Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

(2020) Chiaowen Joyce Hsiao et al.   GENOME RESEARCH

Meltome atlas—thermal proteome stability across the tree of life

(2020) Anna Jarzab et al.   NATURE METHODS

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Targeting UDP-α-d-glucose 6-dehydrogenase inhibits glioblastoma growth and migration

(2018) Olutobi Oyinlade et al.   ONCOGENE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Enhanced validation of antibodies for research applications

(2018) Fredrik Edfors et al.   Nature Communications

The Mcm2–7-interacting domain of human mini-chromosome maintenance 10 (Mcm10) protein is important for stable chromatin association and origin firing

(2017) Masako Izumi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptomic Characterization of the Human Cell Cycle in Individual Unsynchronized Cells

(2017) Joakim Karlsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Image Data Resource: a bioimage data integration and publication platform

(2017) Eleanor Williams et al.   NATURE METHODS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

(2017) Johan Boström et al.   PLoS One

A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer

(2016) Daniel Dominguez et al.   CELL RESEARCH

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

A proposal for validation of antibodies

(2016) Mathias Uhlen et al.   NATURE METHODS

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators

(2016) Nicole St-Denis et al.   Cell Reports

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation

(2015) Katherine Sellers et al.   JOURNAL OF CLINICAL INVESTIGATION

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FUCCI sensors: powerful new tools for analysis of cell proliferation

(2015) N. Zielke et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Dysfunction of Intraflagellar Transport Proteins beyond the Primary Cilium

(2014) P. V. Tran   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

(2014) Alberto Santos et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism

(2014) Maria S. Robles et al.   PLoS Genetics

Ubiquitin Ligases and Cell Cycle Control

(2013) Leonardo K. Teixeira et al.   Annual Review of Biochemistry

Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

(2013) Gavin D. Grant et al.   MOLECULAR BIOLOGY OF THE CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication

(2013) Javier Peña-Diaz et al.   NUCLEIC ACIDS RESEARCH

The Protein Interaction Landscape of the Human CMGC Kinase Group

(2013) Markku Varjosalo et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Effect of estrogen sulfation by SULT1E1 and PAPSS on the development of estrogen-dependent cancers

(2012) Yali Xu et al.   CANCER SCIENCE

Quantitative Proteomics Reveals the Basis for the Biochemical Specificity of the Cell-Cycle Machinery

(2011) Felicia Walton Pagliuca et al.   MOLECULAR CELL

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

(2010) Shinya Ohta et al.   CELL

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

A single fixation protocol for proteome-wide immunofluorescence localization studies

(2009) Charlotte Stadler et al.   Journal of Proteomics

The nuts and bolts of AGC protein kinases

(2009) Laura R. Pearce et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

(2008) Z. Bar-Joseph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA