Volume 21 Supplement 9
Selected Articles from the 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019)
- Open access
- Published: 03 December 2020
Current trend and development in bioinformatics research
- Yuanyuan Fu 1 ,
- Zhougui Ling 1 , 2 ,
- Hamid Arabnia 3 &
- Youping Deng 1
BMC Bioinformatics volume 21 , Article number: 538 ( 2020 ) Cite this article
This is an editorial report of the supplements to BMC Bioinformatics that includes 6 papers selected from the BIOCOMP’19—The 2019 International Conference on Bioinformatics and Computational Biology. These articles reflect current trend and development in bioinformatics research.
The supplement to BMC Bioinformatics was proposed to launch during the BIOCOMP’19—The 2019 International Conference on Bioinformatics and Computational Biology held from July 29 to August 01, 2019 in Las Vegas, Nevada. In this congress, a variety of research areas was discussed, including bioinformatics which was one of the major focuses due to the rapid development and requirement of using bioinformatics approaches in biological data analysis, especially for omics large datasets. Here, six manuscripts were selected after strict peer review, providing an overview of the bioinformatics research trend and its application for interdisciplinary collaboration.
Cancer is one of the leading causes of morbidity and mortality worldwide. There exists an urgent need to identify new biomarkers or signatures for early detection and prognosis. Mona et al. identified biomarker genes from functional network based on the 407 differential expressed genes between lung cancer and healthy populations from a public Gene Expression Omnibus dataset. The lower expression of sixteen gene signature is associated with favorable lung cancer survival, DNA repair, and cell regulation [ 1 ]. A new class of biomarkers such as alternative splicing variants (ASV) have been studied in recent years. Various platforms and methods, for example, Affymetrix Exon-Exon Junction Array, RNA-seq, and liquid chromatography tandem mass spectrometry (LC–MS/MS), have been developed to explore the role of ASV in human disease. Zhang et al. have developed a bioinformatics workflow to combine LC–MS/MS with RNA-seq which provide new opportunities in biomarker discovery. In their study, they identified twenty-six alternative splicing biomarker peptides with one single intron event and one exon skipping event; further pathways indicated the 26 peptides may be involved in cancer, signaling, metabolism, regulation, immune system and hemostasis pathways which validated by the RNA-seq analysis [ 2 ].
Proteins serve crucial functions in essentially all biological processes and the function directly depends on their three-dimensional structures. Traditional approaches to elucidation of protein structures by NMR spectroscopy are time consuming and expensive, however, the faster and more cost-effective methods are critical in the development of personalized medicine. Cole et al. improved the REDRAFT software package in the important areas of usability, accessibility, and the core methodology which resulted in the ability to fold proteins [ 3 ].
The human microbiome is the aggregation of microorganisms that reside on or within human bodies. Rebecca et al. discussed the tissue-associated microbial detection in cancer using next generation sequencing (NGS). Various computational frameworks could shed light on the role of microbiota in cancer pathogenesis [ 4 ]. How to analyze the human microbiome data efficiently is a huge challenge. Zhang et al. developed a nonparametric test based on inter-point distance to evaluate statistical significance from a Bayesian point of view. The proposed test is more efficient and sensitive to the compositional difference compared with the traditional mean-based method [ 5 ].
Human disease is also considered as the cause of the interaction between genetic and environmental factors. In the last decades, there was a growing interest in the effect of metal toxicity on human health. Evaluating the toxicity of chemical mixture and their possible mechanism of action is still a challenge for humans and other organisms, as traditional methods are very time consuming, inefficient, and expensive, so a limited number of chemicals can be tested. In order to develop efficient and accurate predictive models, Yu et al. compared the results among a classification algorithm and identified 15 gene biomarkers with 100% accuracy for metal toxicant using a microarray classifier analysis [ 6 ].
Currently, there is a growing need to convert biological data into knowledge through a bioinformatics approach. We hope these articles can provide up-to-date information of research development and trend in bioinformatics field.
Availability of data and materials
The 2019 International Conference on Bioinformatics and Computational Biology
Liquid chromatography tandem mass spectrometry
Alternative splicing variants
Nuclear Magnetic Resonance
Residual Dipolar Coupling based Residue Assembly and Filter Tool
Next generation sequencing
Mona Maharjan RBT, Chowdhury K, Duan W, Mondal AM. Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies. 2020. https://doi.org/10.1186/s12859-020-3524-8 .
Zhang F, Deng CK, Wang M, Deng B, Barber R, Huang G. Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. Mol Cell Proteomics. 2020;16:1850–63. https://doi.org/10.1186/s12859-020-03824-8 .
Article Google Scholar
Casey Cole CP, Rachele J, Valafar H. Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package. 2020. https://doi.org/10.1186/s12859-020-3522-x .
Rebecca M, Rodriguez VSK, Menor M, Hernandez BY, Deng Y. Tissue-associated microbial detection in cancer using human sequencing data. 2020. https://doi.org/10.1186/s12859-020-03831-9 .
Qingyang Zhang TD. A distance based multisample test for high-dimensional compositional data with applications to the human microbiome . 2020. https://doi.org/10.1186/s12859-020-3530-x .
Yu Z, Fu Y, Ai J, Zhang J, Huang G, Deng Y. Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another. 2020. https://doi.org/10.1186/s12859-020-3525-7 .
This supplement will not be possible without the support of the International Society of Intelligent Biological Medicine (ISIBM).
About this supplement
This article has been published as part of BMC Bioinformatics Volume 21 Supplement 9, 2020: Selected Articles from the 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019). The full contents of the supplement are available online at https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-21-supplement-9 .
Publication of this supplement has been supported by NIH grants R01CA223490 and R01 CA230514 to Youping Deng and 5P30GM114737, P20GM103466, 5U54MD007601 and 5P30CA071789.
Authors and affiliations.
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
Yuanyuan Fu, Zhougui Ling & Youping Deng
Department of Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, China
Department of Computer Science, University of Georgia, Athens, GA, 30602, USA
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YF drafted the manuscript, ZL, HA, and YD revised the manuscript. All authors read and approved the final manuscript.
Correspondence to Youping Deng .
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Fu, Y., Ling, Z., Arabnia, H. et al. Current trend and development in bioinformatics research. BMC Bioinformatics 21 (Suppl 9), 538 (2020). https://doi.org/10.1186/s12859-020-03874-y
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Today, a single laboratory can generate a vast amount of biological data. There is a wealth of data already available in public databases, which makes the modern life sciences almost dependent on bioinformatics. This book brings together an international team of experts to discuss the state-of-the-art from several fields of bioinformatics, from the automatic identification and classification of viruses to the analysis of the transcriptome of single cells and plants, including artificial intelligence algorithms to discover biomarkers and text mining approaches to help in the interpretation of the findings. Machine learning, pattern discovery and analysis, error correction, Bayesian inference and novel computational techniques to discover chromosomal rearrangements continue to play crucial roles in biological discovery, and all of them are explored in chapters of this book. In sum, this book contains high-quality chapters that provide excellent views into key topics of current bioinformatics research, topics that should remain important for the next several years.
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Current Research in Bioinformatics
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Current Research in Bioinformatics, a peer reviewed international journal is launched to publish notable research on the application of information technology to the field of molecular biology. Researchers and scholars are invited to submit their original research / review articles in the field of creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data.
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Title: an evaluation of large language models in bioinformatics research.
Abstract: Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem solving. However, the potential and efficacy of these models in bioinformatics remain incompletely explored. In this work, we study the performance LLMs on a wide spectrum of crucial bioinformatics tasks. These tasks include the identification of potential coding regions, extraction of named entities for genes and proteins, detection of antimicrobial and anti-cancer peptides, molecular optimization, and resolution of educational bioinformatics problems. Our findings indicate that, given appropriate prompts, LLMs like GPT variants can successfully handle most of these tasks. In addition, we provide a thorough analysis of their limitations in the context of complicated bioinformatics tasks. In conclusion, we believe that this work can provide new perspectives and motivate future research in the field of LLMs applications, AI for Science and bioinformatics.
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Emerging issues that could trouble teens
Stanford Medicine’s Vicki Harrison explains the forces impacting youth mental health today, and why it’s so important to involve teens in solutions.
Image credit: Getty Images
One of the most alarming developments across the United States in recent years has been the growing mental health crisis among children and adolescents.
The already dire situation is evolving 2024 already presenting a new set of challenges that Vicki Harrison, the program director at the Stanford Center for Youth Mental Health & Wellbeing , is closely monitoring and responding to.
Stanford Report sat down with Harrison to find out what concerns her the most about the upcoming year. Harrison also talked about some of the promising ways she and her colleagues are responding to the national crisis and the importance of bringing the youth perspective into that response.
Challenging current events
From the 2024 general election to evolving, international conflicts, today’s dialed-in youth have a lot to process. As teens turn to digital and social media sources to learn about current events and figure out where they stand on particular issues, the sheer volume of news online can feel overwhelming, stressful, and confusing.
One way Harrison is helping teens navigate the information they consume online is through Good for Media , a youth-led initiative that grew out of the Stanford Center for Youth Mental Health & Wellbeing to bring teens and young adults together to discuss using social media in a safe and healthy way. In addition to numerous youth-developed tools and videos, the team has a guide with tips to deal with the volume of news online and how to process the emotions that come with it.
Harrison points out that the tone of political discourse today – particularly discussions about reining in the rights a person has based on aspects of their identity, such as their religion, race, national origin, or gender – affects adolescents at a crucial time in their development, a period when they are exploring who they are and what they believe in.
“If their identity is being othered, criticized, or punished in some way, what messages is that sending to young people and how do they feel good about themselves?” Harrison said. “We can’t divorce these political and cultural debates from the mental health of young people.”
Harrison believes that any calls for solving the mental health crisis must acknowledge the critical importance of inclusion, dignity, and respect in supporting the mental health of young people.
Talking about mental health
Adolescence is a crucial time to develop coping skills to respond to stressful situations that arise – a skill not all teens and youth learn.
“It hasn’t always been normalized to talk about mental health and how to address feeling sad or worried about things,” Harrison said. “It’s not something that all of us have been taught to really understand and how to cope with. A lot of young people aren’t comfortable seeking professional services.”
The Stanford Center for Youth Mental Health & Wellbeing is helping young people get that extra bit of support to deal with problems before they get worse.
This year, they are rolling out stand-alone “one-stop-shop” health centers that offer youth 12-25 years old access to a range of clinical and counseling services with both trained professionals and peers. Called allcove , there are three locations open so far – Palo Alto, Redondo Beach, and San Mateo. More are set to open across the state in 2024.
“If we can normalize young people having an access point – and feeling comfortable accessing it – we can put them on a healthier track and get them any help they may need,” Harrison said.
Another emerging issue Harrison is monitoring is the growing role of social media influencers who talk openly about their struggles with mental health and well-being.
While this is helping bring awareness to mental health – which Harrison wants to see more of – she is also concerned about how it could lead some teens to mistake a normal, stressful life experience for a mental disorder and incorrectly self-diagnose themselves or to overgeneralize or misunderstand symptoms of mental health conditions. Says Harrison, “We want to see mental health destigmatized, but not oversimplified or minimized.”
“We can’t divorce these political and cultural debates from the mental health of young people.” —Vicki Harrison Program Director at the Stanford Center for Youth Mental Health & Wellbeing
Eyes on new technologies
Advances in technology – particularly generative AI – offer new approaches to improving teen well-being, such as therapeutic chatbots or detecting symptoms through keywords or patterns in speech.
“Digital solutions are a promising part of the continuum of care, but there’s the risk of rolling out things without the research backing them,” Harrison said.
Social media companies have come under scrutiny in recent years for inadequately safeguarding young adult mental health. Harrison hopes those mishaps serve as a cautionary tale for those applying AI tools more broadly.
There’s an opportunity, she says, to involve adolescents directly in making AI applications safe and effective. She and her team hope to engage young people with policy and industry and involve them in the design process, rather than as an afterthought.
“Can we listen to their ideas for how to make it better and how to make it work for them?” Harrison asks. “Giving them that agency is going to give us great ideas and make a better experience for them and for everyone using it.”
Harrison said she and her team are hoping to engage young people with policy and industry to elevate their ideas into the design process, rather than have it be an afterthought.
“There’s a lot of really motivated young people who see potential to do things differently and want to improve the world they inhabit,” Harrison said. “That’s why I always want to find opportunities to pass them the microphone and listen.”
Read our research on: Immigration & Migration | Podcasts | Election 2024
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How americans view the situation at the u.s.-mexico border, its causes and consequences, 80% say the u.s. government is doing a bad job handling the migrant influx.
Pew Research Center conducted this study to understand the public’s views about the large number of migrants seeking to enter the U.S. at the border with Mexico. For this analysis, we surveyed 5,140 adults from Jan. 16-21, 2024. Everyone who took part in this survey is a member of the Center’s American Trends Panel (ATP), an online survey panel that is recruited through national, random sampling of residential addresses. This way nearly all U.S. adults have a chance of selection. The survey is weighted to be representative of the U.S. adult population by gender, race, ethnicity, partisan affiliation, education and other categories. Read more about the ATP’s methodology .
Here are the questions used for the report and its methodology .
The growing number of migrants seeking entry into the United States at its border with Mexico has strained government resources, divided Congress and emerged as a contentious issue in the 2024 presidential campaign .
Americans overwhelmingly fault the government for how it has handled the migrant situation. Beyond that, however, there are deep differences – over why the migrants are coming to the U.S., proposals for addressing the situation, and even whether it should be described as a “crisis.”
Factors behind the migrant influx
Economic factors – either poor conditions in migrants’ home countries or better economic opportunities in the United States – are widely viewed as major reasons for the migrant influx.
About seven-in-ten Americans (71%), including majorities in both parties, cite better economic opportunities in the U.S. as a major reason.
There are wider partisan differences over other factors.
About two-thirds of Americans (65%) say violence in migrants’ home countries is a major reason for why a large number of immigrants have come to the border.
Democrats and Democratic-leaning independents are 30 percentage points more likely than Republicans and Republican leaners to cite this as a major reason (79% vs. 49%).
By contrast, 76% of Republicans say the belief that U.S. immigration policies will make it easy to stay in the country once they arrive is a major factor. About half as many Democrats (39%) say the same.
For more on Americans’ views of these and other reasons, visit Chapter 2.
How serious is the situation at the border?
A sizable majority of Americans (78%) say the large number of migrants seeking to enter this country at the U.S.-Mexico border is eithera crisis (45%) or a major problem (32%), according to the Pew Research Center survey, conducted Jan. 16-21, 2024, among 5,140 adults.
Related: Migrant encounters at the U.S.-Mexico border hit a record high at the end of 2023 .
- Republicans are much more likely than Democrats to describe the situation as a “crisis”: 70% of Republicans say this, compared with just 22% of Democrats.
- Democrats mostly view the situation as a major problem (44%) or minor problem (26%) for the U.S. Very few Democrats (7%) say it is not a problem.
In an open-ended question , respondents voice their concerns about the migrant influx. They point to numerous issues, including worries about how the migrants are cared for and general problems with the immigration system.
Yet two concerns come up most frequently:
- 22% point to the economic burdens associated with the migrant influx, including the strains migrants place on social services and other government resources.
- 22% also cite security concerns. Many of these responses focus on crime (10%), terrorism (10%) and drugs (3%).
When asked specifically about the impact of the migrant influx on crime in the United States, a majority of Americans (57%) say the large number of migrants seeking to enter the country leads to more crime. Fewer (39%) say this does not have much of an impact on crime in this country.
Republicans (85%) overwhelmingly say the migrant surge leads to increased crime in the U.S. A far smaller share of Democrats (31%) say the same; 63% of Democrats instead say it does not have much of an impact.
Government widely criticized for its handling of migrant influx
For the past several years, the federal government has gotten low ratings for its handling of the situation at the U.S.-Mexico border. (Note: The wording of this question has been modified modestly to reflect circumstances at the time).
However, the current ratings are extraordinarily low.
Just 18% say the U.S. government is doing a good job dealing with the large number of migrants at the border, while 80% say it is doing a bad job, including 45% who say it is doing a very bad job.
- Republicans’ views are overwhelmingly negative (89% say it’s doing a bad job), as they have been since Joe Biden became president.
- 73% of Democrats also give the government negative ratings, the highest share recorded during Biden’s presidency.
For more on Americans’ evaluations of the situation, visit Chapter 1 .
Which policies could improve the border situation?
There is no single policy proposal, among the nine included on the survey, that majorities of both Republicans and Democrats say would improve the situation at the U.S.-Mexico border. There are areas of relative agreement, however.
A 60% majority of Americans say that increasing the number of immigration judges and staff in order to make decisions on asylum more quickly would make the situation better. Only 11% say it would make things worse, while 14% think it would not make much difference.
Nearly as many (56%) say creating more opportunities for people to legally immigrate to the U.S. would make the situation better.
Majorities of Democrats say each of these proposals would make the border situation better.
Republicans are less positive than are Democrats; still, about 40% or more of Republicans say each would improve the situation, while far fewer say they would make things worse.
Opinions on other proposals are more polarized. For example, a 56% majority of Democrats say that adding resources to provide safe and sanitary conditions for migrants arriving in the U.S. would be a positive step forward.
Republicans not only are far less likely than Democrats to view this proposal positively, but far more say it would make the situation worse (43%) than better (17%).
Building or expanding a wall along the U.S.-Mexico border was among the most divisive policies of Donald Trump’s presidency. In 2019, 82% of Republicans favored expanding the border wall , compared with just 6% of Democrats.
Today, 72% of Republicans say substantially expanding the wall along the U.S. border with Mexico would make the situation better. Just 15% of Democrats concur, with most saying either it would not make much of a difference (47%) or it would make things worse (24%).
For more on Americans’ reactions to policy proposals, visit Chapter 3 .
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Spintronics research finds magnetic state of certain materials can be switched using surface induced strain
by Vienna University of Technology
Electronics are based on electrical charges being transported from one place to another. Electrons move, current flows, and signals are transmitted by applying an electrical voltage. However, there is also another way to manipulate electronic currents and signals: using the properties of the spin—the intrinsic magnetic moment of the electron. This is called "spintronics," and it has become an increasingly important field in contemporary electronic research.
An international research team involving TU Wien and the Czech Academy of Sciences has now achieved an important breakthrough. They have managed to switch the spins in an antiferromagnetic material using surface strain. This could lead to an important new line of research in electronic technologies. The research is published in the journal Advanced Functional Materials .
"There are different types of magnetism," explains Sergii Khmelevskyi from the Vienna Scientific Cluster Research Center, TU Wien. "The best known is ferromagnetism. It occurs when the atomic spins in a material are all aligned in parallel. But there is also the opposite, antiferromagnetism. In an antiferromagnetic material, neighboring atoms always have opposite spins." Their effects therefore cancel each other out and no magnetic force can be detected from the outside.
"In 2010, however, scientists at the TU Wien and the Czech Academy of Science came up with the idea that such antiferromagnetic materials have promising properties for spintronic applications," says Khmelevskyi. This was the start of the new research field of "antiferromagnetic spintronics," which has developed quickly ever since.
Intensive work was done recently by TU Wien, the Institute of Physics of Czech Academy of Sciences and Ecole Polytechnique (Paris). The biggest challenge was that the spins in antiferromagnetic materials are difficult to manipulate—but finding a way to manipulate them in a reliable and precise way is crucial. Only if magnetic states can be switched from one state to another in a targeted manner does it become possible to produce computer memory cells (e.g., MRAM).
Magnetic frustration: Tiny effects make all the difference
Manipulating ferromagnets is easy: It is enough to simply apply an external magnetic field to influence its internal magnetic properties. This is not possible with antiferromagnets—but there is a way out: You can work with surface strain.
However, this requires very specific types of crystals. Depending on the geometry and the arrangement of the atoms in the crystal, several different antiferromagnetic spin arrangements may be possible. The crystal assumes the state with the lowest energy. But it might be an situation when several different spin orders have the same energy. This phenomenon is called "magnetic frustration." "In that case, tiny interactions, which would otherwise play no role, can decide which magnetic state the crystal assumes," says Khmelevskyi.
Experiments with uranium dioxide have shown that mechanical stress can be used to compress the crystal lattice a tiny bit, and this is enough to switch the magnetic order of the material.
"We have now shown that antiferromagnets can actually be switched by utilizing the properties of the magnetic frustration existing in many known materials," says Khmelevskyi. "That opens the door to many exciting further developments in the direction of functional antiferromagnetic spintronics."
Provided by Vienna University of Technology
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