. Pacific Symposium on Biocomputing 2009: 353-355 - 2008
- [c3]Michael F. Ochs, John Quackenbush, Ramana Davuluri:
Session Introduction. Pacific Symposium on Biocomputing 2008: 137-140 - 2007
- [c2]John Quackenbush:
Stochasticity and Networks in Genomic Data. BIBE 2007: 2 - 2003
- [c1]Richard Tong, John Quackenbush, Mark Snuffin:
Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track. TREC 2003: 547-551
Reference Works
- 2009
- [r1]Amira Djebbari, Aedín C. Culhane, Alice Armstrong, John Quackenbush:
AI Methods for Analyzing Microarray Data. Encyclopedia of Artificial Intelligence 2009: 65-70
Informal and Other Publications
- 2024
- [i4]Intekhab Hossain, Jonas Fischer, Rebekka Burkholz, John Quackenbush:
Not all tickets are equal and we know it: Guiding pruning with domain-specific knowledge. CoRR abs/2403.04805 (2024) - 2021
- [i3]Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka:
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. CoRR abs/2107.02911 (2021) - 2019
- [i2]Rebekka Burkholz, John Quackenbush:
Cascade Size Distributions and Why They Matter. CoRR abs/1909.05416 (2019) - 2017
- [i1]Jipeng Qiang, Wei Ding, John Quackenbush, Ping Chen:
Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer. CoRR abs/1703.01900 (2017)
Coauthor Index
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