MediaWiki API result

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            "*": "Subscribe to the mediawiki-api-announce mailing list at <https://lists.wikimedia.org/mailman/listinfo/mediawiki-api-announce> for notice of API deprecations and breaking changes."
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            "19": {
                "pageid": 19,
                "ns": 0,
                "title": "Recent News",
                "revisions": [
                    {
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                        "*": "'''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''\n\n'''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''  I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.\n\n'''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''\n\n'''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''\n\n'''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''\n\n'''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''\n\n'''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''\n\n'''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''\n\n'''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''\n\n'''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''\n\n'''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]'''  I put this here because K-C Chou wrote <b>many</b> papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below.  Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]'''  I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals.  Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles.  For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return.  The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.\nThe scientific publishing industry has been manipulated by their lack of attention to these problems.   If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]'''  over '''[https://scholar.google.com/scholar?hl=en&as_sdt=0%2C21&q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons.  The list of these journals is clear from the citation patterns.\n\n'''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]'''   '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''\n\nDon't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''\n'''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''\n'''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''\n'''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''\n'''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''\n\n'''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''\n\n'''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''\n\n'''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''\n\n'''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on \"The Dark Side of the Human Genome\"]'''\n\n'''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''\n\n'''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''\n\n'''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''\n\n'''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News & Views article on our deltaSVM paper]'''\n\n'''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''\n\n'''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''\n\n'''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''\n\n'''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''\n\n'''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/  Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''\n\n'''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/   kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''\n\n'''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html  Dongwon Lee awarded Young Investigator Day Award.] '''"
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                "title": "Research Interests",
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                        "*": "The ultimate goal of our research is to understand how genomic DNA sequence specifies gene regulation. We are currently focused on 1) developing computational tools to identify functional regulatory elements in non-coding DNA, and 2) experimentally testing and characterizing how these elements function.\n\nIn our computational work, we are using microarray gene expression data, genome-wide location analysis, and whole-genome DNA sequence to systematically identify DNA functional elements and infer combinatorial regulatory logic. We use pattern recognition algorithms to identify over-represented and phylogenetically conserved DNA sequence elements (or putative transcription factor binding sites). We then use a probabilistic Bayesian network to find the most likely functional constraints on the position, spacing, orientation, and combinations of these DNA sequence elements. This methodology has generated a large set of high confidence predictions for regulatory interactions, and is in principle applicable to any organism with microarray and genome sequence data.\n\nIn our experimental work, we are testing these computational predictions by rapid generation of transgenic GFP reporter strains in C. elegans via microparticle bombardment. C. elegans is an attractive model system for several reasons:\n\n* Relevance to human disease: About 60% of C. elegans genes have a human homologue (Harris et al., NAR 2004); and 80% of genes implicated in human cancer have a worm homologue (Futreal et al., Nat Rev Cancer 2004; Poulin et al, Oncogene 2004).\n* The high quality of the genome sequence data and microarray tools.\n* Rapid and effective transformation techniques and GFP reporter assays.\n* Availablity of bacterial feeding library for genome wide RNAi screens to further characterize regulatory interactions.\n* Relative ease and cost of strain maintenance."
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