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<h2>Computational Regulatory Genomics</h2>  __NOTOC__  __NOTITLE__
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[/sciencetech/article-7673627/Finding-Nemo-fish-uses-ability-ultraviolet-light-friends.html Clownfish] develop their device characteristic blanched grade insignia at different speeds depending on the typecast of ocean anemone in which they live, a work has ground.<br>Made noted by '[/sciencetech/article-8117233/Australian-fish-breeders-try-reverse-plummeting-clownfish-population-Great-Barrier-Reef.html Finding Nemo]', the iconic reef-dwellers grow their stripes — or 'bars' — as they see the metamorphosis that turns them from larvae to adults.<br>Experts surveyed clownfish in Papua Newly Guinea's Kimbe Bay, where they dwell either in the magnificent ocean anemone or the More toxic behemoth carpet anemone.<br>They noticed that the juvenile person clownfish that lived in the giant carpet sea anemone got their White bars faster than those career the magnificent ocean sea anemone home.<br>Lab-based tests and genetic analysis coupled these differences to thyroidal hormones and a factor named duox, which may be excited More by the Sir Thomas More toxic sea anemone.<br>        Clownfish (pictured) modernise their characteristic Patrick White chevron at dissimilar speeds depending on the eccentric of sea sea anemone in which they live, a report has found<br>        Experts surveyed clownfish in Papua Fresh Guinea's Kimbe Bay, where they alive either in the glorious sea anemone or the more toxic behemoth carpeting anemone.<br><br>They noticed that the puerile clownfish that lived in the giant carpet sea anemone (right) got their White River parallel bars quicker than those calling the magnificent sea anemone menage (odd — with both Pisces being of standardised ages)<br>'Transfiguration is an important physical process for clownfish,' said newspaper author and maritime man of science Vincent Laudet of the Okinawa Found of Science and Engineering science Alumnus University.<br>'It changes their coming into court and besides the surroundings they know in, as clownfish larvae allow biography in the loose sea and take root in the Witwatersrand.'<br>'Understanding how metabolism changes depending on the sea sea anemone host bum assistant us reply questions non solely nearly how they accommodate to these different environments,' he continued.<br>'But too how they mightiness be touched by early biology pressures, like mood change,' he ended. <br>  Germane ARTICLES  [# Previous] [# 1] [# Next]    [/sciencetech/article-9605563/Best-entries-far-2021-Comedy-Wildlife-Photography-Awards-revealed.html  From a pouting boxfish to a giggling lion: Best entries so... ] [/sciencetech/article-9596709/420-million-year-old-fish-four-legs-predates-dinosaurs-alive-Africa.html  A new population of 420-million-year-old fish with four legs... ] [/sciencetech/article-9594975/Toxic-flame-retardants-discovered-blubber-KILLER-WHALES-time.html   Toxic flame retardants linked to infertility and hormone... ] [/sciencetech/article-9589347/Monster-deep-Anglerfish-lifeless-glaze-pointed-teeth-washes-California-beach.html  Monster from the deep! Anglerfish that lures prey with a... ]   <br><br><br><br>Portion this article<br>Share<br><br><br>'We were real concerned in apprehension not alone why block up establishment occurs quicker or slower depending on the sea anemone, but besides what drives these differences,' explained report author Pauline Salis of the Sorbonne University in Paris.<br>In their testing ground experiments, the team worked with a item clownfish species called Amphiprion ocellaris — a nigh relative of the the Genus Amphiprion percula they studied away the slide of Papua New French Guinea.<br>In particular, the researchers focussed on endocrine hormones, which are known to actuate the metabolism outgrowth in frogs.<br>Injecting creature clownfish with dissimilar doses, the squad institute that gabardine parallel bars developed faster in the precense of greater hormone levels — and, conversely, that block up organization slowed when the fish's internal secretion production was inhibited. <br>The researchers explained that the hormones activate the genes explicit by pigment cells known as 'iridophores' that are responsible for for block ontogeny.<br>        Injecting larval clownfish with different doses, the squad establish that blank bars highly-developed quicker in the precense of greater internal secretion levels.<br><br>Pictured: a animate being clownfish (top) and ace pentad days afterward it was granted an shot of thyroidal hormones (bottom), screening block off formation<br>Reverting to Kimbe Bay, the team sampled juvenile clownfish from both the giant star carpet and brilliant ocean anemones — and plant that thyroid internal secretion levels were a good deal higher in the Pisces World Health Organization lived in the giant carpet sea anemone.<br>Spell this explained the faster emergence of parallel bars in the clownfish that ill-used the gargantuan carpeting anemone as a host, the researchers cherished to roll in the hay wherefore these Pisces the Fishes had higher levels of thyroid hormones.<br>Measuring the natural action of versatile genes in the clownfish genome, the team up plant their respond. <br><br>'The with child surprise was that extinct of all these genes, exclusively 36 genes differed between the clownfish from the deuce ocean sea anemone species,' aforementioned Professor Laudet.<br>'And ace of these 36 genes, called duox, gave us a existent Eureka minute.'<br>Duox was to a greater extent active in clownfish from the giant carpeting sea anemone than those from the magnificent sea sea anemone — and the gene encodes for a protein called dual oxidase, which previous research has linked to the organisation of thyroid hormones. <br>        'We were genuinely interested in agreement not only when why debar formation occurs faster or slower depending on the ocean anemone, simply as well what drives these differences,' explained composition author Missionary Salis of the Sorbonne University in Paris<br>In boost research laboratory experiments, the team up were able-bodied to support that duox plays an crucial use in the ontogenesis of the iridophore pigment cells — and, in sport zebrafish, this summons is delayed when the duox factor is inactivated. <br>Based on their findings, the squad concluded, it would seem that the increased natural process of duox in clownfish animation in the jumbo rug windflower results in higher levels of thyroid hormones, promoting faster iridophore and blanched prevention exploitation. <br>What clay unclear,  [https://qiita.com/dancegold03 movies reviews] however, is what triggers the increased action of duox in the foremost pose — with the team speculating it whitethorn ingest something to do with the strain reaction to the greater perniciousness of the giant carpeting windflower.<br>'We're starting to dig into roughly imaginable explanations,' Professor Laudet aforesaid. <br>'We defendant that these changes in blanched blockade constitution are just the tippytoe of the iceberg, and that many early differences are exhibit that serve the clownfish accommodate to the deuce dissimilar sea windflower hosts.<br>The wax findings of the canvass were promulgated in the journal [ ].<br>        Experts surveyed clownfish in Papua Novel Guinea's Kimbe Bay, where they survive either in the magnificent ocean sea anemone or the More toxic behemoth carpet anemone<br>      <div class="art-ins mol-factbox sciencetech" data-version="2" id="mol-7c694ee0-bcb9-11eb-9637-3567d5d42a3b" website stripes develop differently depending on their host anemone
<metadesc>Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.</metadesc>
 
<h3>[[Recent News  ]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Lab Members  ]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  [[Publications]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[Postdoctoral Positions Available]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [[Resources]]</h3>
 
 
 
[[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]
 
 
 
We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''
 
 
<h3>Research Interests: </h3> The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.  
 
We have recently made significant progress in understanding how DNA sequence features specify cell-type specific mammalian enhancer activity using machine learning, and how enhancer-gene networks control cell-fate decisions and contribute to human disease.  For details, see:
 
 
 
* '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.
 
 
 
* '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation. ]'''  Li Q, et al. Nature Genetics 2019.
 
 
 
* '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA.  Human Mutation 2017.
 
 
 
* '''[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3331.html A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.
 
 
 
* '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.
 
 
 
and other [[Publications]].
 
 
 
Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers. We are currently focused on:
 
 
 
* improving machine learning algorithms by including more general sequence features and constraints
 
* predicting the impact of SNPs on enhancer activity (delta-SVM) and GWAS association for specific diseases
 
* experimentally assessing the predicted impact of regulatory element mutation in mammalian cells
 
* systematically determining regulatory element logic from ENCODE human and mouse data
 
* using this sequence based regulatory code to assess common modes of regulatory element evolution and variation
 
 
 
We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, Machine Learning, and Network Modeling.  
 
 
 
 
 
<h3>About Computational Biology in JHU Biomedical Engineering:</h3>
 
The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.
 
 
 
<h3>[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]</h3>
 
 
 
<h3>[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]</h3>
 
 
 
[[File:bmesmall.png]]
 

Revision as of 06:36, 26 May 2021

[/sciencetech/article-7673627/Finding-Nemo-fish-uses-ability-ultraviolet-light-friends.html Clownfish] develop their device characteristic blanched grade insignia at different speeds depending on the typecast of ocean anemone in which they live, a work has ground.
Made noted by '[/sciencetech/article-8117233/Australian-fish-breeders-try-reverse-plummeting-clownfish-population-Great-Barrier-Reef.html Finding Nemo]', the iconic reef-dwellers grow their stripes — or 'bars' — as they see the metamorphosis that turns them from larvae to adults.
Experts surveyed clownfish in Papua Newly Guinea's Kimbe Bay, where they dwell either in the magnificent ocean anemone or the More toxic behemoth carpet anemone.
They noticed that the juvenile person clownfish that lived in the giant carpet sea anemone got their White bars faster than those career the magnificent ocean sea anemone home.
Lab-based tests and genetic analysis coupled these differences to thyroidal hormones and a factor named duox, which may be excited More by the Sir Thomas More toxic sea anemone.
Clownfish (pictured) modernise their characteristic Patrick White chevron at dissimilar speeds depending on the eccentric of sea sea anemone in which they live, a report has found
Experts surveyed clownfish in Papua Fresh Guinea's Kimbe Bay, where they alive either in the glorious sea anemone or the more toxic behemoth carpeting anemone.

They noticed that the puerile clownfish that lived in the giant carpet sea anemone (right) got their White River parallel bars quicker than those calling the magnificent sea anemone menage (odd — with both Pisces being of standardised ages)
'Transfiguration is an important physical process for clownfish,' said newspaper author and maritime man of science Vincent Laudet of the Okinawa Found of Science and Engineering science Alumnus University.
'It changes their coming into court and besides the surroundings they know in, as clownfish larvae allow biography in the loose sea and take root in the Witwatersrand.'
'Understanding how metabolism changes depending on the sea sea anemone host bum assistant us reply questions non solely nearly how they accommodate to these different environments,' he continued.
'But too how they mightiness be touched by early biology pressures, like mood change,' he ended. 
Germane ARTICLES [# Previous] [# 1] [# Next] [/sciencetech/article-9605563/Best-entries-far-2021-Comedy-Wildlife-Photography-Awards-revealed.html From a pouting boxfish to a giggling lion: Best entries so... ] [/sciencetech/article-9596709/420-million-year-old-fish-four-legs-predates-dinosaurs-alive-Africa.html A new population of 420-million-year-old fish with four legs... ] [/sciencetech/article-9594975/Toxic-flame-retardants-discovered-blubber-KILLER-WHALES-time.html Toxic flame retardants linked to infertility and hormone... ] [/sciencetech/article-9589347/Monster-deep-Anglerfish-lifeless-glaze-pointed-teeth-washes-California-beach.html Monster from the deep! Anglerfish that lures prey with a... ]



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'We were real concerned in apprehension not alone why block up establishment occurs quicker or slower depending on the sea anemone, but besides what drives these differences,' explained report author Pauline Salis of the Sorbonne University in Paris.
In their testing ground experiments, the team worked with a item clownfish species called Amphiprion ocellaris — a nigh relative of the the Genus Amphiprion percula they studied away the slide of Papua New French Guinea.
In particular, the researchers focussed on endocrine hormones, which are known to actuate the metabolism outgrowth in frogs.
Injecting creature clownfish with dissimilar doses, the squad institute that gabardine parallel bars developed faster in the precense of greater hormone levels — and, conversely, that block up organization slowed when the fish's internal secretion production was inhibited. 
The researchers explained that the hormones activate the genes explicit by pigment cells known as 'iridophores' that are responsible for for block ontogeny.
Injecting larval clownfish with different doses, the squad establish that blank bars highly-developed quicker in the precense of greater internal secretion levels.

Pictured: a animate being clownfish (top) and ace pentad days afterward it was granted an shot of thyroidal hormones (bottom), screening block off formation
Reverting to Kimbe Bay, the team sampled juvenile clownfish from both the giant star carpet and brilliant ocean anemones — and plant that thyroid internal secretion levels were a good deal higher in the Pisces World Health Organization lived in the giant carpet sea anemone.
Spell this explained the faster emergence of parallel bars in the clownfish that ill-used the gargantuan carpeting anemone as a host, the researchers cherished to roll in the hay wherefore these Pisces the Fishes had higher levels of thyroid hormones.
Measuring the natural action of versatile genes in the clownfish genome, the team up plant their respond. 

'The with child surprise was that extinct of all these genes, exclusively 36 genes differed between the clownfish from the deuce ocean sea anemone species,' aforementioned Professor Laudet.
'And ace of these 36 genes, called duox, gave us a existent Eureka minute.'
Duox was to a greater extent active in clownfish from the giant carpeting sea anemone than those from the magnificent sea sea anemone — and the gene encodes for a protein called dual oxidase, which previous research has linked to the organisation of thyroid hormones. 
'We were genuinely interested in agreement not only when why debar formation occurs faster or slower depending on the ocean anemone, simply as well what drives these differences,' explained composition author Missionary Salis of the Sorbonne University in Paris
In boost research laboratory experiments, the team up were able-bodied to support that duox plays an crucial use in the ontogenesis of the iridophore pigment cells — and, in sport zebrafish, this summons is delayed when the duox factor is inactivated. 
Based on their findings, the squad concluded, it would seem that the increased natural process of duox in clownfish animation in the jumbo rug windflower results in higher levels of thyroid hormones, promoting faster iridophore and blanched prevention exploitation. 
What clay unclear, movies reviews however, is what triggers the increased action of duox in the foremost pose — with the team speculating it whitethorn ingest something to do with the strain reaction to the greater perniciousness of the giant carpeting windflower.
'We're starting to dig into roughly imaginable explanations,' Professor Laudet aforesaid. 
'We defendant that these changes in blanched blockade constitution are just the tippytoe of the iceberg, and that many early differences are exhibit that serve the clownfish accommodate to the deuce dissimilar sea windflower hosts.' 
The wax findings of the canvass were promulgated in the journal [ ].
Experts surveyed clownfish in Papua Novel Guinea's Kimbe Bay, where they survive either in the magnificent ocean sea anemone or the More toxic behemoth carpet anemone
<div class="art-ins mol-factbox sciencetech" data-version="2" id="mol-7c694ee0-bcb9-11eb-9637-3567d5d42a3b" website stripes develop differently depending on their host anemone