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DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction

Pierre Baldi, Richard H. Lathrop
2001 Pacific Symposium on Biocomputing  
There is mounting evidence that DNA structural properties beyond the double helix signi cantly a ect its interactions with proteins and play an important role in a number of biological phenomena ranging  ...  The selected papers address the underlying structural and functional basis by which these interactions can be understood, modeled, and predicted.  ...  Acknowledgments We gratefully thank the session blind reviewers, who helped in the di cult task of choosing the best contributions from many excellent submissions.  ... 
dblp:conf/psb/BaldiL01 fatcat:3fmdt46gszaslope6sf6zzhn2m

Session Introduction

Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund
2008 Pacific Symposium on Biocomputing  
Acknowledgments We are grateful to those who submitted manuscripts for consideration for inclusion in this session, and we thank the numerous reviewers for their valuable expertise and time throughout  ...  various genomes, gene expression data, protein-protein and protein-ligand interactions, and protein-DNA and protein-RNA binding data.  ...  Two of the papers in this session examine methods for predicting the protein residues that make contact with DNA and RNA.  ... 
dblp:conf/psb/BulykFHM08 fatcat:ya4vfwxlubfk3ph3r77pp32fti

Session Introduction

Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo
2007 Pacific Symposium on Biocomputing  
and protein-ligand interactions, and protein-DNA binding data.  ...  In addition, efforts in structural biology are yielding structural data on proteins, protein complexes, and proteinligand interactions.  ...  Acknowledgments We are grateful to those who submitted manuscripts for this session, and we thank the numerous reviewers for their valuable expertise and time in the peer review process.  ... 
dblp:conf/psb/BulykHFS07 fatcat:kxxwtnrniveedjd2qv3frdu5jy

Session Introduction

Yves A. Lussier, Joanne Berghout, Francesca Vitali, Kenneth S. Ramos, Maricel G. Kann, Jason H. Moore
2018 Pacific Symposium on Biocomputing  
This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology.  ...  Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements.  ...  Introduction The majority of the human genome is comprised of noncoding DNA.  ... 
dblp:conf/psb/LussierBVRKM18 fatcat:ozcexmwhcbdddo2tjmjnbboc4a

Session Introduction

Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
2006 Pacific Symposium on Biocomputing  
Acknowledgements The session co-chairs would like to thank the numerous reviewers for their help in selecting the best papers among many excellent submissions.  ...  The goal of this session is to discuss the latest progress in the study of protein interactions and disease.  ...  Bandyopadhyay et al. used a network analysis of gene expression and protein interaction data to identify active pathways related to HIV pathogenesis.  ... 
dblp:conf/psb/KannOPR06 fatcat:ksl5mgv4yzbaherj74uknxoupa

Session Introduction

Trey Ideker, Erik K. Neumann, Vincent Schächter
2004 Pacific Symposium on Biocomputing  
First, it is now possible to systematically measure pathway interactions themselves, such as those between proteins and proteins or between proteins and DNA.  ...  Many of these papers combine more than one large-scale data type, including gene expression profiles, protein-protein interaction data, and/or pathway databases.  ... 
dblp:conf/psb/IdekerNS04 fatcat:ibqeh5c5ffhlxddwccnzomosvq

Session Introduction

Alexander J. Hartemink, Eran Segal
2004 Pacific Symposium on Biocomputing  
protein structural information, and protein-DNA binding data.  ...  Recent technological advances enable us to collect many different types of data at a genome-wide scale, including DNA sequences, gene and protein expression measurements, protein-protein interactions,  ...  for detecting operon structure; combining protein sequences with tertiary structural information for classifying proteins; combining protein-protein interaction data with gene expression for learning  ... 
dblp:conf/psb/HarteminkS04 fatcat:pdp463s5irhrjl4kystyae3e2e

Session Introduction

Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2010 Pacific Symposium on Biocomputing  
Acknowledgements We thank all the authors who submitted papers to the session, and we gratefully acknowledge the reviewers who contributed their time and expertise to the peer review process.  ...  Introduction Until recently, RNA has been viewed as a simple "working copy" of the genomic DNA, simply transporting information from the genome into the proteins.  ...  Specific problems in computational studies of ncRNAs include: • Algorithms for modelling interactions between RNAs and other molecules, particularly RNA-RNA and RNA-protein interactions • Learning thermodynamic  ... 
dblp:conf/psb/BackofenCHSS10 fatcat:4tcxrxo5gfgpvi2oppdqjxtqsq

Session Introduction

Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
2016 Pacific Symposium on Biocomputing  
interfacial residues involved in RNA-protein recognition in RNA-protein complexes and interaction networks.  ...  This conference session includes presentations exploring computational approaches for detecting regulatory RNAs in RNA-Seq data, for analyzing in vivo CLIP data on RNA-protein interactions, and for predicting  ...  Acknowledgements We thank all of the authors who submitted papers for this session and all of the reviewers who contributed their time and expertise.  ... 
dblp:conf/psb/DobbsBHJLM16 fatcat:55nwao3awjhrjeoas7m5h2onae

Session Introduction

Michael F. Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom
2009 Pacific Symposium on Biocomputing  
Fox, Taylor and Slonim link protein interaction data across four species and identify novel features of hub proteins, showing that the interaction partners of hub proteins are more conserved across evolution  ...  Carey and Gentleman present a new data structure within the R/Bioconductor system that integrates SNP, expression, annotation, and phenotypic data and which links to the many existing Bioconductor tools  ... 
dblp:conf/psb/OchsQDR09 fatcat:o37zyl7x25c2pofq6nyaxxcrfe

Session Introduction

Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
2010 Pacific Symposium on Biocomputing  
modification) and protein-DNA interaction.  ...  Introduction Until just recently, bioinformaticians and genomicists did not have access to genomic data from multiple human individuals or many different species due to labor intensiveness and limitations  ... 
dblp:conf/psb/AlkanBEKS10 fatcat:d4puikkmyff4nbedcte3fl755u

Session Introduction

Anna Okula Basile, Anurag Verma, Marta Byrska-Bishop, Sarah P. Pendergrass, Christian Darabos, H. Lester Kirchner
2017 Pacific Symposium on Biocomputing  
an algorithm to define a phenotype status from variety of structured and unstructured free text in EHR.  ...  In a biomedical setting, this may include clinical measurements, drug usage data, mRNA expression levels, and environmental exposures.  ...  of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks".  ... 
dblp:conf/psb/BasileVBPDK17 fatcat:6rxvfi7ktvcnhdi5afl2yzngbi

Session Introduction

Shefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta Byrska-Bishop, Christian Darabos
2018 Pacific Symposium on Biocomputing  
Our session aims to address these challenges in handling big data for designing a study, performing analysis, and interpreting outcomes of these analyses.  ...  In our session, we will present research articles that can help in identifying innovative ways to recognize and overcome newly arising challenges associated with pattern recognition in biomedical data.  ...  The authors conducted a comprehensive network analysis on publicly available data from human protein-protein interaction (PPI) network and DisGeNET database containing protein-disease associations.  ... 
dblp:conf/psb/VermaVBBD18 fatcat:czpyqrfhcrffxajzrykrhu2tge

Session Introduction

Nikolay Samusik, Nima Aghaeepour, Sean Bendall
2017 Pacific Symposium on Biocomputing  
This session is dedicated to computational methods for single-cell analysis in various biological domains, modelling of population heterogeneity, as well as translational applications of single cell data  ...  We thank all of the authors who submitted papers for this session and all of the reviewers who contributed their time and expertise.  ...  We acknowledge the NIH grant R01GM109836 and the Rachford and Carlota A. Harris Endowed Chair for support.  ... 
dblp:conf/psb/SamusikAB17 fatcat:7jax7cr2grhupit6qkgbluxoxy

Session introduction

Lana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush
2019 Pacific Symposium on Biocomputing  
It allows us to explore processes active in bulk tissue samples, survey tissue complexity, characterize heterogeneous cell populations and explore the role of cellular heterogeneity and interactions in  ...  To deal with these new experimental data, new computational methods, software, and data portals to analyze, integrate and interpret the complexity of the system are clearly needed.  ...  Downstream analyses include methods for clustering, differential expression analysis, pathway/ontology enrichment analysis, protein network interaction mapping, and pseudo-time construction.  ... 
dblp:conf/psb/GarmireYFYQ19 fatcat:r4acw4uayvd3zgvvf3scl3vmfe
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