Paul Pavlidis - RankMe

43 papers B 1Misc 2Journal 38Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Using semantic search to find publicly available gene-expression datasets. Bioinform. Grace S. Brown, James Wengler, Aaron Joyce S. Fabelico, Abigail Muir, Anna Tubbs, Amanda Warren, Alexandra N. Millett, Xinrui Xiang Yu, Paul Pavlidis, Sanja Rogic, Stephen R. Piccolo
2025	J	`jnl`	Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics. PLoS Comput. Biol. Alexander M. Morin, Eric Ching-Pan Chu, Paul Pavlidis
2023	J	`jnl`	The Canadian Open Neuroscience Platform - An open science framework for the neuroscience community. PLoS Comput. Biol. Rachel J. Harding, Patrick Bermudez, Alexander Bernier, Michael J. S. Beauvais, Pierre Bellec, Sean L. Hill, Agah Karakuzu, Bartha M. Knoppers, Paul Pavlidis, Jean-Baptiste Poline, Jane Roskams, Nikola Stikov, Jessica Stone, Stephen C. Strother, CONP Consortium, Alan C. Evans
2021	J	`jnl`	Curation of over 10 000 transcriptomic studies to enable data reuse. Database J. Biol. Databases Curation Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, Burak Ogan Mancarci, Jordan Sicherman, Matthew Jacobson, Justin Leong, Patrick Tan, Paul Pavlidis
2021	J	`jnl`	Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PLoS Comput. Biol. Eric Ching-Pan Chu, Alexander M. Morin, Tak Hou Calvin Chang, Tue Nguyen, Yi-Cheng Tsai, Aman Sharma, Chao Chun Liu, Paul Pavlidis
2019	J	`jnl`	Differential coexpression in human tissues and the confounding effect of mean expression levels. Bioinform. Marjan Farahbod, Paul Pavlidis
2019	J	`jnl`	Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes. PLoS Comput. Biol. Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
2017	J	`jnl`	Can we predict protein from mRNA levels? Nat. Nikolaus Fortelny, Christopher M. Overall, Paul Pavlidis, Gabriela V. Cohen Freue
2017	J	`jnl`	EGAD: ultra-fast functional analysis of gene networks. Bioinform. Sara Ballouz, Melanie Weber, Paul Pavlidis, Jesse A. Gillis
2017	J	`jnl`	Transcriptomic correlates of neuron electrophysiological diversity. PLoS Comput. Biol. Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis
2016	—	`conf`	Linking Wikidata to the Rest of the Semantic Web. SWAT4LS Andra Waagmeester, Egon L. Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E. Putman, Julia Turner, Lynn M. Schriml, Paul Pavlidis, Andrew I. Su, Benjamin M. Good
2016	J	`jnl`	Wikidata as a semantic framework for the Gene Wiki initiative. Database J. Biol. Databases Curation Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim E. Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su
2015	J	`jnl`	Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Res. Nikolaus Fortelny, Sharon Yang, Paul Pavlidis, Philipp F. Lange, Christopher M. Overall
2015	J	`jnl`	Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application. Frontiers Neuroinformatics Leon French, Po Liu, Olivia Marais, Tianna Koreman, Lucia Tseng, Artemis Lai, Paul Pavlidis
2013	J	`jnl`	Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinform. Jesse A. Gillis, Paul Pavlidis
2013	J	`jnl`	Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinform. Jesse A. Gillis, Paul Pavlidis
2013	J	`jnl`	Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355-1363]. NeuroImage Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
2012	J	`jnl`	"Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. PLoS Comput. Biol. Jesse A. Gillis, Paul Pavlidis
2012	J	`jnl`	Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. Bioinform. Leon French, Suzanne Lane, Lydia Xu, Celia Siu, Cathy Kwok, Yiqi Chen, Claudia Krebs, Paul Pavlidis
2012	J	`jnl`	Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing. NeuroImage Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
2012	J	`jnl`	Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity. PLoS Comput. Biol. Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
2012	J	`jnl`	Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinform. Anton Zoubarev, Kelsey M. Hamer, Kiran Keshav, E. Luke McCarthy, Joseph Roy C. Santos, Thea Van Rossum, Cameron McDonald, Adam Hall, Xiang Wan, Raymond Lim, Jesse A. Gillis, Paul Pavlidis
2012	J	`jnl`	Progress and challenges in the computational prediction of gene function using networks. F1000Research Paul Pavlidis, Jesse A. Gillis
2011	J	`jnl`	Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. Frontiers Neuroinformatics Leon French, Powell Patrick Cheng Tan, Paul Pavlidis
2011	J	`jnl`	Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain. PLoS Comput. Biol. Leon French, Paul Pavlidis
2011	J	`jnl`	The role of indirect connections in gene networks in predicting function. Bioinform. Jesse A. Gillis, Paul Pavlidis
2009	J	`jnl`	A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinform. Jesse A. Gillis, Paul Pavlidis
2009	J	`jnl`	Application and evaluation of automated semantic annotation of gene expression experiments. Bioinform. Leon French, Suzanne Lane, Tamryn Law, Lydia Xu, Paul Pavlidis
2009	J	`jnl`	Automated recognition of brain region mentions in neuroscience literature. Frontiers Neuroinformatics Leon French, Suzanne Lane, Lydia Xu, Paul Pavlidis
2008	J	`jnl`	Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinform. Meeta Mistry, Paul Pavlidis
2007	J	`jnl`	Informatics in neuroscience. Briefings Bioinform. Leon French, Paul Pavlidis
2007	J	`jnl`	Sharing and Reusing Gene Expression Profiling Data in Neuroscience. Neuroinformatics Xiang Wan, Paul Pavlidis
2005	J	`jnl`	ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinform. Homin K. Lee, William Braynen, Kiran Keshav, Paul Pavlidis
2004	J	`jnl`	Book Review. J. Biomed. Informatics Paul Pavlidis
2004	J	`jnl`	Support vector machine classification on the web. Bioinform. Paul Pavlidis, Ilan Wapinski, William Stafford Noble
2003	J	`jnl`	Matrix2png: a utility for visualizing matrix data. Bioinform. Paul Pavlidis, William Stafford Noble
2003	J	`jnl`	Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinform. Hanga C. Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P. Ellis, J. John Mann, Etienne Sibille, Victoria Arango
2003	J	`jnl`	The effect of replication on gene expression microarray experiments. Bioinform. Paul Pavlidis, Qinghong Li, William Stafford Noble
2002	Misc	`conf`	Exploring Gene Expression Data with Class Scores. Pacific Symposium on Biocomputing Paul Pavlidis, Darrin P. Lewis, William Stafford Noble
2002	J	`jnl`	Learning Gene Functional Classifications from Multiple Data Types. J. Comput. Biol. Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble
2001	—	`conf`	Classification of genes using probabilistic models of microarray expression profiles. BIOKDD Paul Pavlidis, Christopher Tang, William Stafford Noble
2001	B	`conf`	Gene functional classification from heterogeneous data. RECOMB Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy
2001	Misc	`conf`	Promoter Region-Based Classification of Genes. Pacific Symposium on Biocomputing Paul Pavlidis, Terrence S. Furey, M. Liberto, David Haussler, William Noble Grundy