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    Abhishek Kumar
    4,347
    Contribution points 
    (See all users)

    Contributions by role

    Editor 3900
    PeerJ author 200
    Reviewer 175
    PeerJ PrePrints author 70

    Contributions by subject area

    Genomics 1605
    Bioinformatics 1605
    Evolutionary-Studies 1105
    Genetics 970
    Computational-Biology 872
    Microbiology 835
    Computational-Science 500
    Aquaculture,-Fisheries-and-Fish-Science 335
    Infectious-Diseases 335
    Biodiversity 300
    Entomology 300
    Marine-Biology 300
    Mycology 300
    Zoology 300
    Biochemistry 272
    Cell-Biology 235
    Medical-Genetics 235
    Human–Computer-Interaction 200
    Mathematical-Biology 200
    Science-and-Medical-Education 200
    Nutrition 200
    Taxonomy 200
    Public-Health 200
    Data-Mining-and-Machine-Learning 200
    Plant-Science 200
    Ecology 200
    Molecular-Biology 170
    Neuroscience 100
    Animal-Behavior 100
    Psychiatry-and-Psychology 100
    Biogeography 100
    Conservation-biology 100
    Spatial-and-Geographic-Information-Science 100
    Plant-science 100
    Developmental-Biology 100
    Ethical-Issues 100
    Science-Policy 100
    Immunology 100
    Rheumatology 100
    Parasitology 100
    Anthropology 100
    Drugs-and-Devices 100
    Food-Science-and-Technology 100
    Agricultural-Science 100
    Pharmacology 100
    Orthopedics 100
    Biotechnology 70
    Biophysics 2

    By Q&A topic

    General 2
    Academic Editor

    Abhishek Kumar

    ORCID: 0000-0003-4172-4059

    Summary

    Researcher focusing on computational genomics with current interests in genetics, genomics and trancriptomics specially fungi, insects and vertebrates. Current research interests as following
    1. Research Area #1: Application of genomics to human diseases
    2. Research Area #2: Genomics of drug-like molecules from fungi
    3. Research Area #3: Evolutionary Genomics
    4. Research Area #4: Biodiversity Genomics

    Computational Biology Computational Science Evolutionary Studies Genetics Genomics Microbiology Mycology

    Work details

    Research Scientist

    German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)
    Molecular Genetic Epidemiology

    Websites

    • Google Scholar

    PeerJ Contributions

    • Articles 2
    • Preprints 2
    • Edited 31
    • Reviewed 4
    • Questions 3
    October 13, 2015
    Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
    5 citations
    494 downloads
    2,391 views
    Rakesh Kumar Majhi, Somdatta Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
    cell-biology
    evolutionary-studies
    genetics
    genomics
    medical-genetics
    https://doi.org/10.7717/peerj.1310 PubMed 26500819
    June 16, 2015
    Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY
    5 citations
    332 downloads
    2,121 views
    Abhishek Kumar
    aquaculture-fisheries-and-fish-science
    biochemistry
    evolutionary-studies
    genetics
    genomics
    https://doi.org/10.7717/peerj.1026 PubMed 26157611
    May 26, 2015 - Version: 1
    Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY
    165 downloads
    467 views
    Abhishek Kumar
    aquaculture-fisheries-and-fish-science
    biochemistry
    evolutionary-studies
    genetics
    genomics
    https://doi.org/10.7287/peerj.preprints.1126v1
    July 21, 2014 - Version: 1
    Sperm specific expression of temperature-sensitive ion channel TRPM8 correlates with vertebrate evolution
    371 downloads
    1,498 views
    Rakesh Kumar Majhi, Somdatta Saha, Ashutosh Kumar, Nirlipta Swain, Luna Goswami, Pratyush Mohapatra, Apratim A Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
    cell-biology
    evolutionary-studies
    genetics
    genomics
    medical-genetics
    https://doi.org/10.7287/peerj.preprints.440v1

    Academic Editor on

    January 14, 2019
    Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining
    65 downloads
    349 views
    Simon Orozco-Arias, Ana María Núñez-Rincón, Reinel Tabares-Soto, Diana López-Álvarez
    bioinformatics
    ecology
    computational-science
    data-mining-and-machine-learning
    spatial-and-geographic-information-science
    https://doi.org/10.7717/peerj.6193 PubMed 30656067
    March 8, 2017
    The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L
    5 citations
    397 downloads
    1,294 views
    Wei Qing Kong, Jin Hong Yang
    genomics
    plant-science
    https://doi.org/10.7717/peerj.3037 PubMed 28286710
    February 23, 2017
    Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015
    2 citations
    178 downloads
    1,160 views
    Cecylia Łukaszuk, Elżbieta Krajewska-Kułak, Wojciech Kułak
    microbiology
    mycology
    drugs-and-devices
    public-health
    https://doi.org/10.7717/peerj.3038 PubMed 28243540
    January 26, 2017
    Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola
    4 citations
    517 downloads
    1,639 views
    Hong Keat Looi, Yue Fen Toh, Su Mei Yew, Shiang Ling Na, Yung-Chie Tan, Pei-Sin Chong, Jia-Shiun Khoo, Wai-Yan Yee, Kee Peng Ng, Chee Sian Kuan
    genomics
    microbiology
    https://doi.org/10.7717/peerj.2841 PubMed 28149676
    September 20, 2016
    A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
    13 citations
    1,905 downloads
    7,935 views
    Catherine M. Burke, Aaron E. Darling
    bioinformatics
    ecology
    microbiology
    https://doi.org/10.7717/peerj.2492 PubMed 27688981
    July 6, 2016
    Gene expression analysis of overwintering mountain pine beetle larvae suggests multiple systems involved in overwintering stress, cold hardiness, and preparation for spring development
    4 citations
    526 downloads
    1,873 views
    Jeanne A. Robert, Tiffany Bonnett, Caitlin Pitt, Luke J. Spooner, Jordie Fraser, Macaire M.S. Yuen, Christopher I. Keeling, Jörg Bohlmann, Dezene P.W. Huber
    entomology
    genomics
    https://doi.org/10.7717/peerj.2109 PubMed 27441109
    June 28, 2016
    Collecting reliable clades using the Greedy Strict Consensus Merger
    3 citations
    302 downloads
    1,642 views
    Markus Fleischauer, Sebastian Böcker
    bioinformatics
    computational-biology
    evolutionary-studies
    genetics
    taxonomy
    https://doi.org/10.7717/peerj.2172 PubMed 27375971
    June 27, 2016
    Audio segmentation using Flattened Local Trimmed Range for ecological acoustic space analysis
    1 citation
    264 downloads
    1,296 views
    Giovany Vega, Carlos J. Corrada-Bravo, T. Mitchell Aide
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj-cs.70
    May 24, 2016
    De novo assembly and characterization of the Chinese three-keeled pond turtle (Mauremys reevesii) transcriptome: presence of longevity-related genes
    364 downloads
    1,434 views
    Huazong Yin, Liuwang Nie, Feifei Zhao, Huaxing Zhou, Haifeng Li, Xianmei Dong, Huanhuan Zhang, Yuqin Wang, Qiong Shi, Jun Li
    genetics
    genomics
    zoology
    https://doi.org/10.7717/peerj.2062 PubMed 27257545
    May 24, 2016
    Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa
    6 citations
    470 downloads
    1,920 views
    Sandeep Chakraborty, Rafael Nascimento, Paulo A. Zaini, Hossein Gouran, Basuthkar J. Rao, Luiz R. Goulart, Abhaya M. Dandekar
    biochemistry
    bioinformatics
    genomics
    plant-science
    https://doi.org/10.7717/peerj.2007 PubMed 27257535
    May 2, 2016
    De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
    3 citations
    313 downloads
    1,956 views
    Taruna A. Schuelke, Anthony Westbrook, Kirk Broders, Keith Woeste, Matthew D. MacManes
    genomics
    mycology
    https://doi.org/10.7717/peerj.1952 PubMed 27168971
    January 18, 2016
    Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region
    5 citations
    854 downloads
    1,954 views
    Julio Peñas, Sara Barrios, Javier Bobo-Pinilla, Juan Lorite, M. Montserrat Martínez-Ortega
    biodiversity
    biogeography
    conservation-biology
    genetics
    plant-science
    https://doi.org/10.7717/peerj.1474 PubMed 26844014
    September 10, 2015
    The selenium content of SEPP1 versus selenium requirements in vertebrates
    3 citations
    394 downloads
    1,872 views
    Sam Penglase, Kristin Hamre, Ståle Ellingsen
    agricultural-science
    evolutionary-studies
    genomics
    nutrition
    ethical-issues
    https://doi.org/10.7717/peerj.1244 PubMed 26734501
    September 3, 2015
    Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1
    3 citations
    548 downloads
    1,670 views
    Xuefei Yu, Wei Zheng, Somanath Bhat, J. Andrew Aquilina, Ren Zhang
    microbiology
    molecular-biology
    https://doi.org/10.7717/peerj.1230 PubMed 26355338
    August 6, 2015
    Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
    8 citations
    1,021 downloads
    3,833 views
    Nagesh A. Kuravadi, Vijay Yenagi, Kannan Rangiah, HB Mahesh, Anantharamanan Rajamani, Meghana D. Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, Shilpa Siddappa, Aishwarya Ramamurthy, BN Sathyanarayana, Malali Gowda
    genomics
    https://doi.org/10.7717/peerj.1066 PubMed 26290780
    July 9, 2015
    The seasonal reproduction number of dengue fever: impacts of climate on transmission
    13 citations
    1,022 downloads
    3,935 views
    Sittisede Polwiang
    computational-biology
    mathematical-biology
    infectious-diseases
    https://doi.org/10.7717/peerj.1069 PubMed 26213648
    May 21, 2015
    Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species
    6 citations
    338 downloads
    2,550 views
    Katrín Halldórsdóttir, Einar Árnason
    aquaculture-fisheries-and-fish-science
    evolutionary-studies
    genetics
    marine-biology
    immunology
    https://doi.org/10.7717/peerj.976 PubMed 26038731
    May 14, 2015
    Swabs to genomes: a comprehensive workflow
    15 citations
    1,555 downloads
    9,358 views
    Madison I. Dunitz, Jenna M. Lang, Guillaume Jospin, Aaron E. Darling, Jonathan A. Eisen, David A. Coil
    bioinformatics
    genomics
    microbiology
    https://doi.org/10.7717/peerj.960 PubMed 26020012
    December 16, 2014
    Combining physical and virtual contexts through augmented reality: design and evaluation of a prototype using a drug box as a marker for antibiotic training
    1 citation
    854 downloads
    1,992 views
    Sokratis Nifakos, Tanja Tomson, Nabil Zary
    computational-biology
    computational-science
    human-computer-interaction
    pharmacology
    science-and-medical-education
    https://doi.org/10.7717/peerj.697 PubMed 25548733
    December 9, 2014
    The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types
    37 citations
    2,127 downloads
    17,523 views
    Jenna M. Lang, Jonathan A. Eisen, Angela M. Zivkovic
    bioinformatics
    food-science-and-technology
    microbiology
    nutrition
    https://doi.org/10.7717/peerj.659 PubMed 25538865
    December 2, 2014
    Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasite Neospora caninum
    641 downloads
    2,739 views
    Mamdowh M. Alkurashi, Sean T. May, Kenny Kong, Jaume Bacardit, David Haig, Hany M. Elsheikha
    entomology
    evolutionary-studies
    parasitology
    zoology
    infectious-diseases
    https://doi.org/10.7717/peerj.674 PubMed 25493211
    November 20, 2014
    Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin
    1 citation
    564 downloads
    1,823 views
    Agata Perlińska, Marcin Grynberg
    bioinformatics
    computational-biology
    microbiology
    infectious-diseases
    https://doi.org/10.7717/peerj.679 PubMed 25426338
    November 18, 2014
    Genetic reprogramming of human amniotic cells with episomal vectors: neural rosettes as sentinels in candidate selection for validation assays
    382 downloads
    2,270 views
    Patricia G. Wilson, Tiffany Payne
    cell-biology
    developmental-biology
    genetics
    https://doi.org/10.7717/peerj.668 PubMed 25426336
    November 13, 2014
    Cocaine affects foraging behaviour and biogenic amine modulated behavioural reflexes in honey bees
    7 citations
    824 downloads
    2,726 views
    Eirik Søvik, Naïla Even, Catherine W. Radford, Andrew B. Barron
    animal-behavior
    entomology
    evolutionary-studies
    neuroscience
    psychiatry-and-psychology
    https://doi.org/10.7717/peerj.662 PubMed 25405075
    November 13, 2014
    Error correction and diversity analysis of population mixtures determined by NGS
    1 citation
    476 downloads
    1,888 views
    Graham R. Wood, Nigel J. Burroughs, David J. Evans, Eugene V. Ryabov
    biodiversity
    bioinformatics
    computational-biology
    genetics
    mathematical-biology
    https://doi.org/10.7717/peerj.645 PubMed 25405074
    November 4, 2014
    Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array
    1 citation
    539 downloads
    1,265 views
    Xu Zhang, Wenbo Mu, Cong Liu, Wei Zhang
    bioinformatics
    genetics
    https://doi.org/10.7717/peerj.660 PubMed 25392759
    November 4, 2014
    Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
    20 citations
    1,220 downloads
    7,832 views
    Olga Golosova, Ross Henderson, Yuriy Vaskin, Andrei Gabrielian, German Grekhov, Vijayaraj Nagarajan, Andrew J. Oler, Mariam Quiñones, Darrell Hurt, Mikhail Fursov, Yentram Huyen
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj.644 PubMed 25392756
    October 30, 2014
    Horizontal transfer generates genetic variation in an asexual pathogen
    3 citations
    296 downloads
    1,557 views
    Xiaoqiu Huang
    genomics
    mycology
    https://doi.org/10.7717/peerj.650 PubMed 25374789
    September 30, 2014
    Massively parallel read mapping on GPUs with the q-group index and PEANUT
    2 citations
    687 downloads
    2,648 views
    Johannes Köster, Sven Rahmann
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj.606 PubMed 25289191
    August 14, 2014
    Recent genome reduction of Wolbachia in Drosophila recens targets phage WO and narrows candidates for reproductive parasitism
    17 citations
    582 downloads
    3,417 views
    Jason A. Metcalf, Minhee Jo, Sarah R. Bordenstein, John Jaenike, Seth R. Bordenstein
    evolutionary-studies
    genomics
    https://doi.org/10.7717/peerj.529 PubMed 25165636
    August 14, 2014
    Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation
    11 citations
    472 downloads
    3,377 views
    Alex M. Clark, Barry A. Bunin, Nadia K. Litterman, Stephan C. Schürer, Ubbo Visser
    bioinformatics
    computational-science
    https://doi.org/10.7717/peerj.524 PubMed 25165633

    Signed reviews submitted for articles published in PeerJ Note that some articles may not have the review itself made public unless authors have made them open as well.

    November 24, 2016
    Mining SNPs in extracellular vesicular transcriptome of Trypanosoma cruzi: a step closer to early diagnosis of neglected Chagas disease
    2 citations
    347 downloads
    3,229 views
    Pallavi Gaur, Anoop Chaturvedi
    bioinformatics
    computational-biology
    infectious-diseases
    https://doi.org/10.7717/peerj.2693 PubMed 27904804
    March 10, 2016
    Effects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati
    556 downloads
    1,574 views
    Norhayati Yaacob, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Nor Aini Abdul Rahman
    biochemistry
    biotechnology
    https://doi.org/10.7717/peerj.1751 PubMed 26989608
    December 21, 2015
    Genome-wide identification of hypoxia-induced enhancer regions
    1 citation
    438 downloads
    2,146 views
    Nick Kamps-Hughes, Jessica L. Preston, Melissa A. Randel, Eric A. Johnson
    biotechnology
    genomics
    https://doi.org/10.7717/peerj.1527 PubMed 26713262
    November 19, 2015
    Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data
    4 citations
    646 downloads
    5,178 views
    Jose E. Kroll, Jihoon Kim, Lucila Ohno-Machado, Sandro J. de Souza
    bioinformatics
    computational-biology
    molecular-biology
    https://doi.org/10.7717/peerj.1419 PubMed 26618088

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