The document summarizes the editorial process for papers submitted to EMBO Scientific Publishing journals. It discusses how editors read submitted manuscripts in their entirety and make initial decisions based on factors like scope, novelty, and completeness of analysis. If a paper is sent for peer review, referees are selected based on expertise and reputation. Referees provide detailed reports evaluating the work. Editors may invite referee cross-commenting before making a final decision. The process aims to publish papers that will advance science while maintaining scientific integrity.
The aim of this talk is to discusses some of the ethical issues that can arise during scientific publication and the peer review process and discusses their implications. The presentation covers several issue including the scientific publication ethics, misconduct, integrity of the research, authorship and peer review ethics as well as Committee on publication Ethics (COPE) ,
JALA Editor-in-Chief Edward Kai-Hua Chow, Ph.D., of National University of Singapore shared step-by-step advice on how to design and write scientific research papers more clearly and effectively to improve their chances for successful publication at the recently held conference in Washington, DC. Learn what editors want, what they don't want and how reviewers evaluate manuscripts by reviewing slides from the session.
The document discusses ethics in research and provides several examples of ethical issues and misconduct:
- It defines ethics and research, and explains why adhering to ethical norms in research is important. It discusses common ethical principles and codes/policies for research ethics.
- It presents four cases involving ethical dilemmas in research and discusses appropriate responses. It also provides examples of deviations from acceptable research practices, such as fabricating or falsifying data.
- Specifically, it discusses high-profile cases of scientific misconduct like Dr. John Darsee who fabricated research data and Dr. Robert Slutsky who included non-contributing authors. It emphasizes that the most serious crimes in research are fabrication, falsification, and plagiar
The document discusses a clicker test asking whether patients should be able to view doctors' notes. The three response options are: definitely yes, absolutely no, and maybe it depends.
It then cites a 2012 study from the Annals of Internal Medicine that was a quasi-experimental study inviting patients to read their doctors' notes. The study provides a link to the PubMed entry for the study.
Finally, it lists "Finding Medical Information" and "Basis of Medicine, Unit 2, October 2012" suggesting this is part of a lecture presentation on finding medical information.
Resident Presentations - Evidence-Based Medicine for HaematologyRobin Featherstone
This document provides information about a workshop on evidence-based medicine (EBM) for residents. The workshop objectives are to present clinical EBM summaries to peers and critically reflect on applying clinical studies to practice. The document reviews the EBM process and provides worksheets and resources for critically appraising different study designs, including randomized controlled trials, cohort and case-control studies, and systematic reviews. Key points of the critical appraisal worksheets are summarized for each study design. Logistical details are provided for the next workshop.
This document discusses common mistakes in scientific research. It begins by defining scientific research and outlining the research process. It then explains that a flawless research process is difficult for young researchers due to a lack of experience and guidance. Some common mistakes discussed include selecting a research topic that is too broad or narrow, having unclear research objectives, conducting an insufficient literature review, failing to obtain necessary ethical approvals, and not implementing adequate measures to reduce bias. Additional mistakes relate to poor research methodology, errors in data collection and analysis, using improper statistical methods, and plagiarism in writing up results. Throughout, the document emphasizes the importance of learning from mistakes to conduct better research.
This document summarizes a presentation on research ethics and scientific publication. It discusses author responsibilities including submitting original work and obtaining proper permissions. It defines plagiarism, self-plagiarism, and other ethical violations. It provides examples of plagiarized papers that were retracted from journals. It discusses how journals detect problems, handle ethical violations, and work to uphold integrity. It emphasizes sharing knowledge through peer-reviewed publication and the importance of ethical conduct in research.
The aim of this talk is to discusses some of the ethical issues that can arise during scientific publication and the peer review process and discusses their implications. The presentation covers several issue including the scientific publication ethics, misconduct, integrity of the research, authorship and peer review ethics as well as Committee on publication Ethics (COPE) ,
JALA Editor-in-Chief Edward Kai-Hua Chow, Ph.D., of National University of Singapore shared step-by-step advice on how to design and write scientific research papers more clearly and effectively to improve their chances for successful publication at the recently held conference in Washington, DC. Learn what editors want, what they don't want and how reviewers evaluate manuscripts by reviewing slides from the session.
The document discusses ethics in research and provides several examples of ethical issues and misconduct:
- It defines ethics and research, and explains why adhering to ethical norms in research is important. It discusses common ethical principles and codes/policies for research ethics.
- It presents four cases involving ethical dilemmas in research and discusses appropriate responses. It also provides examples of deviations from acceptable research practices, such as fabricating or falsifying data.
- Specifically, it discusses high-profile cases of scientific misconduct like Dr. John Darsee who fabricated research data and Dr. Robert Slutsky who included non-contributing authors. It emphasizes that the most serious crimes in research are fabrication, falsification, and plagiar
The document discusses a clicker test asking whether patients should be able to view doctors' notes. The three response options are: definitely yes, absolutely no, and maybe it depends.
It then cites a 2012 study from the Annals of Internal Medicine that was a quasi-experimental study inviting patients to read their doctors' notes. The study provides a link to the PubMed entry for the study.
Finally, it lists "Finding Medical Information" and "Basis of Medicine, Unit 2, October 2012" suggesting this is part of a lecture presentation on finding medical information.
Resident Presentations - Evidence-Based Medicine for HaematologyRobin Featherstone
This document provides information about a workshop on evidence-based medicine (EBM) for residents. The workshop objectives are to present clinical EBM summaries to peers and critically reflect on applying clinical studies to practice. The document reviews the EBM process and provides worksheets and resources for critically appraising different study designs, including randomized controlled trials, cohort and case-control studies, and systematic reviews. Key points of the critical appraisal worksheets are summarized for each study design. Logistical details are provided for the next workshop.
This document discusses common mistakes in scientific research. It begins by defining scientific research and outlining the research process. It then explains that a flawless research process is difficult for young researchers due to a lack of experience and guidance. Some common mistakes discussed include selecting a research topic that is too broad or narrow, having unclear research objectives, conducting an insufficient literature review, failing to obtain necessary ethical approvals, and not implementing adequate measures to reduce bias. Additional mistakes relate to poor research methodology, errors in data collection and analysis, using improper statistical methods, and plagiarism in writing up results. Throughout, the document emphasizes the importance of learning from mistakes to conduct better research.
This document summarizes a presentation on research ethics and scientific publication. It discusses author responsibilities including submitting original work and obtaining proper permissions. It defines plagiarism, self-plagiarism, and other ethical violations. It provides examples of plagiarized papers that were retracted from journals. It discusses how journals detect problems, handle ethical violations, and work to uphold integrity. It emphasizes sharing knowledge through peer-reviewed publication and the importance of ethical conduct in research.
The document discusses data analysis and negative results in scientific research. It provides examples of how negative results are underreported but still provide valuable information. It emphasizes that negative results:
1) Prevent wasted efforts on experiments that already failed,
2) Help identify false conclusions by focusing only on positive results, and
3) Can still provide important evidence against hypotheses or support the null hypothesis. Examples show how negative results advanced scientific understanding. The document argues negative results should receive the same rigorous interpretation and publication consideration as positive results.
This document provides an agenda for a workshop on research skills and ethics. It begins with an introduction and dedication to the late Dr. Ahmed Zewail, then discusses the differences between scientists and researchers. The second part introduces the Scientific Research Group in Egypt, its members and activities. The third part covers important research skills like reading, referencing, and using social media. The fourth part defines research misconduct behaviors. The fifth part discusses authorship issues and the sixth presents the Committee on Publication Ethics. The document provides guidance on responsible research practices.
This document describes a user study conducted to understand how medical experts search medical literature. 46 medical experts performed search tasks on 3 different systems using topics provided by a medical library. The systems varied from a basic Boolean system to one incorporating topic modeling. The topic modeling system was found to be the most difficult to use. Experts issued fewer queries for familiar topics and viewed fewer results. The study aims to help improve search tools for medical literature based on expert search behavior.
Hands on Modern Knowledge Cycle Research Misconduct & Reference ManagementNermin Osman
This document discusses research ethics and reference management. It notes that ethics is an important topic in research and not all researchers work ethically. It provides excerpts from studies showing increases in research misconduct over time, including fabrication, falsification and plagiarism. It also discusses topics like obtaining research approvals, definitions of plagiarism, plagiarism checkers, paraphrasing tools, citing different reference types (e.g. books, journals, conferences) and reference managers like Mendeley.
The document discusses the steps required to perform a systematic review of animal studies. It outlines that a systematic review involves 1) phrasing a clear research question, 2) defining inclusion and exclusion criteria, 3) systematically searching for all original papers on the topic, 4) selecting relevant papers, 5) assessing study quality and validity, 6) extracting data, 7) analyzing results through meta-analysis if possible, and 8) interpreting and presenting the data. The presentation focuses on how to phrase the research question, define criteria, systematically search the literature, assess study quality, and analyze results through meta-analysis to draw overall conclusions.
This document discusses the history and process of scientific peer review. It begins by outlining some of the earliest documented uses of peer review in the 9th century by Ishaq bin Ali Al-Rahawi and in the 18th century by the Royal Society of London. It then describes how peer review evolved in the early 1900s in scientific journals and was facilitated by the introduction of photocopiers. The document outlines different peer review systems and their advantages and disadvantages. It also discusses ways to improve peer review, including the roles of authors, editors, reviewers, and publishers. Overall, the document provides a high-level overview of the development and current state of scientific peer review.
This document outlines the key topics in biomedical ethics that are covered in a course on the subject. It discusses the importance of ethics for biomedical engineering to minimize risks and allow research. It defines ethics, morals, and law and explains the need to consider subjects' welfare, respect for persons, and justice. It also addresses the importance of protecting data privacy and obtaining informed consent. The goal is to learn how to design ethical studies and research while avoiding harm.
This document provides information about using the PubMed database to conduct scientific research. It begins by stating the goals of explaining what PubMed is, how to search it, manage search results, and link to full-text articles. It then discusses key steps in the research process like selecting a topic and question, identifying relevant literature, and using databases to search for sources. Several biomedical literature databases are listed, including PubMed which provides free access to MEDLINE citations and abstracts. Overall, the document offers guidance on utilizing PubMed and other resources to review prior studies for a research topic.
Agent-based modelling,laboratory experiments,and observation in the wildBruce Edmonds
An invited talk at the workshop on "Social complexity and laboratory experiments – testing assumptions and predictions of social simulation models with experiments" at Social Simulation 2018, Stockholm
systematic reviews and what the library can do to helpIsla Kuhn
The document provides information about systematic reviews including:
- How systematic reviews differ from traditional reviews by being more comprehensive and methodical.
- The typical stages in a systematic review including developing a question, searching, screening, data extraction and synthesis.
- Potential biases that can affect systematic reviews like publication bias.
- Tools and resources available from the medical library to help with developing search strategies, managing references and data, and publishing open access reviews.
The document summarizes the results of a project that used a business intelligence software to identify potential drug discovery opportunities in oncology research related to cancer stem cells. The project searched literature databases to identify novel targets, compounds, and assays from research in the US and China since 2008. Key findings included several novel targets, compounds, and assays of interest to pharmaceutical companies, as well as identification of major researchers and institutions involved in related work in the US and China.
Reporting research: writing papers, responding to reviewers, and appealingTrish Groves
- Dr. Trish Groves is the Head of Research at BMJ and editor-in-chief of BMJ Open. She gave a presentation on reporting research, including writing papers, responding to reviewers, and appealing rejections.
- She discussed key stages in the research reporting process like following reporting guidelines, structuring papers using IMRAD, addressing reviewer feedback or appealing rejections, and common reasons why papers are rejected like methodological flaws or incomplete reporting.
- Groves provided guidance on writing different sections of a research paper effectively like the introduction, methods, results, and discussion, and highlighted principles for clear scientific writing.
This document provides an overview of a PubMed workshop being held. The workshop objectives are to teach participants how to effectively search PubMed using Medical Subject Headings (MeSH), subheadings, Boolean operators, filters, and publisher links. The document provides examples of searches on topics such as hearing loss and AIDS, chronic fatigue syndrome, multiple sclerosis, breast cancer and tamoxifen, type 2 diabetes prevention, and non-alcoholic fatty liver disease. Participants will complete a search assignment involving a case study patient.
This document discusses the peer review process for Ayurveda research publications. It covers what peer review is, specific points reviewers examine in manuscripts, strengths and weaknesses of peer review, and common problems with Ayurveda manuscripts. Peer review aims to select quality research for publication and funding by having experts evaluate manuscripts. Reviewers check that studies are scientifically sound and address important problems. However, peer review also has weaknesses like bias, and Ayurveda research faces issues like limited specialized journals and unfamiliarity with international standards. The document advocates for training researchers in writing for publication and following reporting guidelines to strengthen Ayurveda research.
This document provides an overview of important considerations for designing a successful clinical research study. It discusses how to begin by defining research questions and assessing feasibility. It then covers common study design types including experimental, observational, descriptive, and analytical designs. Examples are given of randomized clinical trials, cohort studies, cross-sectional studies, and case-control studies that could be used to study the relationship between hormone therapy and coronary heart disease. Statistical issues like sample size calculations and analytic approaches are also highlighted.
Raising the Bar: New Expectations in Forensic Sciences.Dr. David Burrows
This is a seminar I gave at CLE seminar for North Carolina and South Carolina attorneys in September 2015. The National Commission on Forensic Sciences (NCFS) has several work products in draft and adopted to bring Forensic Sciences from its birth to the standards of today.
PO 397 Introduction to Social Science Research atrantham
This document outlines the key principles and methods of the scientific method. It discusses that science is based on investigating natural processes through logical and systematic methods (1). Key aspects covered include that nature can be understood through order, patterns, and natural causes (2); knowledge is built on empirical evidence and experience rather than assumptions (3); and the goal is to continually improve knowledge rather than remain ignorant (4). It also contrasts deductive and inductive reasoning approaches and covers quantitative and qualitative analysis methods.
Ethics is not based on scientific principles but rather on personal value systems. Three key points about research ethics are:
1) Researchers must respect all individuals affected by their research through honest, respectful treatment and ensuring no unreasonable demands are made.
2) Informed consent is required where participants are made aware of how their information will be used and how they will be involved.
3) Confidentiality of personal information must be maintained and anonymity ensured where possible.
Publishers are caretakers of science. Part of that work is maintaining the integrity of scientific literature. Science builds directly upon past work, so we need to be sure that we are building upon a solid foundation and not faulty research. Publishers need to take an active role in monitoring and tracking faulty, retracted research and its influence. I'm asking publishers to (1) clearly mark retracted papers; (2) alert authors who have already cited a retracted paper; and (3) before publishing an article, check its bibliography for retracted papers.
Retracted papers should be clearly marked everywhere they appear, but today that is not the case. Publishers can also use the CrossRef CrossMark service, which lets readers check for article updates (such as retraction) from a little red ribbon at the top of an article. Checking for citations to retracted articles, and limiting future citations, can help science self-correct by shoring up its foundations.
The document discusses data analysis and negative results in scientific research. It provides examples of how negative results are underreported but still provide valuable information. It emphasizes that negative results:
1) Prevent wasted efforts on experiments that already failed,
2) Help identify false conclusions by focusing only on positive results, and
3) Can still provide important evidence against hypotheses or support the null hypothesis. Examples show how negative results advanced scientific understanding. The document argues negative results should receive the same rigorous interpretation and publication consideration as positive results.
This document provides an agenda for a workshop on research skills and ethics. It begins with an introduction and dedication to the late Dr. Ahmed Zewail, then discusses the differences between scientists and researchers. The second part introduces the Scientific Research Group in Egypt, its members and activities. The third part covers important research skills like reading, referencing, and using social media. The fourth part defines research misconduct behaviors. The fifth part discusses authorship issues and the sixth presents the Committee on Publication Ethics. The document provides guidance on responsible research practices.
This document describes a user study conducted to understand how medical experts search medical literature. 46 medical experts performed search tasks on 3 different systems using topics provided by a medical library. The systems varied from a basic Boolean system to one incorporating topic modeling. The topic modeling system was found to be the most difficult to use. Experts issued fewer queries for familiar topics and viewed fewer results. The study aims to help improve search tools for medical literature based on expert search behavior.
Hands on Modern Knowledge Cycle Research Misconduct & Reference ManagementNermin Osman
This document discusses research ethics and reference management. It notes that ethics is an important topic in research and not all researchers work ethically. It provides excerpts from studies showing increases in research misconduct over time, including fabrication, falsification and plagiarism. It also discusses topics like obtaining research approvals, definitions of plagiarism, plagiarism checkers, paraphrasing tools, citing different reference types (e.g. books, journals, conferences) and reference managers like Mendeley.
The document discusses the steps required to perform a systematic review of animal studies. It outlines that a systematic review involves 1) phrasing a clear research question, 2) defining inclusion and exclusion criteria, 3) systematically searching for all original papers on the topic, 4) selecting relevant papers, 5) assessing study quality and validity, 6) extracting data, 7) analyzing results through meta-analysis if possible, and 8) interpreting and presenting the data. The presentation focuses on how to phrase the research question, define criteria, systematically search the literature, assess study quality, and analyze results through meta-analysis to draw overall conclusions.
This document discusses the history and process of scientific peer review. It begins by outlining some of the earliest documented uses of peer review in the 9th century by Ishaq bin Ali Al-Rahawi and in the 18th century by the Royal Society of London. It then describes how peer review evolved in the early 1900s in scientific journals and was facilitated by the introduction of photocopiers. The document outlines different peer review systems and their advantages and disadvantages. It also discusses ways to improve peer review, including the roles of authors, editors, reviewers, and publishers. Overall, the document provides a high-level overview of the development and current state of scientific peer review.
This document outlines the key topics in biomedical ethics that are covered in a course on the subject. It discusses the importance of ethics for biomedical engineering to minimize risks and allow research. It defines ethics, morals, and law and explains the need to consider subjects' welfare, respect for persons, and justice. It also addresses the importance of protecting data privacy and obtaining informed consent. The goal is to learn how to design ethical studies and research while avoiding harm.
This document provides information about using the PubMed database to conduct scientific research. It begins by stating the goals of explaining what PubMed is, how to search it, manage search results, and link to full-text articles. It then discusses key steps in the research process like selecting a topic and question, identifying relevant literature, and using databases to search for sources. Several biomedical literature databases are listed, including PubMed which provides free access to MEDLINE citations and abstracts. Overall, the document offers guidance on utilizing PubMed and other resources to review prior studies for a research topic.
Agent-based modelling,laboratory experiments,and observation in the wildBruce Edmonds
An invited talk at the workshop on "Social complexity and laboratory experiments – testing assumptions and predictions of social simulation models with experiments" at Social Simulation 2018, Stockholm
systematic reviews and what the library can do to helpIsla Kuhn
The document provides information about systematic reviews including:
- How systematic reviews differ from traditional reviews by being more comprehensive and methodical.
- The typical stages in a systematic review including developing a question, searching, screening, data extraction and synthesis.
- Potential biases that can affect systematic reviews like publication bias.
- Tools and resources available from the medical library to help with developing search strategies, managing references and data, and publishing open access reviews.
The document summarizes the results of a project that used a business intelligence software to identify potential drug discovery opportunities in oncology research related to cancer stem cells. The project searched literature databases to identify novel targets, compounds, and assays from research in the US and China since 2008. Key findings included several novel targets, compounds, and assays of interest to pharmaceutical companies, as well as identification of major researchers and institutions involved in related work in the US and China.
Reporting research: writing papers, responding to reviewers, and appealingTrish Groves
- Dr. Trish Groves is the Head of Research at BMJ and editor-in-chief of BMJ Open. She gave a presentation on reporting research, including writing papers, responding to reviewers, and appealing rejections.
- She discussed key stages in the research reporting process like following reporting guidelines, structuring papers using IMRAD, addressing reviewer feedback or appealing rejections, and common reasons why papers are rejected like methodological flaws or incomplete reporting.
- Groves provided guidance on writing different sections of a research paper effectively like the introduction, methods, results, and discussion, and highlighted principles for clear scientific writing.
This document provides an overview of a PubMed workshop being held. The workshop objectives are to teach participants how to effectively search PubMed using Medical Subject Headings (MeSH), subheadings, Boolean operators, filters, and publisher links. The document provides examples of searches on topics such as hearing loss and AIDS, chronic fatigue syndrome, multiple sclerosis, breast cancer and tamoxifen, type 2 diabetes prevention, and non-alcoholic fatty liver disease. Participants will complete a search assignment involving a case study patient.
This document discusses the peer review process for Ayurveda research publications. It covers what peer review is, specific points reviewers examine in manuscripts, strengths and weaknesses of peer review, and common problems with Ayurveda manuscripts. Peer review aims to select quality research for publication and funding by having experts evaluate manuscripts. Reviewers check that studies are scientifically sound and address important problems. However, peer review also has weaknesses like bias, and Ayurveda research faces issues like limited specialized journals and unfamiliarity with international standards. The document advocates for training researchers in writing for publication and following reporting guidelines to strengthen Ayurveda research.
This document provides an overview of important considerations for designing a successful clinical research study. It discusses how to begin by defining research questions and assessing feasibility. It then covers common study design types including experimental, observational, descriptive, and analytical designs. Examples are given of randomized clinical trials, cohort studies, cross-sectional studies, and case-control studies that could be used to study the relationship between hormone therapy and coronary heart disease. Statistical issues like sample size calculations and analytic approaches are also highlighted.
Raising the Bar: New Expectations in Forensic Sciences.Dr. David Burrows
This is a seminar I gave at CLE seminar for North Carolina and South Carolina attorneys in September 2015. The National Commission on Forensic Sciences (NCFS) has several work products in draft and adopted to bring Forensic Sciences from its birth to the standards of today.
PO 397 Introduction to Social Science Research atrantham
This document outlines the key principles and methods of the scientific method. It discusses that science is based on investigating natural processes through logical and systematic methods (1). Key aspects covered include that nature can be understood through order, patterns, and natural causes (2); knowledge is built on empirical evidence and experience rather than assumptions (3); and the goal is to continually improve knowledge rather than remain ignorant (4). It also contrasts deductive and inductive reasoning approaches and covers quantitative and qualitative analysis methods.
Ethics is not based on scientific principles but rather on personal value systems. Three key points about research ethics are:
1) Researchers must respect all individuals affected by their research through honest, respectful treatment and ensuring no unreasonable demands are made.
2) Informed consent is required where participants are made aware of how their information will be used and how they will be involved.
3) Confidentiality of personal information must be maintained and anonymity ensured where possible.
Publishers are caretakers of science. Part of that work is maintaining the integrity of scientific literature. Science builds directly upon past work, so we need to be sure that we are building upon a solid foundation and not faulty research. Publishers need to take an active role in monitoring and tracking faulty, retracted research and its influence. I'm asking publishers to (1) clearly mark retracted papers; (2) alert authors who have already cited a retracted paper; and (3) before publishing an article, check its bibliography for retracted papers.
Retracted papers should be clearly marked everywhere they appear, but today that is not the case. Publishers can also use the CrossRef CrossMark service, which lets readers check for article updates (such as retraction) from a little red ribbon at the top of an article. Checking for citations to retracted articles, and limiting future citations, can help science self-correct by shoring up its foundations.
This document provides an introduction to research integrity, also known as responsible conduct of research or research ethics. It outlines some of the main areas of focus, including research misconduct, collaboration issues, peer review, conflicts of interest, and human/animal subject research. The document discusses how research ethics is not just about intentionally bad acts, but also imperfect or questionable practices that may seem justified. It provides examples of issues that have arisen in areas like authorship, data sharing and ownership, and socially acceptable practices that are now deemed unethical. Overall, the document provides an overview of the moral foundations and key considerations of research integrity.
PLOS Biology is launching a new section focused on meta-research to increase transparency in biosciences research. Meta-research examines issues related to research design, methods, reporting, evaluation and rewards. This will include exploring sources of bias, data sharing standards, and assessment metrics. Registered Reports will also be introduced, which accept studies for publication based on proposed methods rather than results, reducing bias against negative findings. However, most research data is lost within 10-15 years, highlighting the need for improved data sharing policies to maximize the value of research findings.
This document provides an overview of the scholarly publishing process. It discusses the roles of publishers in soliciting, managing, and reviewing submissions; producing, publishing, and disseminating scholarly works; and archiving content. It also touches on how publishers add value through innovation and technology, such as developing digital platforms and mobile content. The rest of the document focuses on further reading resources for authors, reviewers, editors, and other topics related to scholarly publishing.
This is an instance of fabrication. Abo created fake data and reports about preliminary studies that were never actually conducted.
The consequences could include retraction of any publications containing the fabricated data, loss of funding, loss of job or position, loss of trust and credibility in the research community, and possible legal or institutional sanctions.
To avoid this situation, Abo should have been upfront with the grant agency that preliminary studies had not yet been conducted, but that he believed his proposed methods would be successful based on related work and scientific rationale. He could have requested pilot or feasibility funding to conduct initial studies before applying for a larger grant. Fabricating data is never acceptable.
This document provides an overview of research methodology. It defines research as a systematic process using scientific methods to gain new knowledge. The document discusses why research is important, noting it allows for progress through inquiry. It also outlines the typical steps in conducting research, including selecting a topic, reviewing literature, developing research questions and objectives, determining methodology, collecting and analyzing data, discussing results, and presenting conclusions. Finally, it provides guidance on writing research articles, such as how to structure the paper, format references, and address ethical considerations.
The document discusses identifying bias in scientific studies. It states that good science minimizes bias through random sampling, minimizing measurement bias, and accounting for multiple factors. Bias can come from the language used, data reported, and source of the data. The scientific community engages in quality control like independent duplication of results and peer review to eliminate bias.
The document discusses identifying bias in scientific studies. It states that good science minimizes bias through random sampling, minimizing measurement bias, and having a large enough sample size. Bias can influence results and different scientists may find different solutions to the same problem. The scientific community engages in quality control like independent duplication of studies and peer review to eliminate bias. Results are more reliable if verified through these methods.
EBD is sequential, systematic process of addressing a clinical or community relevant problems.
EBD components are;
Clinical expertise
Patient’s preferences & values
Highest level of evidence
This document provides an overview of the IRB approval process at James R. Galt's institution. It discusses why IRB approval is needed, what types of research require approval, and the key components of the IRB submission process, including study protocols, informed consent documents, and other approvals that may be required. It aims to help researchers understand the steps involved in obtaining IRB approval for their studies involving human subjects.
This document discusses research misconduct and issues of reproducibility. It defines research misconduct as fabrication, falsification, or plagiarism. While science aims to be self-correcting, many published findings are not reproducible or trustworthy. Several factors make results less likely to be true, such as small studies, small effect sizes, and conflicts of interest. Efforts are underway to improve reproducibility through replicating studies, publishing negative results, and establishing standards for transparent and ethical research.
This document discusses what science is and is not. It begins by stating that science attempts to disprove ideas rather than prove them, and is concerned with understanding the natural world through observation and experimentation. It notes several misconceptions, such as the idea that science can prove anything or that there is a linear progression from hypothesis to theory to law. Good science minimizes bias through random sampling, appropriate measurement techniques, and independent verification. It emphasizes that science provides the most reliable knowledge about the natural world but does not claim certainty, only degrees of probability. Overall, the document provides a concise overview of the scientific process and addresses common misconceptions about the limitations and objectives of science.
The document discusses the benefits of clinical trial authors submitting supplemental materials and making raw trial data publicly available, such as enabling other researchers to verify results, test secondary hypotheses, and aid the design of future trials, while also outlining some arguments against data sharing and proposing a code of conduct for data sharing. It concludes by suggesting medical journals require data availability for publication to help address issues around researchers restricting access to trial data.
The document discusses the benefits of clinical trial authors submitting supplemental materials and making raw trial data publicly available, such as enabling other researchers to verify results, test secondary hypotheses, and aid the design of future trials, while also outlining some arguments researchers give against data sharing and proposing a code of conduct for data sharing.
Workshop Part 2: Publication Ethics for Biomedical Researchers (BioMed Centra...balaram_biomedcentral
The second presentation in the 2015 BioMed Central author workshop presented at institutions in Brazil.
In this segment, Dr. Maria Kowalczuk, Biology Editor, shares information on research ethics and publication ethics, drawing from her experience as a member of the BioMed Central Research Integrity Group.
The document discusses ethics in research and provides examples of ethical and unethical research practices. It defines ethics as norms for acceptable versus unacceptable behavior. Research ethics are important to promote transparency, accountability, and public trust in research. Common ethical principles discussed include honesty, integrity, and respect for colleagues. The document outlines various codes and policies for research ethics from government agencies and professional societies. It also discusses how to make ethical decisions and identifies the most serious offenses as fabrication, falsification, and plagiarism. Examples are given of past cases of scientific misconduct.
This document discusses the need for open science due to a reproducibility crisis in many scientific disciplines. It notes that many published findings cannot be replicated and estimates that at least two-thirds of published results in psychology and biomedicine may be incorrect. This represents a credibility crisis that undermines public trust in science. The document argues that adopting practices of open science such as preregistration, open data, and detailed documentation can help address this crisis by reducing biases, enabling replication, and increasing transparency and reproducibility. Open science is presented as a means of improving research quality and accelerating discovery for the benefit of both science and society.
Similar to Scientific papers as open discovery tools (20)
I would not recommend including details about prior rejections from other journals in your cover letter. The editors will not have access to those previous reviews, so it does not provide useful context. Focus instead on clearly explaining the significance and novelty of your findings for the specific readership of the journal you are submitting to.
Here are a few things not to include in a cover letter when submitting a revised manuscript:
- Details about previous rejections from other journals
- Criticism of previous reviewers/editors' assessments
- Apologies for lack of impact or interest
- Excessive focus on the manuscript's weaknesses or limitations
- Requests for special treatment or exceptions to normal policies
The cover letter should focus on addressing issues raised in the previous review, changes made to strengthen the work, and why the revised manuscript is a good fit for the journal. It's best to maintain a positive tone that emphasizes the manuscript's strengths and significance within the journal's scope.
The reviewer critiques a paper that aimed to identify genetic elements from metagenomic DNA that confer tolerance to inhibitory compounds in E. coli. The reviewer argues that: 1) Using E. coli to screen metagenomic DNA libraries for novel functions is not a novel approach. 2) The paper does not demonstrate how the identified tolerance genes improve E. coli for biomass conversion as claimed. 3) There is no evidence the identified genes confer combined tolerance to mixtures of inhibitors. 4) The identified genes appear to encode general "housekeeping" functions rather than dedicated resistance mechanisms. The reviewer concludes the short study does not provide new insights and would not qualify for publication in specialist journals.
The document discusses scientific publishing and the editorial process. It notes that the goal of publishing is to advance science by having authors disclose their findings in exchange for credit. The editorial process involves peer review, where editors select reviewers with relevant expertise. Reviewers provide feedback to help editors decide whether to accept, reject, or request revisions to manuscripts. The process aims to critically evaluate works and ensure high quality through transparency.
This document discusses systems biology and provides examples of regulatory networks and dynamics modeling in systems biology. It summarizes that systems biology aims to understand biological processes using a systems-level approach by integrating 'omics data, quantitative analysis, and computational modeling to study biological systems at various scales, from pathways to whole organisms. It also notes the rapid expansion of the field since 2000 and discusses current and future directions, including data integration, modeling dynamics, placing networks in spatial and temporal contexts, and applications to medicine.
The editorial process involves authors submitting manuscripts that are reviewed by editors and peer reviewers to determine if a paper should be published. If selected for review, the manuscript is sent to 3-4 peer reviewers with relevant expertise. Based on the reviews, the editor decides to reject the paper, ask for revisions, or accept it for publication. The goal is to publish papers that advance science while maintaining a high standard of quality through a rigorous review process.
In his public lecture, Christian Timmerer provides insights into the fascinating history of video streaming, starting from its humble beginnings before YouTube to the groundbreaking technologies that now dominate platforms like Netflix and ORF ON. Timmerer also presents provocative contributions of his own that have significantly influenced the industry. He concludes by looking at future challenges and invites the audience to join in a discussion.
Cosa hanno in comune un mattoncino Lego e la backdoor XZ?Speck&Tech
ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune.
Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile.
BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).
GraphSummit Singapore | The Future of Agility: Supercharging Digital Transfor...Neo4j
Leonard Jayamohan, Partner & Generative AI Lead, Deloitte
This keynote will reveal how Deloitte leverages Neo4j’s graph power for groundbreaking digital twin solutions, achieving a staggering 100x performance boost. Discover the essential role knowledge graphs play in successful generative AI implementations. Plus, get an exclusive look at an innovative Neo4j + Generative AI solution Deloitte is developing in-house.
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
Infrastructure Challenges in Scaling RAG with Custom AI modelsZilliz
Building Retrieval-Augmented Generation (RAG) systems with open-source and custom AI models is a complex task. This talk explores the challenges in productionizing RAG systems, including retrieval performance, response synthesis, and evaluation. We’ll discuss how to leverage open-source models like text embeddings, language models, and custom fine-tuned models to enhance RAG performance. Additionally, we’ll cover how BentoML can help orchestrate and scale these AI components efficiently, ensuring seamless deployment and management of RAG systems in the cloud.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/building-and-scaling-ai-applications-with-the-nx-ai-manager-a-presentation-from-network-optix/
Robin van Emden, Senior Director of Data Science at Network Optix, presents the “Building and Scaling AI Applications with the Nx AI Manager,” tutorial at the May 2024 Embedded Vision Summit.
In this presentation, van Emden covers the basics of scaling edge AI solutions using the Nx tool kit. He emphasizes the process of developing AI models and deploying them globally. He also showcases the conversion of AI models and the creation of effective edge AI pipelines, with a focus on pre-processing, model conversion, selecting the appropriate inference engine for the target hardware and post-processing.
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Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
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Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdf
Scientific papers as open discovery tools
1. EMBO Scientific Publishing
Thomas Lemberger
Chief Editor, Molecular Systems Biology
Deputy Head of Publications, EMBO
1. Editorial Process
2. Scientific integrity
3. Integrating data in papers
2. Scientific
publishing
“The publication of scientific
information is intended to move
science forward. More
specifically, the act of publishing
is a quid pro quo in which
authors receive credit and
acknowledgment in exchange
for disclosure of their scientific
findings.”
11. EMBO Scientific Publications
• All areas of molecular &
cell biology
• All areas of molecular &
cell biology
• First journal launched by • Short-format papers
EMBO (1982)
• Science & Society
section
• Systems biology,
synthetic biology,
systems medicine
• At the interface between
basic and clinical life
sciences
• Open Access
• Open Access
14. OPEN
ACCESS
R Aebersold
GM Church
E Liu
L Hood
Scope & general
policies
Senior Editors
Advisory Board
P Bork
EMBO Editors:
Thomas Lemberger
Maria Polychronidou
Julie Ahringer
Charles Auffray
Ewan Birney
Tom Blundell
Thomas S. Deisboeck
Jan Ellenberg
Michael Elowitz
Alan Fersht
Stan Fields
Mark Gerstein
Frank Holstege
Sung Hou Kim
Hiroaki Kitano
Doron Lancet
Andrew J. Link
Stephen Oliver
Jeremy Nicholson
Bernhard Palsson
Rama Ranganathan
Uwe Sauer
Luis Serrano
Lucy Shapiro
Pamela Silver
Michael Snyder
Janet Thornton
Masaru Tomita
Marc Vidal
Hans V. Westerhoff
Lothar Willmitzer
John Yates
18. First editorial decision
EMBO editors read the entire manuscript (yes!)
Decision on a balance of multiple factors:
•
•
•
•
•
Scope
Novelty & conceptual advance
Mechanistic, functional, biological insights
Utility of methods, dataset, resource
Completeness and conclusiveness of the analysis
19. In case of doubt...
R Aebersold
GM Church
E Liu
L Hood
Senior Editors
Advisory Board
P Bork
EMBO Editors:
Thomas Lemberger
Maria Polychronidou
Julie Ahringer
Charles Auffray
Ewan Birney
Tom Blundell
Thomas S. Deisboeck
Jan Ellenberg
Michael Elowitz
Alan Fersht
Stan Fields
Mark Gerstein
Frank Holstege
Sung Hou Kim
Hiroaki Kitano
Doron Lancet
Andrew J. Link
Stephen Oliver
Jeremy Nicholson
Bernhard Palsson
Rama Ranganathan
Uwe Sauer
Luis Serrano
Lucy Shapiro
Pamela Silver
Michael Snyder
Janet Thornton
Masaru Tomita
Marc Vidal
Hans V. Westerhoff
Lothar Willmitzer
John Yates
21. To review or not to review...
time
review
editorial
rejection
reject
revise
reject
accept
22. Peer-review
Referees are invited based on:
• Balance of expertise
• Reputation as researcher
• Reputation as reviewer
• No conflict of interest (positive or negative)
3 (4) reviewers / manuscript
24. Referee report
1.
Summary
• Describe your understanding of the story
• What are the key conclusions: findings and concepts
• What are the methodology and model system
2.
General remarks
• Are you convinced of the key conclusions?
• Place the work in its context.
• What is the nature of the advance (conceptual, technical, clinical)?
• How important is the advance as compared to previous knowledge?
• What audience will be interested in this?
3.
Major points
• Specific criticisms related to key conclusions
• Specify experiments or analyses required to demonstrate the conclusions
• Motivate your critique with relevant citations and argumentation
4.
Minor points
• Easily addressable points
• Presentation and style
• Trivial mistakes
27. Cross-commenting
Ref #3
Ref #2
Ref #1
Ref #2 cross-comments
“…[it] settles a controversy in the field which has been going
on for more than ten years. In summary, this is a landmark
paper. I cannot support publication in your journal strongly
enough!”
“As written, the paper is focused on the methods, which is
fine given that's where it makes its most substantial
contribution. But the writing is quite technical and could
benefit from more explanation of the high-level logic of their
approach.”
“After reading through this nicely-executed technical work,
one is left with an impression that after all we really have not
gained much new mechanistic insights.
…in addition to the XXX data that should be generated
under their current framework…”
…Each reviewer has numerous suggestions about how to
do this. It will likely be impossible to incorporate them all
while retaining a coherent narrative. […]
Reviewer 3 also calls for an additional experiment including XXX stains in the current dataset. To incorporate
this into their current analytical framework, the authors
would have to find parameters and reagents to allow
simultaneous imaging of 5 genes (not just the 4 presented
here). Moreover, they would then have to reacquire all
images using the 5-stain protocol.
While I agree that it would be useful to have XXX data
included, I also believe that this is beyond the scope of this
paper.
29. Transparent Process
• Transparent Anonymous Peer Review:
Anonymous referee reports and editorial correspondence are published alongside papers
• Single Round of Major Revision:
More than 90% of invited revisions are published at Molecular Systems Biology
• Referee Discussion before Decision:
Referees are invited to comment on each other's reports before the editor makes a decision
• Scooping Protection:
Findings that are published by others during review or revision are not a criterion for rejection
• Source Data for Figures:
Authors can archive and make available the data underlying their published figures
• Flexible Formatting:
No journal-specific formatting required at submission
30. Scientific
publishing
“The publication of scientific
information is intended to move
science forward. More
specifically, the act of publishing
is a quid pro quo in which
authors receive credit and
acknowledgment in exchange
for disclosure of their scientific
findings.”
31. Scientific publishing
The publication of scientific information is intended to
move science forward. More specifically, the act of
publishing is a quid pro quo in which authors receive
credit and acknowledgment in exchange for
disclosure of their scientific findings.
Implies:
• Originality
• Integrity
• Authenticity
Respect of:
• Laws and ethics
• Safety and security
• Societal context
32. Data integrity
Beautification
• Clarification
• Aesthetics
Selective reporting
• Misrepresentation of the
data
• Biasing data to fit a
particular hypothesis
Fabrication
• Deliberate
manufacturin of
data
45. Seoul National University's report on Dr. Hwang Woo Suk:
The data in the 2005 article including test results from
• DNA fingerprinting,
• photographs of teratoma,
• embryoid bodies,
• MHC-HLA isotype matches and
• karyotyping
have all been fabricated.
http://www.useoul.edu/snunews?bm=v&bbsidx=71494&page=63
46. Figure 2F
Figure 6D
(F) NT-ESC colony with typical
morphology derived from a caffeinetreated SCNT human blastocyst.
(D) Human NT-ESCs expressed standard pluripotency
markers detected by immunocytochemistry for
antibodies against OCT4, NANOG, SOX2, SSEA-4,
TRA-1–60, and TRA-1–81. Original magnification, ×200;
Ph, phase contrast.
47. In Figures 2F and S5 (upper-right), we presented two phase-contrast photos of fields of cells, correctly labeled as SCNT-derived
hESO-NT1 and IVF-derived hESO-7, respectively. These images are the same fields of cells shown in the top two images of
Figure 6D; however, in Figure 6D, we inadvertently switched the labels on the images. This re-use of the images was intentional,
but we should have indicated this in the original legend for Figure 6. We have corrected the labeling error in Figure 6D.
We would also like to note that the Scientific Integrity Committee at Oregon Health & Science University has carefully assessed
the paper and the errors and has concluded that there is no evidence of fabrication, falsification, or plagiarism that would warrant
further inquiry or investigation into research misconduct.
Figure 2F
Figure 6D
(F) NT-ESC colony with typical
morphology derived from a caffeinetreated SCNT human blastocyst.
(D) Human NT-ESCs expressed standard pluripotency
markers detected by immunocytochemistry for
antibodies against OCT4, NANOG, SOX2, SSEA-4,
TRA-1–60, and TRA-1–81. Original magnification, ×200;
Ph, phase contrast. Note that the upper-left image for
hESO-NT1 is the same shown in Figure 2F.
48. What can PIs do?
•
•
•
•
•
•
•
Provide guidance to students and postdocs
View original data
Organize good data management practice
Maintain an open lab environment
Accept only relevant authorship
Cooperate with editors
Retract/correct as appropriate
49. What can journals do?
•
•
•
•
Rigorous peer review
Check by editors before publication
Investigation and retraction policy
Data transparency
55. • Data archival service
• Data‘transparency‟
• Data reuse
• Data-oriented search
56. 15/27
Structured metadata:
„perturbation-observation-assay‟
(Level 0:metadata associated to individual panels.)
Level 1: „object-oriented‟ representation of
experimental variables as a list of chemical
and biological components.
Level 2: represent the causality of the experimental
design: “Measurement of Y as a function of A,
B, C, using assay P in biological system S.”
Level 3: machine-readable representation with
standard identifiers.
experimental system
perturbed
component
measured
component
assayed
property
57. 9/27
SourceData
Tools to publish figures as structured digital objects
that link the human-readable illustrations with
machine-readable metadata and „source data‟ in
order to
•improve data transparency;
•make published data useable;
•enable data-oriented search.
58. 19/27
drug Z
activity
kinase Y
kinase Y
protein X
Paper 3
Paper 2
Paper 1
Data-oriented search
gene x
P
tissue T
disease
D
Resulting hypothesis: test drug Z in disease D.
60. Scientific publishing
• Dominant channel for the
dissemination of peer-reviewed
data.
• Journals function as a proxy for
quality in research assessment
• The rate of publishing keeps
increasing.
• Papers are human-readable but
poorly machine-readable.
62. The Paper of the Future?
Search
<!DOCTYPE article PUBLIC "-//NLM//DTD
Journal Archiving and Interchange DTD v2.3
20070202//EN" "archivearticle.dtd">
<article article-type="researcharticle"><?properties no_embargo?>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Mol Syst
Biol</journal-id>
<journal-title>Molecular Systems
Biology</journal-title>
<issn pub-type="epub">1744-4292</issn>
<publisher>
<publisher-name>Nature Publishing
Group</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-idtype="pmc">2238715</article-id>
Data
Methods
Claims
Authors
Models
63.
64.
65. Future directions in systems biology
• Genome-wide genetics of human diseases
• Translational systems biology or systems
medicine
• Genome-scale engineering & synthetic biology
• Temporal structure of biological processes
• ‘In vivo biochemistry’ with single-cell singlemolecule assays
• Bridge the gap between ‘omics’ and mechanistic
models
66.
67. “How do we get from the
Jimome & Craigome to
systems biology?”
George M Church, Senior Editor
68. Multi-omics data integration
Global analysis of genome, transcriptome and
proteome reveals the response to aneuploidy in
human cells.
Zuzana Storchova, Mol Syst Biol. 2012 8:608.
Integration of clinical data with a genome-scale metabolic model of the
human adipocyte.
Jens Nielsen and colleagues, Mol Syst Biol. 2013;9:649.
69. Comparative omics for functional discoveries
Human disease locus
discovery and mapping to
molecular pathways through
phylogenetic profiling.
Gary Ruvkun and colleagues,
Mol Syst Biol. 2013 9:692
19 017 human genes
Phylogenetic profiles of across 86 eukaryotic genomes.
71. Spatial patterns
Waks et al, 2011 Mol Syst Biol 7:506
Di Vetura and Sourjik , 2011 Mol Syst Biol 7:457
72. Temporal patterns
Promoter decoding of transcription factor dynamics involves a tradeoff between noise and control of gene expression.
Hansen AS, O'Shea EK. Mol Syst Biol. 2013 9:704
73. Cell population & dynamics
Digital cell quantification identifies global immune cell dynamics during influenza
infection.
Ido Amit and colleagues, 2014 Mol Syst Biol. 10:720
74. Microbiome & metagenomics
A top-down systems biology view of microbiomemammalian metabolic interactions in a mouse
model.
J. Nicholson and colleagues, Mol Syst Biol. 2007 3:112.
Toward molecular trait-based ecology through integration of
biogeochemical, geographical and metagenomic data.
Peer Bork and colleagues, Mol Syst Biol. 2011 7:473