Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks

(2011) Filippo Menolascina et al.   AUTOMATICA

Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering

(2011) T. Alexandrov et al.   BIOINFORMATICS

Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism

(2011) Shakti Gupta et al.   BMC Systems Biology

Inferring causal genomic alterations in breast cancer using gene expression data

(2011) Linh M Tran et al.   BMC Systems Biology

Integrative Genomics Identifies Molecular Alterations that Challenge the Linear Model of Melanoma Progression

(2011) A. E. Rose et al.   CANCER RESEARCH

Adaptive Control Model Reveals Systematic Feedback and Key Molecules in Metabolic Pathway Regulation

(2011) Chang F. Quo et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing

(2011) Zhifu Sun et al.   PLoS One

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

(2011) Lesia Bilitchenko et al.   PLoS One

Insights gained from the reverse engineering of gene networks in keloid fibroblasts

(2011) Brandon NS Ooi et al.   Theoretical Biology and Medical Modelling

Minimum Information About a Simulation Experiment (MIASE)

(2011) Dagmar Waltemath et al.   PLoS Computational Biology

Nanostructure-Initiator Mass Spectrometry Metabolite Analysis and Imaging

(2010) Matthew P. Greving et al.   ANALYTICAL CHEMISTRY

Noise and Robustness in Prokaryotic Regulatory Networks

(2010) Rafael Silva-Rocha et al.   Annual Review of Microbiology

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

(2010) Eva Freyhult et al.   BMC BIOINFORMATICS

Comparison study of microarray meta-analysis methods

(2010) Anna Campain et al.   BMC BIOINFORMATICS

Class prediction for high-dimensional class-imbalanced data

(2010) Rok Blagus et al.   BMC BIOINFORMATICS

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

(2010) E. Weeding et al.   BRIEFINGS IN BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM)

(2010) Hannah Carter et al.   CANCER BIOLOGY & THERAPY

DNA Microarrays Are Predictive of Cancer Prognosis: A Re-evaluation

(2010) X. Fan et al.   CLINICAL CANCER RESEARCH

Application of the Principles of Systems Biology and Wiener's Cybernetics for Analysis of Regulation of Energy Fluxes in Muscle Cells in Vivo

(2010) Rita Guzun et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Classification of HER2 Receptor Status in Breast Cancer Tissues by MALDI Imaging Mass Spectrometry

(2010) Sandra Rauser et al.   JOURNAL OF PROTEOME RESEARCH

Elevation of sulfatides in ovarian cancer: An integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry

(2010) Ying Liu et al.   Molecular Cancer

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Integrative genomics identifies LMO1 as a neuroblastoma oncogene

(2010) Kai Wang et al.   NATURE

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pairwise selection assembly for sequence-independent construction of long-length DNA

(2010) William J. Blake et al.   NUCLEIC ACIDS RESEARCH

A synthetic low-frequency mammalian oscillator

(2010) Marcel Tigges et al.   NUCLEIC ACIDS RESEARCH

A synthetic circuit for selectively arresting daughter cells to create aging populations

(2010) Bruno Afonso et al.   NUCLEIC ACIDS RESEARCH

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

Tuning and controlling gene expression noise in synthetic gene networks

(2010) Kevin F. Murphy et al.   NUCLEIC ACIDS RESEARCH

Consistency of predictive signature genes and classifiers generated using different microarray platforms

(2010) X Fan et al.   PHARMACOGENOMICS JOURNAL

k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction

(2010) R M Parry et al.   PHARMACOGENOMICS JOURNAL

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

Reverse Engineering of Bacterial Chemotaxis Pathway via Frequency Domain Analysis

(2010) Junjie Luo et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is a gene-centric human proteome project the best way for proteomics to serve biology?

(2010) Thierry Rabilloud et al.   PROTEOMICS

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

BglBricks: A flexible standard for biological part assembly

(2010) J Christopher Anderson et al.   Journal of Biological Engineering

Over-optimism in bioinformatics research

(2009) A.-L. Boulesteix   BIOINFORMATICS

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The systems analysis approach to mechanosensory coding

(2009) Andrew S. French   BIOLOGICAL CYBERNETICS

Considerations for the design and construction of a synthetic platform cell for biotechnological applications

(2009) P.L. Foley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Optimal classifier selection and negative bias in error rate estimation: an empirical study on high-dimensional prediction

(2009) Anne-Laure Boulesteix et al.   BMC Medical Research Methodology

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

Multi-enzymatic synthesis

(2009) Fernando Lopez-Gallego et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

BING: Biomedical informatics pipeline for Next Generation Sequencing

(2009) Jeffrey Kriseman et al.   JOURNAL OF BIOMEDICAL INFORMATICS

MALDI-Ion Mobility Separation-Mass Spectrometry Imaging of Glucose-Regulated Protein 78 kDa (Grp78) in Human Formalin-Fixed, Paraffin-Embedded Pancreatic Adenocarcinoma Tissue Sections

(2009) Marie-Claude Djidja et al.   JOURNAL OF PROTEOME RESEARCH

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

(2009) David Yu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

Synthetic protein scaffolds provide modular control over metabolic flux

(2009) John E Dueber et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Data clustering: 50 years beyond K-means

(2009) Anil K. Jain   PATTERN RECOGNITION LETTERS

The brainstem respiratory network: An overview of a half century of research

(2009) Armand L. Bianchi et al.   RESPIRATORY PHYSIOLOGY & NEUROBIOLOGY

Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment

(2009) John H. Phan et al.   TRENDS IN BIOTECHNOLOGY

Managing and Analyzing Next-Generation Sequence Data

(2009) Brent G. Richter et al.   PLoS Computational Biology

Self-correcting networks: Function, robustness, and motif distributions in biological signal processing

(2008) Pablo Kaluza et al.   CHAOS

On the Epistemological Crisis in Genomics

(2008) Edward Dougherty   CURRENT GENOMICS

Mass Spectrometry Image Correlation: Quantifying Colocalization

(2008) Liam A. McDonnell et al.   JOURNAL OF PROTEOME RESEARCH

MALDI Imaging Combined with Hierarchical Clustering as a New Tool for the Interpretation of Complex Human Cancers

(2008) Sören-Oliver Deininger et al.   JOURNAL OF PROTEOME RESEARCH

Metabolic gene regulation in a dynamically changing environment

(2008) Matthew R. Bennett et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

(2008) Chris F Taylor et al.   NATURE BIOTECHNOLOGY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Integrative biology — a strategy for systems biomedicine

(2008) Edison T. Liu   NATURE REVIEWS GENETICS

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH

Cross-validation and bootstrapping are unreliable in small sample classification

(2008) A. Isaksson et al.   PATTERN RECOGNITION LETTERS

The Immune System and Its Ecology*

(2008) Alfred I. Tauber   PHILOSOPHY OF SCIENCE

Feedback Loops Shape Cellular Signals in Space and Time

(2008) O. Brandman et al.   SCIENCE

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Structural robustness of metabolic networks with respect to multiple knockouts

(2007) Jörn Behre et al.   JOURNAL OF THEORETICAL BIOLOGY