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John Quackenbush
Person information
- affiliation: Dana-Farber Cancer Institute, Boston, USA
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2020 – today
- 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 - [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) - 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) - 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 - [i3]Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka:
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. CoRR abs/2107.02911 (2021) - 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) - [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
2010 – 2019
- 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) - [c7]Lana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush:
Session introduction. PSB 2019: 332-337 - [i2]Rebekka Burkholz, John Quackenbush:
Cascade Size Distributions and Why They Matter. CoRR abs/1909.05416 (2019) - 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 - 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) - [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) - 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) - [c5]Kimberly Glass
, John Quackenbush, Jeremy Kepner:
High performance computing of gene regulatory networks using a message-passing model. HPEC 2015: 1-6 - 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)
2000 – 2009
- 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) - [c4]Michael F. Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom:
Session Introduction. Pacific Symposium on Biocomputing 2009: 353-355 - [r1]Amira Djebbari, Aedín C. Culhane, Alice Armstrong, John Quackenbush:
AI Methods for Analyzing Microarray Data. Encyclopedia of Artificial Intelligence 2009: 65-70 - 2008
- [j14]Amira Djebbari, John Quackenbush
:
Seeded Bayesian Networks: Constructing genetic networks from microarray data. BMC Syst. Biol. 2: 57 (2008) - [c3]Michael F. Ochs, John Quackenbush, Ramana Davuluri:
Session Introduction. Pacific Symposium on Biocomputing 2008: 137-140 - 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) - [c2]John Quackenbush:
Stochasticity and Networks in Genomic Data. BIBE 2007: 2 - 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
- [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 - [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) - [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 - 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)
Coauthor Index
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