John Quackenbush

73 papers A* 7B 3C 1Misc 3Journal 55Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	B	`conf`	FACT: Gated Fusion-Augmented Causal Mask Transformer for Pseudotime Analysis. IEEE Big Data Zhen Lu, Chengjie Zheng, Iris Shen, John Quackenbush, Viola Fanfani, Wei Ding, Ping Chen
2024	B	`conf`	BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. RECOMB 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
2024	J	`jnl`	Higher-order correction of persistent batch effects in correlation networks. Bioinform. Soel Micheletti, Daniel Schlauch, John Quackenbush, Marouen Ben Guebila
2024	J	`jnl`	Not all tickets are equal and we know it: Guiding pruning with domain-specific knowledge. CoRR Intekhab Hossain, Jonas Fischer, Rebekka Burkholz, John Quackenbush
2024	A*	`conf`	Pruning neural network models for gene regulatory dynamics using data and domain knowledge. NeurIPS Intekhab Hossain, Jonas Fischer, Rebekka Burkholz, John Quackenbush
2024	B	`conf`	SpaCeNet: Spatial Cellular Networks from Omics Data. RECOMB 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
2022	J	`jnl`	GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 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
2022	J	`jnl`	Looking back at the first twenty years of genomics. Quant. Biol. John Quackenbush
2021	A*	`conf`	Cascade Size Distributions: Why They Matter and How to Compute Them Efficiently. AAAI Rebekka Burkholz, John Quackenbush
2021	A*	`conf`	Gene Regulatory Network Inference as Relaxed Graph Matching. AAAI Deborah A. Weighill, Marouen Ben Guebila, Camila Miranda Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig, Rebekka Burkholz
2021	A*	`conf`	Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. NeurIPS Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka
2021	J	`jnl`	Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. CoRR Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka
2020	A*	`conf`	A Novel Deep Learning Model by Stacking Conditional Restricted Boltzmann Machine and Deep Neural Network. KDD Tianyu Kang, Ping Chen, John Quackenbush, Wei Ding
2020	A*	`conf`	Catalysis Clustering with GAN by Incorporating Domain Knowledge. KDD Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
2020	J	`jnl`	Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE Access Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
2020	J	`jnl`	PUMA: PANDA Using MicroRNA Associations. Bioinform. Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass
2019	J	`jnl`	Cascade Size Distributions and Why They Matter. CoRR Rebekka Burkholz, John Quackenbush
2019	J	`jnl`	Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinform. Sheila M. Gaynor, Ryan Sun, Xihong Lin, John Quackenbush
2019	Misc	`conf`	Session introduction. PSB Lana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush
2018	A*	`conf`	Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping. ICDM Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding
2017	J	`jnl`	Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinform. 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
2017	J	`jnl`	Estimating gene regulatory networks with pandaR. Bioinform. Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush
2017	J	`jnl`	Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer. CoRR Jipeng Qiang, Wei Ding, John Quackenbush, Ping Chen
2017	J	`jnl`	Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinform. Joseph N. Paulson, Cho-Yi Chen, Camila Miranda Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
2016	J	`jnl`	BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinform. Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson
2016	J	`jnl`	Bipartite Community Structure of eQTLs. PLoS Comput. Biol. John Platig, Peter J. Castaldi, Dawn L. DeMeo, John Quackenbush
2016	J	`jnl`	PyPanda: a Python package for gene regulatory network reconstruction. Bioinform. David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer
2016	J	`jnl`	Safikhani Nat. 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
2015	J	`jnl`	A network model for angiogenesis in ovarian cancer. BMC Bioinform. Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan
2015	—	`conf`	High performance computing of gene regulatory networks using a message-passing model. HPEC Kimberly Glass, John Quackenbush, Jeremy Kepner
2015	J	`jnl`	Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Syst. Biol. Megha Padi, John Quackenbush
2014	J	`jnl`	Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. BMC Syst. Biol. 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
2014	J	`jnl`	Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst. Biol. Kimberly Glass, John Quackenbush, Edwin K. Silverman, Bartolome Celli, Stephen I. Rennard, Guo-Cheng Yuan, Dawn L. DeMeo
2013	J	`jnl`	Inconsistency in large pharmacogenomic studies. Nat. Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush
2013	J	`jnl`	RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinform. Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains
2013	J	`jnl`	Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains
2013	J	`jnl`	Significance Analysis of Prognostic Signatures. PLoS Comput. Biol. 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
2012	J	`jnl`	GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 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
2012	J	`jnl`	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush
2012	J	`jnl`	Viral Perturbations of Host Networks Reflect Disease Etiology. PLoS Comput. Biol. 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
2012	J	`jnl`	iBBiG: iterative binary bi-clustering of gene sets. Bioinform. Daniel Gusenleitner, Eleanor Howe, Stefan Bentink, John Quackenbush, Aedín C. Culhane
2012	J	`jnl`	nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinform. 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
2011	J	`jnl`	Defining an informativeness metric for clustering gene expression data. Bioinform. Jessica Cara Mar, Christine A. Wells, John Quackenbush
2011	J	`jnl`	Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinform. Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson
2011	J	`jnl`	GCOD - GeneChip Oncology Database. BMC Bioinform. Fenglong Liu, Joseph White, Corina Antonescu, John Quackenbush
2011	J	`jnl`	Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush
2011	J	`jnl`	RNA-Seq analysis in MeV. Bioinform. Eleanor Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush
2010	J	`jnl`	GeneSigDB - a curated database of gene expression signatures. Nucleic Acids Res. 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
2009	—	`ch.`	AI Methods for Analyzing Microarray Data. Encyclopedia of Artificial Intelligence Amira Djebbari, Aedín C. Culhane, Alice Armstrong, John Quackenbush
2009	J	`jnl`	An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinform. Martin J. Aryee, José A. Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush
2009	J	`jnl`	Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinform. Jessica Cara Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush
2009	J	`jnl`	Decomposition of Gene Expression State Space Trajectories. PLoS Comput. Biol. Jessica Cara Mar, John Quackenbush
2009	J	`jnl`	Editorial. Bioinform. Alex Bateman, John Quackenbush
2009	J	`jnl`	Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
2009	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Michael F. Ochs, John Quackenbush, Ramana V. Davuluri, Habtom W. Ressom
2008	J	`jnl`	Seeded Bayesian Networks: Constructing genetic networks from microarray data. BMC Syst. Biol. Amira Djebbari, John Quackenbush
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Michael F. Ochs, John Quackenbush, Ramana V. Davuluri
2007	J	`jnl`	Microarray blob-defect removal improves array analysis. Bioinform. Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu
2007	C	`conf`	Stochasticity and Networks in Genomic Data. BIBE John Quackenbush
2006	J	`jnl`	A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 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
2006	J	`jnl`	It is time to end the patenting of software. Bioinform. John Quackenbush, Steven Salzberg
2006	J	`jnl`	The TIGR Maize Database. Nucleic Acids Res. 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
2005	J	`jnl`	CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinform. Adam A. Margolin, Joel Greshock, Tara L. Naylor, Yael Mosse, John M. Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, Barbara L. Weber
2005	J	`jnl`	MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinform. Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
2005	J	`jnl`	The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush
2003	—	`conf`	Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track. TREC Richard Tong, John Quackenbush, Mark Snuffin
2003	—	`book`	Microarray gene expression data analysis - a beginner's guide. Helen C. Causton, John Quackenbush, Alvis Brazma
2003	J	`jnl`	TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinform. Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush
2003	J	`jnl`	The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard B. Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell
2002	J	`jnl`	An open letter to the scientific journals. Bioinform. 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
2002	J	`jnl`	Genesis: cluster analysis of microarray data. Bioinform. Alexander Sturn, John Quackenbush, Zlatko Trajanoski
2001	J	`jnl`	The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Joseph White
2000	J	`jnl`	The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, Jonathan Upton