Vivek Krishnakumar
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Explore the profile of Vivek Krishnakumar including associated specialties, affiliations and a list of published articles.
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16
Citations
2103
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Recent Articles
1.
Tang H, Krishnakumar V, Zeng X, Xu Z, Taranto A, Lomas J, et al.
Imeta
. 2024 Aug;
3(4):e211.
PMID: 39135687
The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a...
2.
Sullivan A, Purohit P, Freese N, Pasha A, Esteban E, Waese J, et al.
Plant J
. 2019 Jul;
100(3):641-654.
PMID: 31350781
Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data...
3.
Xiong J, Yang W, Chen K, Jiang C, Ma Y, Chai X, et al.
PLoS Biol
. 2019 Jun;
17(6):e3000294.
PMID: 31158217
A morphospecies is defined as a taxonomic species based wholly on morphology, but often morphospecies consist of clusters of cryptic species that can be identified genetically or molecularly. The nature...
4.
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology
Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, et al.
Plant Cell
. 2017 Aug;
29(8):1806-1821.
PMID: 28808136
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required...
5.
Krishnakumar V, Contrino S, Cheng C, Belyaeva I, Ferlanti E, Miller J, et al.
Plant Cell Physiol
. 2016 Dec;
58(1):e4.
PMID: 28013278
ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and...
6.
Hamilton E, Kapusta A, Huvos P, Bidwell S, Zafar N, Tang H, et al.
Elife
. 2016 Nov;
5.
PMID: 27892853
The germline genome of the binucleated ciliate undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline...
7.
Cheng C, Krishnakumar V, Chan A, Thibaud-Nissen F, Schobel S, Town C
Plant J
. 2016 Nov;
89(4):789-804.
PMID: 27862469
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the...
8.
Chamala S, Garcia N, Godden G, Krishnakumar V, Jordon-Thaden I, De Smet R, et al.
Appl Plant Sci
. 2015 Apr;
3(4).
PMID: 25909041
Premise Of The Study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic...
9.
Zhang X, Rosen B, Tang H, Krishnakumar V, Town C
PLoS One
. 2015 Feb;
10(2):e0117699.
PMID: 25706651
Recent RNA-seq studies reveal that the transcriptomes in animals and plants are more complex than previously thought, leading to the inclusion of many more splice isoforms in annotated genomes. However,...
10.
Krishnakumar V, Choi Y, Beck E, Wu Q, Luo A, Sylvester A, et al.
Plant Cell Physiol
. 2014 Nov;
56(1):e12.
PMID: 25432973
Maize is a global crop and a powerful system among grain crops for genetic and genomic studies. However, the development of novel biological tools and resources to aid in the...