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Epigenetics
non-coding RNA
Synthetic Biology
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Conference Highlights

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dnam

Book Review: Epigenetics – Current Research and Emerging Trends

Edited by Brian P. Chadwick and composed of 17 chapters from thought leaders in academia and industry, this is one text you don’t want to miss. It covers a wide breadth of topics ranging from DNA methylation to Chromatin to ncRNA, with insight from across the tree of life and related human disorders. The perspective […]

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dnam

5fC is Stable in Mammalian Brains

DNA methylation has been undergoing dramatic change lately. 6mA shook things up by showing Cytosine can’t claim all the glory and now a talented team from the UK have shown 5-formylcytosine (5fC) is starting to follow in 5hmC’s independent footsteps. The team profiled 5hmC, 5fC, and 5caC using: in vivo isotope labeling of methionine to penetrate […]

read more...
synb

Gene Editing Future Brightens with paCas9

We knew it was coming.  No, not another Jurassic Park sequel.  No, not another installment of Star Wars.  More inevitable than the revival of the Terminator franchise: we now have photoactivatable CRISPR/Cas9. Yes, as surely as the sun rises, scientists have developed a way to use that light (or at least the blue part) to […]

read more...
stem

Stem Cell Reprogramming – Leaner, Quicker, Cheaper, Better

“More for less” is a phrase that generally gets most people excited, and scientists trying to make induced pluripotent stem cells (iPSCs) are no exception. The reprogramming of somatic cells to generate iPSCs aims to bring patient-specific cell replacement therapies to the masses, but the process currently suffers from obstacles common to new technologies – […]

read more...
stem

Nukes Aid Stem Cell Research in the Heart

Researchers from the laboratory of Jonas Frisén at the Karolinska Institutet in Sweden have recently put radioactive carbon from nuclear bomb tests to good use, testing whether the adult human heart has the ability to repair itself. So how does that work? Well, a sharp rise in atmospheric radioactive carbon in the 1950-60s due to […]

read more...
tech

Advances in ChIP-based Technologies for Profiling Epigenomic Landscapes and Gene Regulatory Networks

Abstract: Gene expression is regulated by a combination of transcription factor binding and the distribution of epigenetic modifications across regulatory regions. Much of what we know about the epigenome and gene regulation stems from our ability to determine the genome-wide distribution of histone modifications and transcription factors using chromatin immunoprecipitation followed by next generation sequencing […]

read more...
tech

Locus-Specific Biochemical Analysis of Genome Functions Using enChIP with CRISPR

Abstract Elucidation of molecular mechanisms of genome functions such as transcription and epigenetic regulation requires identification of components mediating the genome functions. To this end, we recently developed the locus-specific chromatin immunoprecipitation (ChIP) (locus-specific ChIP) technologies to identify molecules interacting with a given genomic region of interest in vivo. Locus-specific ChIP consists of insertional ChIP […]

read more...
stem

KeyGenes Helps Predict Differentiated Humans iPSCs

Cells differentiated from embryonic stem cells are generally phenotypically immature, so identifying what cell type they are can be a bit like trying to figure out what exactly the picture your child drew for you in kindergarten is supposed to be. “That’s lovely darling but…” Luckily, for biologists at least, a team of Dutch researchers […]

read more...
dnam

CpH Methylation Gets A Tissue Specific Makeover

In the latest show of the power of teamwork we see some of the biggest names in epigenetics join forces to unravel the mysteries of the methylome across different tissues, including the molecular cartographers who tackled the brain and the researchers who brought forth the predictive powers of Epigram. The talented team from the Salk Institute and UCSD have […]

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chr

A TAD of Disruption Shows the Importance of Boundaries

If you’ve ever seen a polydactyl cat you might (understandably) live in fear of cats with thumbs. If we want to prevent the takeover by our feline friends we need to understand the cause of this limb anomaly. Luckily, researchers led by Stefan Mundlos have done just that by asking if 3D chromosome structure data […]

read more...

Epigenetics

dnam

5fC is Stable in Mammalian Brains

DNA methylation has been undergoing dramatic change lately. 6mA shook things up by showing Cytosine can’t claim all the glory and now a talented team from the UK have shown 5-formylcytosine (5fC) is starting to follow in 5hmC’s independent footsteps. The team profiled 5hmC, 5fC, and 5caC using: in vivo isotope labeling of methionine to penetrate […]

read more...
tech

Advances in ChIP-based Technologies for Profiling Epigenomic Landscapes and Gene Regulatory Networks

Abstract: Gene expression is regulated by a combination of transcription factor binding and the distribution of epigenetic modifications across regulatory regions. Much of what we know about the epigenome and gene regulation stems from our ability to determine the genome-wide distribution of histone modifications and transcription factors using chromatin immunoprecipitation followed by next generation sequencing […]

read more...
tech

Locus-Specific Biochemical Analysis of Genome Functions Using enChIP with CRISPR

Abstract Elucidation of molecular mechanisms of genome functions such as transcription and epigenetic regulation requires identification of components mediating the genome functions. To this end, we recently developed the locus-specific chromatin immunoprecipitation (ChIP) (locus-specific ChIP) technologies to identify molecules interacting with a given genomic region of interest in vivo. Locus-specific ChIP consists of insertional ChIP […]

read more...
dnam

CpH Methylation Gets A Tissue Specific Makeover

In the latest show of the power of teamwork we see some of the biggest names in epigenetics join forces to unravel the mysteries of the methylome across different tissues, including the molecular cartographers who tackled the brain and the researchers who brought forth the predictive powers of Epigram. The talented team from the Salk Institute and UCSD have […]

read more...
chr

A TAD of Disruption Shows the Importance of Boundaries

If you’ve ever seen a polydactyl cat you might (understandably) live in fear of cats with thumbs. If we want to prevent the takeover by our feline friends we need to understand the cause of this limb anomaly. Luckily, researchers led by Stefan Mundlos have done just that by asking if 3D chromosome structure data […]

read more...
chr

Could Chromatin Organization be the Key to Eternal Youth?

For thousands of years great men such as Alexander the Great and Ponce de León have searched far and wide in their search for the fountain of youth and the hope of eternal life. But where they previously failed, an enterprising group of scientists may have now just succeeded! A report published recently in Science […]

read more...
dnam

Twins Team Up to Help Unravel DNA Methylation in Schizophrenia

While they can’t see through lead or stop bullets with their chest, twins do have a superpower of their own – when it comes to unraveling the complex genomic and epigenomic changes underlying diseases and disorders. In their latest adventure monozygotic twins are helping to understand the DNA methylation changes associated with schizophrenia. The epigenomics of […]

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stem

A TET-à-TET Between SIRT6 and 5hmC Controls Embryonic Stem Cell Fate

With many political parties fighting it out for influence in the UK general election last week, it is nice to see the spirit of cooperation alive and well in embryonic stem cells. In their latest study, Raul Mostoslavsky and colleagues show that two giants of epigenetic regulation, histone acetylation and DNA hydroxymethylation, team up to […]

read more...
dnam

6mA Makes the Grade as a Eukaryotic Epigenetic Mark

There’s no denying that we love DNA methylation, so we are delighted to learn of another form of DNA methylation that has come on the scene as an epigenetic mark. N6-Methyladenosine (6mA or m6A) refers to the methylation of adenosine at its nitrogen-6 position, as opposed to 5mC and related oxidative marks (5hmC, 5fC, 5caC) that occur on […]

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dnam

Upcycling the Epigenome in the Brain Help Neurons Stay in Touch

Upcycling is the latest of many green crazes where people keep hold of old furniture and instead of throwing it away, they repurpose it to give new life. It seems that the brain might be doing the same for methylation. It’s been a long held belief that DNA methylation is fixed in differentiated cells, yet there is […]

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non-coding RNA

ncrna

miRNA-Switches Makes Stem Cell Selection Pure and Simple

As any sports coach, hopeful lottery winner, or child in a candy store will tell you, an effective selection strategy is vitally important to a successful outcome. Selection is also an important concept for scientists and clinicians hoping to take advantage of the ability that human pluripotent stem cells (hPSCs) have to differentiate into multiple […]

read more...
ncrna

Get in the Loop of Antisense Mediated Transcriptional Regulation

Long non-coding RNA research isn’t just a load of HOTAIR; since their initial discovery long non-coding RNAs have revealed their importance in regulating the genome. One such insight is the observation that lncRNA express antisense transcripts, which are abundantly found either partially or completely overlapping with transcripts from the opposite strand. These have been shown […]

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ncrna

Novel Primate- and Tissue Specific miRNAs with Dr Isidore Rigoutsos

In this interview Dr Isidore Rigoutsos discusses his recent paper ‘Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs‘ published in PNAS, February 2015. This paper shows the presence of many more miRNAs than previously thought and uncovers that the majority of these are in fact, cell-type […]

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chr

A cHi-C Way of Capturing Chromatin Conformation

Identifying cancer risk loci is like trying to find a key you lost somewhere in your apartment. You know that it’s there and by combining experience with indistinct recollection you can even narrow it down to a few square meters. Now imagine you not only have to find the key but also map all the […]

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ncrna

Gene Expression Comes Full CircRNA

Circular RNAs (circRNAs) are a diverse RNA species that regulate gene expression in some funky ways, like functioning as super absorbent miRNA sponges in mammalian cells. However, they also seem to be particularly relevant to the brain. Recent research adds a new function to this ‘outside of the box’ method of regulating gene expression by observing circRNAs […]

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ncrna

m6Ajor New Function for MicroRNAs in RNA Methylation

It’s no secret that microRNAs are pretty busy molecules. A single microRNA can regulate the expression of several, maybe even hundreds, of transcripts. If that wasn’t enough, researchers at the Chinese Academy of Sciences, Beijing now add another function to this packed list of duties: the control of m6A RNA methylation, which is emerging as an […]

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ncrna

Expressed Long Non-coding RNAs Snitch on Tissue-specific Enhancers

Predicting tissue-specific enhancers is a tricky business. While histone marks such as H3K4me1 and binding of p300 are good enhancer predictors, pointing out which enhancers are tissue-specific is more of a challenge. That is, of course, unless you have PreSTIGE – an algorithm developed by the Scacheri lab that identifies tissue-specific enhancers by combining H3K4me1 […]

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ncrna

From Neuron to Germline: Inheritance by Mobile RNAs

We’ve got transgenerational epigenetic inheritance on the mind and now strangely enough it seems that the mind also causes transgenerational epigenetic inheritance?! Researchers have just shown the strangest case of inheritance yet: soma to germline. A talented team from the University of Maryland have been tracing double stranded RNA (dsRNA) in C. elegans and have made some interesting observations […]

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stem

Plotting the Path to Pluripotency Uncovers Key Role of DNA Methylation

If you’ve read our recent piece ‘Reprogramming Roadmap Reveals Fuzzy New Stem Cells‘ you’ll already know how “Project Grandiose” [1, 2], the brainchild of Andras Nagy, identified a new pluripotent state (the F-class  stem cell). While the discovery of this new class is thrilling, the main purpose of this grand project was to uncover the […]

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stem

A “Grandiose” Project Provides a Fuzzy New Future for iPSC Research

Induced pluripotent stem cell (iPSCs) research burst on to the scene in 2006 with a paper which has since spawned thousands of studies and has proved to be a quantum leap for regenerative medicine. This reached a crescendo this year when a Japanese patient became the first recipient of retinal cells generated from iPSCs made […]

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Synthetic Biology

synb

Gene Editing Future Brightens with paCas9

We knew it was coming.  No, not another Jurassic Park sequel.  No, not another installment of Star Wars.  More inevitable than the revival of the Terminator franchise: we now have photoactivatable CRISPR/Cas9. Yes, as surely as the sun rises, scientists have developed a way to use that light (or at least the blue part) to […]

read more...
synb

MINimize Your Genome Engineering Efforts with CRISPR and Bxb1

CRISPR is for genome engineering what Mike Tyson was for boxing: simple, efficient and almost a guarantee to see a knockout in the first round.  While in boxing a knockout typically results in an involuntary power nap of the opponent, the phenotype of a gene knockout is often not so clear-cut. Besides potential problems caused […]

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synb

None Shall Pass! Genome Editing Stops Heritable Diseases in Their Tracks

The scientific world is still reeling from the news of the first genome editing of human embryos to treat genetic disease, as we have reported previously here on Epigenie. Unfortunately, the paper suggested that this strategy may need huge improvement or may never be applicable. However, another recently published study, from the laboratory of Juan Carlos […]

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synb

Spray Your Way Free of Cystic Fibrosis with a Gene Editing Nasal Spray

With allergy season around the corner, you might be turning to nasal sprays to relieve the symptoms. But now Marie Egan’s lab at Yale University have developed a very different type of nasal spray that helps overcome a disorder much more devastating: Cystic Fibrosis. Earlier attempts to correct the F508del CFTR mutation have been undertaken using CRISPRs in […]

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synb

Cas9 Gets an Illuminating Upgrade: Light-activatable Genome Editing

While dead Cas9 (dCas9) has been coupled to optogenetic systems to enable on the fly effector domain action, the not so dead Cas9 has just gotten a very different form of light induction that works with genome editing. The designer genome editing system, developed by a talented team from the University of Pittsburgh and the University of North Carolina at Chapel Hill, […]

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synb

CRISPR-Cas9 Gene Editing of Human Embryos: A Look at the Science

Unless you were on Mars or in the middle of a Netflix binge, you couldn’t have missed the paper that has been hitting the headlines all over the world this week – the first example of the genetic modification of human embryos. The study led by Junjiu Huang (Sun Yat-sen University, Guangzhou) used CRISPR-Cas9 gene […]

read more...
synb

CRISPR Goes Back to its Roots to Fight HIV

All the cool techniques people are developing with CRISPR-Cas9 are great and all, but sometimes a repurposed natural genetic system just has to go back to its roots. If CRISPR was originally a virus defense system in bacteria, why not forget about all this genome engineering whatnot for a minute and just use it to […]

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synb

Cancer Therapy Gets a Little Personal

Just like snowflakes we are all unique (at least genetically speaking), and unfortunately for modern medicine so are our cancers. This individuality in cancers, even of the same type or subtype, means that there is no single cure-all. However, researchers, like those at the from Washington University in St. Louis and The University of Oklahoma, […]

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synb

The Little Blue Pill Gets an Optogenetic Upgrade

While there’s no denying that optogenetics is one stimulating piece of biotechnology, the double entendre of optogenetics being a ‘turn on‘ has now become fact. The lab of Martin Fussenegger at ETH Zurich’s Department of Biosystems in Basel, Switzerland has developed a synthetic optogenetic technology that allows for the blue Viagra® pill to be skipped by a blue light that induces penile […]

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synb

CRISPR Gets Creative with Histone Acetylation

There’s been a lot of firsts in the world of genome editing happening lately, from its application in human embryonic stem cells,  the identification of a smaller more versatile Cas9, to its upgrade to efficiently using homology-directed repair. Now CRISPR-Cas9 is getting its feet wet with epigenome editing thanks to the clever folks in the Gersbach lab […]

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Stem Cells

stem

Stem Cell Reprogramming – Leaner, Quicker, Cheaper, Better

“More for less” is a phrase that generally gets most people excited, and scientists trying to make induced pluripotent stem cells (iPSCs) are no exception. The reprogramming of somatic cells to generate iPSCs aims to bring patient-specific cell replacement therapies to the masses, but the process currently suffers from obstacles common to new technologies – […]

read more...
stem

Nukes Aid Stem Cell Research in the Heart

Researchers from the laboratory of Jonas Frisén at the Karolinska Institutet in Sweden have recently put radioactive carbon from nuclear bomb tests to good use, testing whether the adult human heart has the ability to repair itself. So how does that work? Well, a sharp rise in atmospheric radioactive carbon in the 1950-60s due to […]

read more...
stem

KeyGenes Helps Predict Differentiated Humans iPSCs

Cells differentiated from embryonic stem cells are generally phenotypically immature, so identifying what cell type they are can be a bit like trying to figure out what exactly the picture your child drew for you in kindergarten is supposed to be. “That’s lovely darling but…” Luckily, for biologists at least, a team of Dutch researchers […]

read more...
ncrna

miRNA-Switches Makes Stem Cell Selection Pure and Simple

As any sports coach, hopeful lottery winner, or child in a candy store will tell you, an effective selection strategy is vitally important to a successful outcome. Selection is also an important concept for scientists and clinicians hoping to take advantage of the ability that human pluripotent stem cells (hPSCs) have to differentiate into multiple […]

read more...
chr

Could Chromatin Organization be the Key to Eternal Youth?

For thousands of years great men such as Alexander the Great and Ponce de León have searched far and wide in their search for the fountain of youth and the hope of eternal life. But where they previously failed, an enterprising group of scientists may have now just succeeded! A report published recently in Science […]

read more...
stem

A TET-à-TET Between SIRT6 and 5hmC Controls Embryonic Stem Cell Fate

With many political parties fighting it out for influence in the UK general election last week, it is nice to see the spirit of cooperation alive and well in embryonic stem cells. In their latest study, Raul Mostoslavsky and colleagues show that two giants of epigenetic regulation, histone acetylation and DNA hydroxymethylation, team up to […]

read more...
synb

CRISPR-Cas9 Gene Editing of Human Embryos: A Look at the Science

Unless you were on Mars or in the middle of a Netflix binge, you couldn’t have missed the paper that has been hitting the headlines all over the world this week – the first example of the genetic modification of human embryos. The study led by Junjiu Huang (Sun Yat-sen University, Guangzhou) used CRISPR-Cas9 gene […]

read more...
stem

Pioneering Transcription Factors Wiggle Towards Pluripotency

Canoes, camels, cars and catamarans have carried human pioneers far and wide; taking us to undiscovered lands to encounter unseen beauty, encouraged by the hope of fame, glory, and a lust for adventure. How pioneer transcription factors brave the inhospitable exterior of a compacted DNA-histone complex to induce transcription of tightly guarded genes is, however, […]

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stem

Human Preimplantation Embryos Go Retroviral

Our genomes are littered with tales of our evolutionary past, including infections from retroviruses that have left their mark in the vast expanses of the human genome. While most of the endogenous retroviruses (ERVs) have lost their protein coding potential, a class of human specific ERVs (HERVs) still possess intact open reading frames. Inspired by […]

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dnam

The Differentiation Race: Not all Cells Move at the Same Speed

Christoph Bock discusses his recent paper ‘Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics‘ published in Cell Reports. Epigenetic Regulation of Cell States In this first section Christoph tells us why he is interested in studying the epigenetic regulation of cell states and how his new method helps to look at the epigenetics of […]

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Conference Highlights

Name City Country Date
Name City Country Date
DNA Repair and Genome Stability within Chromatin Environments Mainz Germany 03 Jun 2015
EMBO Chromatin and Epigenetics 2015 Heidelberg Germany 02 Jun 2015
Neuroepigenetics 2015 Santa Fe USA 22 Feb 2015
microRNAs Europe Meeting 2014 Cambridge UK 03 Nov 2014
Epigenomics of Common Diseases 2014 Cambridge UK 27 Oct 2014
Epigenetic plasticity: Implications in Neural (dys)function 2014 Braga Portugal 22 Oct 2014
Chromatin and Epigenetics: From Omics to Single Cells Strasbourg France 14 Oct 2014
World Congress of Psychiatric Genetics 2014 Copenhagen Denmark 12 Oct 2014
Nuclear RNA, Gene Regulation, and Chromatin Structure (2014 IMB Conference) Mainz Germany 09 Oct 2014
Transcription and Chromatin Heidelberg Germany 23 Aug 2014
EpiCongress-Boston 2014 Boston USA 22 Jul 2014
Canadian Conference on Epigenetics: Epigenetics, Eh! 2014 London Canada 22 Jun 2014
RNA-Seq 2014 Boston USA 17 Jun 2014
Cambridge Epigenetics Symposium 2014 Babraham United Kingdom 10 Jun 2014
Linking Metabolism to Epigenetics 2014 Cambridge USA 01 May 2014
Chromatin: from Nucleosomes to Chromosomes Cambridge UK 30 Apr 2014
Long Noncoding RNAs: Marching toward Mechanism Santa Fe USA 27 Feb 2014
Cancer Epigenetics 2014 Santa Fe USA 04 Feb 2014
EpiCongress London 2013 London UK 19 Nov 2013
Chromatin Structure & Function 2013 Grand Cayman Island 11 Nov 2013
3rd Wellcome Trust Epigenomics of Common Diseases Cambridge UK 07 Nov 2013
Next-Generation Histone Deacetylase Inhibitors Boston USA 25 Sep 2013
Targeting Histone Demethylases Boston USA 25 Sep 2013
Targeting Epigenetic Readers Boston 24 Sep 2013
The Clinical Epigenome Conference San Francisco 26 Jun 2013
Chromatin and Epigenetics 2013 Heidelberg Germany 08 May 2013
Non-Coding RNA, Epigenetics and Transgenerational Inheritance Cambridge UK 11 Apr 2013
NCI Symposium on Chromosome Biology: Epigenetics in Development Bethesda, 04 Apr 2013
Epigenetic Marks and Cancer Drugs 2013 Santa Fe USA 20 Mar 2013
Epigenetics & Chromatin: Interactions and Processes 2013 Boston USA 11 Mar 2013
Noncoding RNAs in Development and Cancer 2013 Vancouver Canada 20 Jan 2013
4th World Epigenetics Summit 2012 London UK 04 Dec 2012
Epigenetics and Stem Cells 2012 Cambridge UK 16 Oct 2012
Discovery On Target – Histone Methyltransferases & Demethylases 2012 Boston USA 02 Oct 2012
10th Transcription and Chromatin 2012 Heidelberg Germany 24 Aug 2012
World Epigenetics Summit 2012 Boston USA 24 Jul 2012
Regulation of Adult Neurogenesis: From Epigenetics to Behavior Barcelona Spain 12 Jul 2012
Chromatin: From Structure to Epigenetics Strasbourg France 26 Jun 2012
Epigenetic Regulation: From Mechanism to Intervention 2012 London UK 20 Jun 2012
ISSCR Annual Meeting 2012 Yokohama Japan 13 Jun 2012
DIA-ChIP 2012 Swansea UK 11 Jun 2012
The Contribution of Epigenetics in Pediatric Environmental Health San Francisco USA 30 May 2012
Epigenetics 2012 Adelaide Australia 07 May 2012
Genomics Research 2012 Boston USA 19 Apr 2012
Epigenetic Control of Skin Development and Regeneration 2012 Bradford UK 02 Apr 2012
Non-Coding RNAs Snowbird USA 31 Mar 2012
X-Gen Congress: Epigenetics 2012 San Diego USA 05 Mar 2012
Gene Silencing by Small RNAs Vancouver Canada 07 Feb 2012
Stem Cells 2012 San Diego USA 02 Feb 2012
Epigenomics and Chromatin Dynamics Keystone USA 17 Jan 2012
2nd World Epigenetics Summit Munich Germany 14 Dec 2011
Chromatin Structure and Function 2011 Aruba 05 Dec 2011
SFN Neuroscience 2011 Meeting Highlights Washington, D.C. United States 28 Nov 2011
ESF-EMBO Epigenetics in Context: Ecology to Evolution Sant Feliu de Guixols Spain 03 Oct 2011
Epigenetics Europe 2011 Munich Germany 28 Sep 2011
A Day with Andy Feinberg Symposium Melbourne Australia 31 Aug 2011
World Epigenetics Summit 2011 Boston United States 18 Aug 2011
EMBO Conference: Chromatin and Epigenetics 2011 Heidelberg Germany 16 Jul 2011
ISSCR Annual Meeting 2011 Toronto Canada 06 Jul 2011
Epigenetic World Congress 2011 Boston USA 17 May 2011
Environmental Epigenomics and Disease Susceptibility 2011 Asheville USA 27 Mar 2011
NYAS Behavioral Epigenetics 2010 Boston USA 29 Oct 2010
Epigenetics Europe Conference 2010 Dublin Ireland 14 Sep 2010
Epigenetics and Stem Cells 2010 Copenhagen Denmark 25 Aug 2010
ISSCR 2010 San Francisco USA 16 Jun 2010
Epigenetics World Congress Boston USA 26 May 2010
CHI X Gen Congress San Diego United States 17 Mar 2010
Keystone Molecular Basis for Chromatin Structure and Regulation Taos United States 28 Feb 2010
Keystone Symposia RNA Silencing – Mechanism, Biology and Application Keystone United States 02 Feb 2010
Epigenetics 2009 Melbourne Australia 15 Dec 2009
Abcam’s Fifth Chromatin: Structure & Function Conference Guanacaste Costa Rica 01 Dec 2009
EMBO Conference on Chromatin and Epigenetics Heidelberg Germany 18 Jun 2009
Emerging Evidence for Epigenomic Changes in Human Disease Bethesda United States 25 Mar 2009