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Cindy Duarte Castelão

Cindy received a Biomedical degree in 2011, and a MsC in Molecular Biology and Genetics in 2011. Her career so far has been in the Molecular Genetics field, working closely with deep-sequencing techniques, and how these techniques can help to unveil the secrets of the genome and epigenome. Join me in uncovering the mystery. Publications by Cindy Duarte Castelão

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Articles by Cindy Duarte Castelão

DNA sequence MLPA

Multiplex Ligation-dependent Probe Amplification (MLPA)

By Cindy Duarte Castelão | December 27, 2018

Multiplex ligation-dependent probe amplification (MLPA) is a molecular technique developed by MRC-Holland back in 2002. In a nutshell, MLPA is a sensitive technique that allows quantification of nucleic acid sequences, quickly and efficiently. It is performed in many laboratories worldwide, and can be applied to detect copy number changes (like deletions or duplications) of a…

DNA sequence

Studying the Epigenome by Next Generation Sequencing

By Cindy Duarte Castelão | December 14, 2018

The epigenome has been in the research spotlight, and for good reason. Not only has it been associated with the developmental stages of an organism, but epigenetic alterations lead to disorders and have been linked to many human diseases. So, the question stands: what exactly is an epigenome? What Is the Epigenome? Simply put, the…

Using dbSNP and ClinVar to Classify Gene Variants

Using dbSNP and ClinVar to Classify Gene Variants

By Cindy Duarte Castelão | October 18, 2018

As we discussed previously, the gaps in our understanding of the human genome make variant classification an extremely difficult job. However, with each passing day our knowledge increases, and the tools to help us become increasingly more efficient. Let’s pick up where we left off in our first article about variants. After checking Ensemble to…

Small child hiding in hallway, playing hide and seek

A Beginner’s Guide to Single-Cell RNA Sequencing

By Cindy Duarte Castelão | May 18, 2018

Since our early steps in Science we have been told that every cell in our body has the exact same genetic information (minus one or two alterations). Therefore, the great variety of cells in our body comes from gene expression – each cell must express one set of genes and repress another set to function…

How to Use Ensembl to Classify Gene Variants

How to Use Ensembl to Classify Gene Variants

By Cindy Duarte Castelão | January 2, 2018

Even though our knowledge about genomes grows daily, and in huge leaps, we sometimes need to remind ourselves that DNA was first isolated in 1869 and its molecular structure was only identified in 1953. The PCR reaction only hit the scientific community as recently as 1983! So even though we are growing fast, we are…

How to Survive a Difficult PCR

How to Survive a Difficult PCR

By Cindy Duarte Castelão | October 12, 2017

I am sure many of you have been there. Everything is going smoothly, and your project seems to be working out perfectly. And then there is this one PCR. For some reason, it just won’t work. It is a black dot on your record. Even though I have a scientific mind, I have to be…

Next Gen Sequencing Challenges

By Cindy Duarte Castelão | September 5, 2017

Next generation sequencing opened the doors to our genome. It gives massive amounts of information in a week – whereas Sanger sequencing takes thrice as long, and causes lab lesions due to the abusive use of pipettes. Indeed, with minimal hands-on procedures we obtain a lot of data. But nothing in Science is ever easy.…

maxam-gilbert sequencing

Maxam-Gilbert Sequencing: What Was It, and Why It Isn’t Anymore

By Cindy Duarte Castelão | July 26, 2017

In the mid-1970s, two methods were developed for directly sequencing DNA: the Maxam-Gilbert sequencing (or chemical sequencing) method and the Sanger chain-termination method. Indeed, in 1980, both Walter Gilbert and Frederick Sanger were awarded The Nobel Prize in Chemistry for “their contributions concerning the determination of base sequences in nucleic acids”. Actually, each got a…

nanopore sequencing

An Introduction to Nanopore Sequencing

By Cindy Duarte Castelão | July 18, 2017

DNA sequencing is the most powerful method to reveal genetic variations at the molecular level, leading to a better understanding of our body in physiological settings, and pathological conditions. It is the beginning of the long road towards better diagnostics and personalized medicine. Even though there have been great advances in DNA sequencing technologies there…

oligo purification

Oligo Purification Methods: How, Why and for What?

By Cindy Duarte Castelão | July 18, 2017

Who amongst us hasn’t had the need for oligonucleotides in an experiment? It is a cornerstone in many procedures and techniques. Depending on the goal, it can be very hard to design just the right oligo for your experiment.  Oligos must have the right length; the right amount of C-G, T-A; they can’t form secondary…

deep sequencing

Demystifying NGS: Depth Coverage and Deep Sequencing

By Cindy Duarte Castelão | April 18, 2017

NGS is not a three-headed monster. However, it can be a difficult concept to grasp—especially when you are getting started.  There is a lot of new terminology, and a whole new world to discover: both in the lab bench and in interpreting your results. It helps to start somewhere. So, let’s start! Depth of Coverage…


How to Focus When Your Colleagues Are Wreaking Havoc Around You

By Cindy Duarte Castelão | March 29, 2017

Now, we all love our colleagues – true, some are more loveable than others, but still. However, sometimes they can be very noisy. Especially when you need to focus.  For example, when you are in the middle of some important breakthrough, or trying to decipher a cryptic, but important paper. If you work in a…

Variations on the ChIP-seq Theme and Challenges of Befriending Large Datasets

Variations on the ChIP-seq Theme and Challenges of Befriending Large Datasets

By Cindy Duarte Castelão | January 31, 2017

ChIP-seq has proved amazing. Through these new techniques, we can obtain big datasets in a matter of days, making our lives in the lab easier and more efficient. ChiP-seq combines chromatin immunoprecipitation (ChIP) assays with whole genome sequencing. This makes it possible to understand where proteins bind to DNA and epigenetic modifications. Humans are not only their…

7 Tips for using Magnetic Beads for DNA Cleanup

7 Tips for using Magnetic Beads for DNA Cleanup

By Cindy Duarte Castelão | November 3, 2016

Whatever molecular biology techniques you use, at some point you will have to clean up your DNA samples to remove things like buffers, contaminants and nucleotides from you precious sample, so that you have perfectly pure DNA for your downstream experiments. Magnetic beads are one DNA cleanup option. They are simple and effective—and their reassuringly…

new laboratory group

How to Fit in With a New Laboratory Group

By Cindy Duarte Castelão | July 9, 2016

Change is never easy, especially when you are trying to fit in with a new laboratory group. Here are some tips to make your transition bearable. Or even pleasant.

PhD topic

How to Choose a PhD Topic

By Cindy Duarte Castelão | July 9, 2016

Choosing a PhD topic can be very hard. There are a lot of things to consider from the subject to the supervisor. Here are some tips to help you choose. Find out what you really like This is the first topic because it is the most important. My first advice would be to get some…

Want NGS Success? Consider These Three Factors

Want NGS Success? Consider These Three Factors

By Cindy Duarte Castelão | July 9, 2016

NGS is still something a little scary for most operators. Mainly because of the price, which can make the pipette, in the hand of the best of us, shake a little with fear. And even though the protocols have a tendency for getting simpler, faster, and more appropriate for a routine, there are still crucial…

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