the Non-Coding RNA Group

Example Page 1

Sun, 05 May 2019 00:00:00 +0100

In this tutorial, I’ll share my top 10 tips for getting started with Academic:

Tip 1

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellus ac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. Sed ac faucibus dolor, scelerisque sollicitudin nisi. Cras purus urna, suscipit quis sapien eu, pulvinar tempor diam. Quisque risus orci, mollis id ante sit amet, gravida egestas nisl. Sed ac tempus magna. Proin in dui enim. Donec condimentum, sem id dapibus fringilla, tellus enim condimentum arcu, nec volutpat est felis vel metus. Vestibulum sit amet erat at nulla eleifend gravida.

Nullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.

Cras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.

Suspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.

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Tip 2

Example Page 2

Sun, 05 May 2019 00:00:00 +0100

Here are some more tips for getting started with Academic:

Tip 3

Tip 4

Example Talk

Sat, 01 Jun 2030 13:00:00 +0000

Click on the Slides button above to view the built-in slides feature.

Slides can be added in a few ways:

Create slides using Academic’s Slides feature and link using slides parameter in the front matter of the talk file
Upload an existing slide deck to static/ and link using url_slides parameter in the front matter of the talk file
Embed your slides (e.g. Google Slides) or presentation video on this page using shortcodes.

Further talk details can easily be added to this page using Markdown and $\rm \LaTeX$ math code.

HCMV

Sat, 10 Oct 2020 00:00:00 +0000

HCMV is present in humans with seroprevalence ranging from 45 to 96% globally (about 96% in China). HCMV infection occurs throughout the body, is always mild and asymptomatic in healthy populations, but is symptomatic or even lethal in immunocompromised/immune-immature people, such as HIV-infected patients, transplant recipients and new-borns infected in utero. The virus can enter latency after primary infection, but can be re-activated at any time.

In the general population, the immune system restricts HCMV infection to latency and is asymptomatic. However, HCMV infection causes severe diseases in immune-immature and immune-compromised patients. This includes transplant recipients, who often suffer severe complications including pneumonia, hepatitis and gastrointestinal ulcerations after transplantation. This is a consequence of their impaired immune system which allows the latent HCMV infection to be reactivated. Consequently, transplant recipients always receive pre-emptive or prophylactic antiviral therapy but nevertheless have a high risk of developing drug resistance and HCMV reactivation.

To date, no effective vaccine is available for HCMV, and only four licensed drugs (ganciclovir/valganciclovir, cidofovir and foscarnet, which all target viral DNA replication) are available. Most recently, in the US in 2017, letermovir, which targets viral DNA packaging, was licenced for prophylaxis in bone marrow patients. However, all of these drugs can cause severe side effects and, in the long-term, drug resistance inevitably occurs due to accumulation of mutations in the HCMV genome. In spite of these problems, HCMV drug resistance has not been well characterized, leaving a huge gap in options for clinical therapy and treatment.

HCMV studies to date have primarily been experimental and have used “classical” approaches to identify key proteins and clarify their roles in the infection process. Computational methods can assist in genome characterization and is widely used in the study of other viral and bacterial genomes, but this approach has not been widely adopted in the investigation of the HCMV genome. We are developing computational methods to perform genome wide comparison of HCMV strains, including both coding and non-coding (miRNA) regions. In this work, we collaboratiing with the lab of Luo Minhua in Wuhan Institute of Virology and hospitals in Beijing and Changsha who have been collecting viral isolates from transplant patients. This work is supported by a Scientia Fellowship from UiO

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Thu, 01 Oct 2020 00:00:00 +0000

Ethnicity

Wed, 17 Jun 2020 00:00:00 +0000

A 2016 report on the ethnic composition of WES and WGS studies found that 84% of studies involved Europeans, only 14% & 3% of samples originated from Asia and Africa respectively. The bias is even more pronounced for studies of the non-coding genome, with only a handful of reports on population SNVs. Even though the situation is improving, the majority of studies remain biased towards Caucasian populations. This lack of variation among populations can impact awareness of how efficacious a drug may be or how likely it is to cause adverse events. However, the advent of large-scale WGS with broader populations means it is now possible to consider population specific variation within NC genomic regions.

In this work we are using publicly available data from the 1000 genomes project and the African Variome Project and combining it with data from collaborators in Africa and China to identify variations in specific populations that occur within miRNA associated regions. This work is funded by a Research Council of Norway FRIPRO grant.

Data Standards

Mon, 27 Apr 2020 00:00:00 +0000

The life sciences have been revolutionized by technical advances in experimental methodology. Nowadays, researchers not only generate huge amounts of data in a single experiment but the types of data they are collecting have also become highly divergent. Thus, biology is making the transition towards a data science and a ‘life cycle’ view of research data. Researchers now face the challenges associated with handling large amounts of heterogeneous data in a digital format. Some of these challenges include consolidating the data; translating it into a format that can be read by complex analysis pipelines; determining the most suitable analysis parameters; and making the data publicly available for reuse. There is growing evidence to suggest that many published results will not be reproducible over time. Thus, robust data management and stewardship plans are essential to ensure the long-term sustainability of digital data.

The Findable, Accessible, Interoperable, and Reusable FAIR data initiative was created in 2016 to address these issues by providing a framework for defining the minimum elements required for good data management. However, adopting FAIR principles is not straightforward as it requires knowledge of metadata, schemata, protocols, policies, and community agreements. Moreover, the lack of exactness in the original FAIR principles means that is a lack of clear guidelines regarding implementation of different elements. Even when robust solutions exist, data providers may have to choose among different and not necessarily compatible implementations.

The organ on chip research environment is one area where FAIR concepts are needed, but are yet to be incorporated. Organ on chip seeks to simulate the activities, mechanisms and physiological response of organs or organ systems. A major data challenge is that organ on chip research collects huge amounts of highly diverse types of data that need to be integrated to understand the mechanics of an organoid design. Currently, no standards exist in the field and, in addition to the challenges of integrating the data, there is also the problem of how to compare results among different research groups. For example, there are several Liver on Chip designs, but no way to compare performance.

Within the Hybrid Technology Hub Organ on Chip centre of excellence at the University of Oslo, we are developing the Global Accessible Distribution Data Sharing (GADDS) platform, an all-in-one cloud platform to facilitate data archiving and sharing with a level of FAIRness. GADDS uses decentralization technologies and a tamper proof blockchain algorithm as a metadata quality control. By providing a browser-based client interface, GADDs can simplify the implementation of FAIRness in the data collection and storage process. The platform is specifically developed for the Organ on Chip environment but has general application in any data collection and integration process requiring a level of data FAIRness. GADDS integrates version control, cloud storage and data as an all-in-one platform.

miRAW

Mon, 27 Apr 2020 00:00:00 +0000

miRAW is a miRNA target prediction based on Deep Learning (DL) which, rather than incorporating any knowledge (such as seed regions), investigates the entire miRNA and 3’UTR mRNA nucleotides to learn a uninhibited set of feature descriptors related to the targeting process.

The trained model is based on more than 150,000 experimentally validated homo sapiens miRNA:gene targets cross referenced with different CLIP-Seq, CLASH and iPAR-CLIP datasets to obtain ∼20,000 validated miRNA:gene exact target sites.

Using this data, we implemented and trained a deep neural network—composed of autoencoders and a feed-forward network—able to automatically learn features describing miRNA-mRNA interactions and assess functionality. Predictions were then refined using information such as site location or site accessibility energy. In a comparison using independent datasets, our DL approach consistently outperformed existing prediction methods, recognizing the seed region as a common feature in the targeting process, but also identifying the role of pairings outside this region. Thermodynamic analysis also suggests that site accessibility plays a role in targeting but that it cannot be used as a sole indicator for functionality.

miRBaseMiner

Mon, 27 Apr 2020 00:00:00 +0000

microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successive releases. A further consideration is that each new miRBase release contains entries that have had limited review and which may subsequently be removed in a future release to ensure the quality of annotation. To aid the miRBase user, we developed a software tool, miRBaseMiner, for investigating miRBase annotation and generating custom annotation sets.

We apply the tool to characterize each release from v9.2 to v22 to examine how annotation has changed across releases and highlight some of the annotation features that users should keep in mind when using for miRBase for data analysis.

These include:

entries with identical or very similar sequences;
entries with multiple annotated genome locations;
hairpin precursor entries with extremely low-estimated minimum free energy;
entries possessing reverse complementary;
entries with 3ʹ poly(A) ends.

As each of these factors can impact the identification of dysregulated features and subsequent clinical or biological conclusions, miRBaseMiner is a valuable resource for any user using miRBase as a reference source.

miRNAs

Mon, 27 Apr 2020 00:00:00 +0000

There are more than 45 000 miRNA related publications in PubMed. While some studies investigate miRNA biogenesis, function and decay, the majority of work has focused on identifying specific miRNAs with roles in disease and developmental processes. In the most common approach, miRNA association studies are performed using microarray or Next Generation Sequencing (NGS) platforms to compare two conditions (e.g. healthy versus cancer) and identify miRNAs that have statistically significant differences in expression levels. The mRNA targets of these miRNAs are predicted using computational tools such as TargetScan3 and functionally interesting ones may be also experimentally verified.

However, these studies implicitly assume an oversimplistic model of miRNA function

Annotation: miRNA studies are dependent on annotation and the primary reference resource is miRBase. The quality of this resource is variable and different versions can return different results in miRNA expression studies (i.e. identification of differentially expressed miRNAs). A further complication is that miRBase includes highly similar or duplicate miRNAs, and miRNAs that have multiple copies.
isomiRs: In most miRNA expression studies it is assumed that miRNAs exist as a well-defined and stable entity, i.e., the single sequence specified in miRBase is the exact form in which a miRNA is expressed. In reality, a miRNA is expressed as a series of highly similar isoforms, or isomiRs, which have demonstrated functional roles18. Microarray based studies are unable to capture this variation, and most NGS Small RNA Sequencing (Small RNA Seq) studies generally fail to consider such deviations.
Ethnicity: This is rarely considered in miRNA studies. miRBase annotation is based on the standard reference genome, GrCh38.p13, but ethnicity can impact miRNA studies by (i) failing to map reads to features containing population specific SNVs, and (ii) failing to incorporate population specific variation in the 3’UTR targets.
Targeting: Due to cost and throughput issues, determining miRNA targets is heavily dependent on computational prediction tools. Many of these are rule based, i.e., they incorporate knowledge into the prediction process - in particular, they require the presence of seed region binding (nt2 to nt7/8 in a miRNA). Even machine learning based approaches used by tools such as TargetScan incorporate this information into their models. While this helps to improve model performance, it biases the model to identify targeting events based on existing knowledge, rather than providing new insight into the targeting process.

Rabies

Mon, 27 Apr 2020 00:00:00 +0000

China has been facing an ongoing rabies epizootic since the middle of the 1990s that, consistent with many other countries experiencing major extended rabies outbreaks, is primarily spread by domestic dogs transmitting the rabies virus (RABV), a species of the Genus Lyssavirus. The southern and eastern parts of the country report the majority of human cases, but almost all provinces have experienced some degree of impact from the disease. For several years now, we have been working with the Chinese Center for Disease Control and Prevention to investigate surveillance data (in the form of demographics and sequence data collected from isolates) From this, we have built up a detailed picture of the current epizootic so that we can identify the origin of new cases (i.e., from dogs, or wildlife). This is important as it allows us to determine whether existing control techniques are effectively controlling the spread of the current epizootic and if current checkpoints at national borders are preventing the introduction of new cases from neighboring countries.

TBGEN

Mon, 27 Apr 2020 00:00:00 +0000

Jasmine: a Java pipeline for isomiR characterization in miRNA-seq Data

Sun, 01 Mar 2020 00:00:00 +0000

3D cell culture models and organ‐on‐a‐chip: Meet separation science and mass spectrometry

Wed, 01 Jan 2020 00:00:00 +0000

Systematic assessment of commercially available low-input miRNA library preparation kits

Wed, 01 Jan 2020 00:00:00 +0000

miRBaseMiner, a tool for investigating miRBase content

Fri, 01 Nov 2019 00:00:00 +0000

Writing technical content in Academic

Fri, 12 Jul 2019 00:00:00 +0000

Academic is designed to give technical content creators a seamless experience. You can focus on the content and Academic handles the rest.

Highlight your code snippets, take notes on math classes, and draw diagrams from textual representation.

On this page, you’ll find some examples of the types of technical content that can be rendered with Academic.

Examples

Code

Academic supports a Markdown extension for highlighting code syntax. You can enable this feature by toggling the highlight option in your config/_default/params.toml file.

```python
import pandas as pd
data = pd.read_csv("data.csv")
data.head()
```

renders as

import pandas as pd
data = pd.read_csv("data.csv")
data.head()

Math

Academic supports a Markdown extension for $\LaTeX$ math. You can enable this feature by toggling the math option in your config/_default/params.toml file.

To render inline or block math, wrap your LaTeX math with $...$ or $$...$$, respectively.

Example math block:

$$\gamma_{n} = \frac{ 
\left | \left (\mathbf x_{n} - \mathbf x_{n-1} \right )^T 
\left [\nabla F (\mathbf x_{n}) - \nabla F (\mathbf x_{n-1}) \right ] \right |}
{\left \|\nabla F(\mathbf{x}_{n}) - \nabla F(\mathbf{x}_{n-1}) \right \|^2}$$

renders as

$$\gamma_{n} = \frac{ \left | \left (\mathbf x_{n} - \mathbf x_{n-1} \right )^T \left [\nabla F (\mathbf x_{n}) - \nabla F (\mathbf x_{n-1}) \right ] \right |}{\left |\nabla F(\mathbf{x}_{n}) - \nabla F(\mathbf{x}_{n-1}) \right |^2}$$

Example inline math $\nabla F(\mathbf{x}_{n})$ renders as $\nabla F(\mathbf{x}_{n})$.

Example multi-line math using the \\\\ math linebreak:

$$f(k;p_0^*) = \begin{cases} p_0^* & \text{if }k=1, \\\\
1-p_0^* & \text {if }k=0.\end{cases}$$

renders as

$$f(k;p_0^) = \begin{cases} p_0^ & \text{if }k=1, \\
1-p_0^* & \text {if }k=0.\end{cases}$$

Diagrams

Academic supports a Markdown extension for diagrams. You can enable this feature by toggling the diagram option in your config/_default/params.toml file or by adding diagram: true to your page front matter.

An example flowchart:

```mermaid
graph TD
A[Hard] -->|Text| B(Round)
B --> C{Decision}
C -->|One| D[Result 1]
C -->|Two| E[Result 2]
```

renders as

graph TD
A[Hard] -->|Text| B(Round)
B --> C{Decision}
C -->|One| D[Result 1]
C -->|Two| E[Result 2]

An example sequence diagram:

```mermaid
sequenceDiagram
Alice->>John: Hello John, how are you?
loop Healthcheck
    John->>John: Fight against hypochondria
end
Note right of John: Rational thoughts!
John-->>Alice: Great!
John->>Bob: How about you?
Bob-->>John: Jolly good!
```

renders as

sequenceDiagram
Alice->>John: Hello John, how are you?
loop Healthcheck
    John->>John: Fight against hypochondria
end
Note right of John: Rational thoughts!
John-->>Alice: Great!
John->>Bob: How about you?
Bob-->>John: Jolly good!

An example Gantt diagram:

```mermaid
gantt
section Section
Completed :done,    des1, 2014-01-06,2014-01-08
Active        :active,  des2, 2014-01-07, 3d
Parallel 1   :         des3, after des1, 1d
Parallel 2   :         des4, after des1, 1d
Parallel 3   :         des5, after des3, 1d
Parallel 4   :         des6, after des4, 1d
```

renders as

gantt
section Section
Completed :done,    des1, 2014-01-06,2014-01-08
Active        :active,  des2, 2014-01-07, 3d
Parallel 1   :         des3, after des1, 1d
Parallel 2   :         des4, after des1, 1d
Parallel 3   :         des5, after des3, 1d
Parallel 4   :         des6, after des4, 1d

An example class diagram:

```mermaid
classDiagram
Class01 <|-- AveryLongClass : Cool
<<interface>> Class01
Class09 --> C2 : Where am i?
Class09 --* C3
Class09 --|> Class07
Class07 : equals()
Class07 : Object[] elementData
Class01 : size()
Class01 : int chimp
Class01 : int gorilla
class Class10 {
  <<service>>
  int id
  size()
}
```

renders as

classDiagram
Class01 <|-- AveryLongClass : Cool
<<interface>> Class01
Class09 --> C2 : Where am i?
Class09 --* C3
Class09 --|> Class07
Class07 : equals()
Class07 : Object[] elementData
Class01 : size()
Class01 : int chimp
Class01 : int gorilla
class Class10 {
  <<service>>
  int id
  size()
}

An example state diagram:

```mermaid
stateDiagram
[*] --> Still
Still --> [*]
Still --> Moving
Moving --> Still
Moving --> Crash
Crash --> [*]
```

renders as

stateDiagram
[*] --> Still
Still --> [*]
Still --> Moving
Moving --> Still
Moving --> Crash
Crash --> [*]

Todo lists

You can even write your todo lists in Academic too:

- [x] Write math example
- [x] Write diagram example
- [ ] Do something else

renders as

Write math example
Write diagram example
Do something else

Tables

Represent your data in tables:

| First Header  | Second Header |
| ------------- | ------------- |
| Content Cell  | Content Cell  |
| Content Cell  | Content Cell  |

renders as

First Header	Second Header
Content Cell	Content Cell
Content Cell	Content Cell

Asides

Academic supports a shortcode for asides, also referred to as notices, hints, or alerts. By wrapping a paragraph in {{% alert note %}} ... {{% /alert %}}, it will render as an aside.

{{% alert note %}}
A Markdown aside is useful for displaying notices, hints, or definitions to your readers.
{{% /alert %}}

renders as

A Markdown aside is useful for displaying notices, hints, or definitions to your readers.

Spoilers

Add a spoiler to a page to reveal text, such as an answer to a question, after a button is clicked.

{{< spoiler text="Click to view the spoiler" >}}
You found me!
{{< /spoiler >}}

renders as

Click to view the spoiler

You found me!

Icons

Academic enables you to use a wide range of icons from Font Awesome and Academicons in addition to emojis.

Here are some examples using the icon shortcode to render icons:

{{< icon name="terminal" pack="fas" >}} Terminal  
{{< icon name="python" pack="fab" >}} Python  
{{< icon name="r-project" pack="fab" >}} R

renders as

Terminal
Python
R

Display Jupyter Notebooks with Academic

Tue, 05 Feb 2019 00:00:00 +0000

from IPython.core.display import Image
Image('https://www.python.org/static/community_logos/python-logo-master-v3-TM-flattened.png')

print("Welcome to Academic!")

Welcome to Academic!

Install Python and JupyterLab

Install Anaconda which includes Python 3 and JupyterLab.

Alternatively, install JupyterLab with pip3 install jupyterlab.

Create or upload a Jupyter notebook

Run the following commands in your Terminal, substituting <MY-WEBSITE-FOLDER> and <SHORT-POST-TITLE> with the file path to your Academic website folder and a short title for your blog post (use hyphens instead of spaces), respectively:

mkdir -p <MY-WEBSITE-FOLDER>/content/post/<SHORT-POST-TITLE>/
cd <MY-WEBSITE-FOLDER>/content/post/<SHORT-POST-TITLE>/
jupyter lab index.ipynb

The jupyter command above will launch the JupyterLab editor, allowing us to add Academic metadata and write the content.

Edit your post metadata

The first cell of your Jupter notebook will contain your post metadata ( front matter).

In Jupter, choose Markdown as the type of the first cell and wrap your Academic metadata in three dashes, indicating that it is YAML front matter:

---
title: My post's title
date: 2019-09-01

# Put any other Academic metadata here...
---

Edit the metadata of your post, using the documentation as a guide to the available options.

To set a featured image, place an image named featured into your post’s folder.

For other tips, such as using math, see the guide on writing content with Academic.

Convert notebook to Markdown

jupyter nbconvert index.ipynb --to markdown --NbConvertApp.output_files_dir=.

Example

This post was created with Jupyter. The orginal files can be found at https://github.com/gcushen/hugo-academic/tree/master/exampleSite/content/post/jupyter

Slides

Tue, 05 Feb 2019 00:00:00 +0000

Create slides in Markdown with Academic

Academic | Documentation

Features

Efficiently write slides in Markdown
3-in-1: Create, Present, and Publish your slides
Supports speaker notes
Mobile friendly slides

Controls

Next: Right Arrow or Space
Previous: Left Arrow
Start: Home
Finish: End
Overview: Esc
Speaker notes: S
Fullscreen: F
Zoom: Alt + Click
PDF Export: E

Code Highlighting

Inline code: variable

Code block:

porridge = "blueberry"
if porridge == "blueberry":
    print("Eating...")

Math

In-line math: $x + y = z$

Block math:

$$ f\left( x \right) = ;\frac{{2\left( {x + 4} \right)\left( {x - 4} \right)}}{{\left( {x + 4} \right)\left( {x + 1} \right)}} $$

Fragments

Make content appear incrementally

{{% fragment %}} One {{% /fragment %}}
{{% fragment %}} **Two** {{% /fragment %}}
{{% fragment %}} Three {{% /fragment %}}

Press Space to play!

One Two Three

A fragment can accept two optional parameters:

class: use a custom style (requires definition in custom CSS)
weight: sets the order in which a fragment appears

Speaker Notes

Add speaker notes to your presentation

{{% speaker_note %}}
- Only the speaker can read these notes
- Press `S` key to view
{{% /speaker_note %}}

Press the S key to view the speaker notes!

Themes

black: Black background, white text, blue links (default)
white: White background, black text, blue links
league: Gray background, white text, blue links
beige: Beige background, dark text, brown links
sky: Blue background, thin dark text, blue links

night: Black background, thick white text, orange links
serif: Cappuccino background, gray text, brown links
simple: White background, black text, blue links
solarized: Cream-colored background, dark green text, blue links

Custom Slide

Customize the slide style and background

{{< slide background-image="/media/boards.jpg" >}}
{{< slide background-color="#0000FF" >}}
{{< slide class="my-style" >}}

Custom CSS Example

Let’s make headers navy colored.

Create assets/css/reveal_custom.css with:

.reveal section h1,
.reveal section h2,
.reveal section h3 {
  color: navy;
}

Questions?

Ask

Documentation

The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China

Tue, 01 Jan 2019 00:00:00 +0000

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

Sun, 01 Jul 2018 00:00:00 +0000

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Sun, 01 Jan 2017 00:00:00 +0000

Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells

Sun, 01 Jan 2017 00:00:00 +0000

Identification and BAC construction of Han, the first characterized HCMV clinical strain in China

Sun, 01 May 2016 00:00:00 +0000

Jasmine

Wed, 27 Apr 2016 00:00:00 +0000

The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard allows investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences.

Jasmine is a software tool that incorporates a hierarchal framework for characterizing isomiR populations. Jasmine is a Java application that can process raw read data in fastq/fasta format, or mapped reads in SAM format to produce a detailed characterization of isomiR populations. Thus, Jasmine can reveal structure not apparent in a standard miRNA-Seq analysis pipeline.

The Non-Coding Genome

Wed, 27 Apr 2016 00:00:00 +0000

Less than 2% of the human genome consists of protein-coding genes. Initially, the remainder of the genome was assumed to be ‘junk’ DNA but it is now clear that these regions play important regulatory roles. We are interested in the regions that encode miRNA related information (e.g. transcription recognition sites, pre-miRNAs and 3’UTRs ) and how they deviate from the information in miRBase, the most commonly used miRNA reference resource. These deviations can be significant as they can impact miRNA expression studies (in the form of microArray, qPCR or Next Generation Sequencing). For example, in Next Generation Sequencing, can be in the form of miscounted miRNA reads. When combined with changes in 3’UTR targets, this can disrupt the miRNA-mRNA target events.

We are interested in investigating these effects in the context of ethnicity as reference resources rarely take this factor into account. This work is financed by a Research Council of Norway FRIPRO grant.

Academic: the website builder for Hugo

Wed, 20 Apr 2016 00:00:00 +0000

Create a free website with Academic using Markdown, Jupyter, or RStudio. Choose a beautiful color theme and build anything with the Page Builder - over 40 widgets, themes, and language packs included!

Check out the latest demo of what you’ll get in less than 10 minutes, or view the showcase of personal, project, and business sites.

👉 Get Started
📚 View the documentation
💬 Ask a question on the forum
👥 Chat with the community
🐦 Twitter: @source_themes @GeorgeCushen #MadeWithAcademic
💡 Request a feature or report a bug
⬆️ Updating? View the Update Guide and Release Notes
❤️ Support development of Academic:
- ☕️ Donate a coffee
- 💵 Become a backer on Patreon
- 🖼️ Decorate your laptop or journal with an Academic sticker
- 👕 Wear the T-shirt
- 👩‍💻 Contribute

Academic is mobile first with a responsive design to ensure that your site looks stunning on every device.

Key features:

Page builder - Create anything with widgets and elements
Edit any type of content - Blog posts, publications, talks, slides, projects, and more!
Create content in Markdown, Jupyter, or RStudio
Plugin System - Fully customizable color and font themes
Display Code and Math - Code highlighting and LaTeX math supported
Integrations - Google Analytics, Disqus commenting, Maps, Contact Forms, and more!
Beautiful Site - Simple and refreshing one page design
Industry-Leading SEO - Help get your website found on search engines and social media
Media Galleries - Display your images and videos with captions in a customizable gallery
Mobile Friendly - Look amazing on every screen with a mobile friendly version of your site
Multi-language - 15+ language packs including English, 中文, and Português
Multi-user - Each author gets their own profile page
Privacy Pack - Assists with GDPR
Stand Out - Bring your site to life with animation, parallax backgrounds, and scroll effects
One-Click Deployment - No servers. No databases. Only files.

Themes

Academic comes with automatic day (light) and night (dark) mode built-in. Alternatively, visitors can choose their preferred mode - click the sun/moon icon in the top right of the Demo to see it in action! Day/night mode can also be disabled by the site admin in params.toml.

Choose a stunning theme and font for your site. Themes are fully customizable.

Ecosystem

Academic Admin: An admin tool to import publications from BibTeX or import assets for an offline site
Academic Scripts: Scripts to help migrate content to new versions of Academic

Install

You can choose from one of the following four methods to install:

Then personalize and deploy your new site.

Updating

View the Update Guide.

Feel free to star the project on Github to help keep track of updates.

License

Released under the MIT license.

Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus

Tue, 01 Dec 2015 00:00:00 +0000

Resistant mutations and quasispecies complexity of hepatitis B virus during telbivudine treatment"

Sun, 01 Nov 2015 00:00:00 +0000

BlastGraph: a comparative genomics tool based on BLAST and graph algorithms

Thu, 01 Oct 2015 00:00:00 +0000

Rabies cases in the west of China have two distinct origins

Thu, 01 Oct 2015 00:00:00 +0000

Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa

Mon, 01 Jun 2015 00:00:00 +0000

MicroRNA miR-21 attenuates human cytomegalovirus replication in neural cells by targeting Cdc25a

Thu, 01 Jan 2015 00:00:00 +0000

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Mon, 01 Dec 2014 00:00:00 +0000

Comparison of genotypes I and III in Japanese encephalitis virus reveals distinct differences in their genetic and host diversity

Wed, 01 Oct 2014 00:00:00 +0000

Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks

Thu, 01 May 2014 00:00:00 +0000

Reassortment and migration analysis of Crimean–Congo haemorrhagic fever virus

Tue, 01 Oct 2013 00:00:00 +0000

Molecular phylodynamic analysis indicates lineage displacement occurred in Chinese rabies epidemics between 1949 to 2010

Mon, 01 Jul 2013 00:00:00 +0000

Computational evolutionary analysis of the overlapped surface (S) and polymerase (P) region in hepatitis B virus indicates the spacer domain in P is crucial for survival

Mon, 01 Apr 2013 00:00:00 +0000

Genetic characterization and transmitted drug resistance of the HIV type 1 epidemic in men who have sex with men in Beijing, China

Fri, 01 Mar 2013 00:00:00 +0000

Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus

Tue, 01 Jan 2013 00:00:00 +0000

National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries

Tue, 01 Jan 2013 00:00:00 +0000

Observation of non-principal plane neutral points in the upwelling polarized light field above a water surface

Wed, 01 Aug 2012 00:00:00 +0000

The spatial and temporal dynamics of rabies in China

Sun, 01 Jan 2012 00:00:00 +0000

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

Thu, 01 Dec 2011 00:00:00 +0000

Emergence of genotype I of Japanese encephalitis virus as the dominant genotype in Asia

Sat, 01 Oct 2011 00:00:00 +0000

the Non-Coding RNA Group

Example Page 1

Tip 1

Tip 2

Example Page 2

Tip 3

Tip 4

Example Talk

HCMV

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Ethnicity

Data Standards

miRAW

miRBaseMiner

miRNAs

Rabies

TBGEN

Jasmine: a Java pipeline for isomiR characterization in miRNA-seq Data

3D cell culture models and organ‐on‐a‐chip: Meet separation science and mass spectrometry

Systematic assessment of commercially available low-input miRNA library preparation kits

miRBaseMiner, a tool for investigating miRBase content

Writing technical content in Academic

Examples

Code

Math

Diagrams

Todo lists

Tables

Asides

Spoilers

Icons

Did you find this page helpful? Consider sharing it 🙌

Display Jupyter Notebooks with Academic

Install Python and JupyterLab

Create or upload a Jupyter notebook

Edit your post metadata

Convert notebook to Markdown

Example

Slides

Create slides in Markdown with Academic

Features

Controls

Code Highlighting

Math

Fragments

Speaker Notes

Themes

Custom Slide

Custom CSS Example

Questions?

The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells

Identification and BAC construction of Han, the first characterized HCMV clinical strain in China

Jasmine

The Non-Coding Genome

Academic: the website builder for Hugo

Themes

Ecosystem

Install

Updating

License

Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus

Resistant mutations and quasispecies complexity of hepatitis B virus during telbivudine treatment"

BlastGraph: a comparative genomics tool based on BLAST and graph algorithms

Rabies cases in the west of China have two distinct origins

Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa

MicroRNA miR-21 attenuates human cytomegalovirus replication in neural cells by targeting Cdc25a

Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS?

Comparison of genotypes I and III in Japanese encephalitis virus reveals distinct differences in their genetic and host diversity

Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks

Reassortment and migration analysis of Crimean–Congo haemorrhagic fever virus

Molecular phylodynamic analysis indicates lineage displacement occurred in Chinese rabies epidemics between 1949 to 2010

Computational evolutionary analysis of the overlapped surface (S) and polymerase (P) region in hepatitis B virus indicates the spacer domain in P is crucial for survival

Genetic characterization and transmitted drug resistance of the HIV type 1 epidemic in men who have sex with men in Beijing, China

Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus

National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries

Observation of non-principal plane neutral points in the upwelling polarized light field above a water surface

The spatial and temporal dynamics of rabies in China