PubRank

Chris Sander

Author PubWeight™ 603.81‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Human MicroRNA targets. PLoS Biol 2004 34.51
2 A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007 34.03
3 Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007 27.10
4 The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012 26.98
5 Integrative genomic profiling of human prostate cancer. Cancer Cell 2010 23.61
6 MicroRNA targets in Drosophila. Genome Biol 2003 23.59
7 Global mapping of the yeast genetic interaction network. Science 2004 21.34
8 International network of cancer genome projects. Nature 2010 20.35
9 Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013 19.54
10 The microRNA.org resource: targets and expression. Nucleic Acids Res 2007 16.26
11 The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol 2004 16.08
12 Characterizing gene sets with FuncAssociate. Bioinformatics 2003 14.10
13 Identification of microRNAs of the herpesvirus family. Nat Methods 2005 12.98
14 Identification of virus-encoded microRNAs. Science 2004 12.56
15 The somatic genomic landscape of glioblastoma. Cell 2013 11.73
16 The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 2013 11.29
17 Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011 10.99
18 The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010 9.19
19 Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2010 9.18
20 A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006 8.80
21 The Systems Biology Graphical Notation. Nat Biotechnol 2009 8.53
22 Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 2011 7.22
23 Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010 7.15
24 Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A 2007 6.79
25 (V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A 2009 6.78
26 Genome sequencing identifies a basis for everolimus sensitivity. Science 2012 6.71
27 Emerging landscape of oncogenic signatures across human cancers. Nat Genet 2013 6.48
28 miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol 2004 6.44
29 Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet 2010 6.10
30 Pathguide: a pathway resource list. Nucleic Acids Res 2006 6.05
31 Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015 5.71
32 Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet 2009 5.31
33 MicroRNA profiling of the murine hematopoietic system. Genome Biol 2005 4.94
34 Protein 3D structure computed from evolutionary sequence variation. PLoS One 2011 4.71
35 Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev 2009 4.43
36 Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun 2013 4.35
37 Functional copy-number alterations in cancer. PLoS One 2008 4.27
38 Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A 2011 4.08
39 Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 2005 3.95
40 Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009 3.66
41 Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood 2007 3.64
42 Automated network analysis identifies core pathways in glioblastoma. PLoS One 2010 3.64
43 A series of PDB related databases for everyday needs. Nucleic Acids Res 2010 3.60
44 Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol 2007 3.46
45 The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet 2011 3.41
46 Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol 2010 3.37
47 Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron 2009 3.27
48 cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 2006 3.24
49 A specificity map for the PDZ domain family. PLoS Biol 2008 3.16
50 Three-dimensional structures of membrane proteins from genomic sequencing. Cell 2012 3.02
51 CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res 2006 3.00
52 Pathway information for systems biology. FEBS Lett 2005 2.97
53 The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 2005 2.94
54 Introducing meta-services for biomedical information extraction. Genome Biol 2008 2.78
55 A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 2012 2.72
56 Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 2003 2.66
57 NetPath: a public resource of curated signal transduction pathways. Genome Biol 2010 2.62
58 The amino-acid mutational spectrum of human genetic disease. Genome Biol 2003 2.55
59 Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet 2009 2.51
60 Protein structure prediction from sequence variation. Nat Biotechnol 2012 2.50
61 DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A 2008 2.49
62 RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol 2011 2.46
63 Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res 2007 2.44
64 Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol 2008 2.33
65 Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res 2013 2.26
66 The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A 2009 2.09
67 Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol 2013 1.92
68 Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov 2011 1.85
69 The mutational landscape of adenoid cystic carcinoma. Nat Genet 2013 1.83
70 An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell 2016 1.79
71 ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics 2009 1.76
72 Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One 2012 1.76
73 Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell 2011 1.74
74 Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors. Cancer Res 2012 1.71
75 Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods 2013 1.64
76 Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A 2013 1.60
77 Prediction of human microRNA targets. Methods Mol Biol 2006 1.60
78 Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy. Clin Cancer Res 2014 1.57
79 Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev 2011 1.55
80 Signal processing in the TGF-beta superfamily ligand-receptor network. PLoS Comput Biol 2006 1.54
81 Using biological pathway data with paxtools. PLoS Comput Biol 2013 1.50
82 Genomic complexity and AKT dependence in serous ovarian cancer. Cancer Discov 2012 1.50
83 miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis. PLoS One 2012 1.44
84 An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. J Natl Cancer Inst 2013 1.42
85 Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol 2013 1.41
86 Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res 2011 1.40
87 MYC cooperates with AKT in prostate tumorigenesis and alters sensitivity to mTOR inhibitors. PLoS One 2011 1.38
88 Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. J Clin Invest 2016 1.36
89 18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Res 2011 1.36
90 Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol 2007 1.36
91 Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proc Natl Acad Sci U S A 2011 1.30
92 Integrative subtype discovery in glioblastoma using iCluster. PLoS One 2012 1.29
93 From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol 2007 1.27
94 Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol 2011 1.26
95 mRNA turnover rate limits siRNA and microRNA efficacy. Mol Syst Biol 2010 1.21
96 MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. J Pathol 2013 1.17
97 Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics 2008 1.16
98 Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. PLoS One 2011 1.09
99 Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. Sci Signal 2013 1.08
100 Discovering modulators of gene expression. Nucleic Acids Res 2010 1.07
101 The molecular diversity of Luminal A breast tumors. Breast Cancer Res Treat 2013 1.07
102 Detection of activity centers in cellular pathways using transcript profiling. J Biopharm Stat 2004 1.00
103 Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One 2013 0.99
104 ZIC1 overexpression is oncogenic in liposarcoma. Cancer Res 2010 0.95
105 Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics 2014 0.94
106 Pattern search in BioPAX models. Bioinformatics 2013 0.93
107 Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods 2013 0.92
108 Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma. BMC Med Genet 2007 0.89
109 PiHelper: an open source framework for drug-target and antibody-target data. Bioinformatics 2013 0.86
110 The BioPAX Validator. Bioinformatics 2013 0.85
111 Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol 2008 0.84
112 Using MEMo to discover mutual exclusivity modules in cancer. Curr Protoc Bioinformatics 2013 0.84
113 Principle of system balance for drug interactions. N Engl J Med 2010 0.80
114 Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 2017 0.75