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Bioinformatics and Systems Biology Graduate Program
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top-articles
Bioinformatics and Systems Biology Graduate Program
56
(top 2%)
papers
3.0K
(top 1%)
citations
29
(top 1%)
h
-index
53
(top 1%)
g
-index
85
all documents
4.1K
doc citations
1.0K
citing journals
Top Articles
#
Title
Journal
Year
Citations
1
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming
Cell Research
2012
452
2
The emergence of SARS-CoV-2 in Europe and North America
Science
2020
331
3
Network Context and Selection in the Evolution to Enzyme Specificity
Science
2012
249
4
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
Nature Genetics
2019
236
5
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
Science
2022
192
6
Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegans
PLoS Pathogens
2014
184
7
Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells
Proceedings of the National Academy of Sciences of the United States of America
2012
152
8
Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function
Nature Communications
2018
129
9
Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase
Nature Structural and Molecular Biology
2019
123
10
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
Science
2022
123
11
Structural Systems Biology Evaluation of Metabolic Thermotolerance in
Escherichia coli
Science
2013
111
12
Timing the SARS-CoV-2 index case in Hubei province
Science
2021
109
13
Experimental selection of hypoxia-tolerant Drosophila melanogaster
Proceedings of the National Academy of Sciences of the United States of America
2011
105
14
TreeCluster: Clustering biological sequences using phylogenetic trees
PLoS ONE
2019
99
15
Systems biology analysis of longitudinal functional response of endothelial cells to shear stress
Proceedings of the National Academy of Sciences of the United States of America
2017
95
16
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
PLoS Computational Biology
2019
86
17
Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
Nature Communications
2019
82
18
Technical Variations in Low-Input RNA-seq Methodologies
Scientific Reports
2014
75
19
Properties of structural variants and short tandem repeats associated with gene expression and complex traits
Nature Communications
2020
67
20
A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements
PLoS Genetics
2011
65
21
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
Nature Communications
2021
65
22
Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
Nature
2022
60
23
AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications
Nature Communications
2020
49
24
TET methylcytosine oxidases: new insights from a decade of research
Journal of Biosciences
2020
49
25
Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesicles
Proceedings of the National Academy of Sciences of the United States of America
2012
48
26
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences
Bioinformatics
2019
45
27
Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories
Stem Cell Reports
2019
44
28
Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions
Proceedings of the National Academy of Sciences of the United States of America
2021
43
29
Quantitative Transcriptomics using Designed Primer-based Amplification
Scientific Reports
2013
38
30
Immune DNA signature of T-cell infiltration in breast tumor exomes
Scientific Reports
2016
30
31
De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads
PLoS ONE
2010
29
32
High-Resolution Mutational Profiling Suggests the Genetic Validity of Glioblastoma Patient-Derived Pre-Clinical Models
PLoS ONE
2013
25
33
Fast and accurate distance‐based phylogenetic placement using divide and conquer
Molecular Ecology Resources
2022
25
34
Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
Nature Communications
2020
22
35
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Nature Communications
2022
22
36
Identification of therapeutic targets for glioblastoma by network analysis
Oncogene
2016
18
37
Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain
Cell Research
2022
16
38
Rapid Analysis of Saccharomyces cerevisiae Genome Rearrangements by Multiplex Ligation–Dependent Probe Amplification
PLoS Genetics
2012
15
39
The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ
Npj Breast Cancer
2022
13
40
DEPP: Deep Learning Enables Extending Species Trees using Single Genes
Systematic Biology
2023
11
41
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
Nature Biotechnology
2023
9
42
Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
Nucleic Acids Research
2021
8
43
Wnt Pathway Activation Increases Hypoxia Tolerance during Development
PLoS ONE
2014
8
44
Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and Opportunities
Frontiers in Endocrinology
2021
8
45
A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition
Systematic Biology
2018
5
46
Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021
Journal of Infectious Diseases
2022
5
47
Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions
Nature Communications
2022
5
48
Tests of Selection in Pooled Case-Control Data: An Empirical Study
Frontiers in Genetics
2011
3
49
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling
Cell Systems
2022
3
50
Whole-genome CRISPR screening identifies PI3K/AKT as a downstream component of the oncogenic GNAQ–focal adhesion kinase signaling circuitry
Journal of Biological Chemistry
2023
3
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