This is how to find scientific papers when you are doing a literature review (or "lit review" or "lit search"). I recommend using multiple methods because each has its limitations. A multi-website approach will give you better results.
PubMed
PubMed.gov is the National Institutes of Health (NIH) government-funded search engine for biomedical research, biology, chemistry, and other topics of interest to human health. It indexes specific journals that fit this criteria and any articles (human-focused or not) that are published in those journals. For example, my plant RNA regulation and alternative splicing paper is indexed on PubMed. Plant research is relevant for human health as well, from nutrition to medical advances. PubMed thus includes a lot of basic biology research and sociology research.
PubMed provides links to articles for the original publisher's website (which might be behind a paywall) and links to PubMed Central (which releases articles free to the public after 1 year post-publication, if the research is NIH-funded). PubMed Central is a great way to get free access to NIH-funded research articles.
Find raw data through PubMed:
Scroll down past the abstract, similar articles, cited by, and references sections. You will find useful links to other NIH data repositories under section "Related information". For example, search my Gonzalez et al 2018 placenta RNA-seq paper on PubMed and click on the "GEO DataSets" link for my paper, then click again on the title to reach the NCBI GEO accession GSE109082, where you can download the gene counts which we input into our DESeq2 analysis. You can re-create my results with these raw counts.
Limitations of PubMed:
PubMed's focus is biomedical research and basic life sciences research. It decides what is included by selecting specific journals to index that fit this interest. Although its reach is broad, PubMed is not the best place to search for topics such as abstract mathematics, engineering, law, quantum physics, etc. You will find some papers on these topics, but you won't find everything so you will need to supplement your search with other engines. For example, the citation for the famous Benjamini-Hochberg false discovery rate statistics method, utilized almost universally for all current RNA-sequencing publications, is not on PubMed.
Google Scholar
Google Scholar (scholar.google.com) is Google's search engine for research papers. It has a broader range than PubMed because it includes research that isn't life sciences. If you are looking for physics, law, mathematical, and sociology research, Google Scholar may be a better search engine than PubMed.
Google Scholar also includes patent searches which allows you to find more information on commercial products such as RNAlater.
Due to their image-to-text technology, Google Scholar is also better for finding old pre-1990s papers with pdf files created from scans. If your interest is historical articles, Google Scholar will find more results than PubMed.
Follow manuscripts using the "Cited by ___" link under search results. Sometimes you find a useful paper but it is old and you are looking for follow up or recent related articles. Click on the "Cited by ___" link to find later papers.
Additionally, if you are specifically looking for RECENT publications, use the publication time filters on the left-hand side (e.g. "Since 2024"). This is especially important for fast moving fields and for new technologies like single cell RNA-seq.
Limitations of Google Scholar:
Google Scholar does not cross-reference the NIH repositories. It will link to the publisher's website preferentially, so you might hit paywalls for articles that are otherwise freely available to the public (no paywall) on PubMed Central. For biomedical research, I recommend using PubMed.gov first, Google Scholar second. Ideally use both.
ResearchGate
ResearchGate.net is a social media platform for researchers, not an official index or search engine for journal articles. Its focus is researcher bios, linking people together (allowing you to follow other researchers), encouraging researchers to upload pdf copies of their papers (public or private), and Q&As to help troubleshoot experiments and interpret data. If you can't find an article elsewhere and see the authors on ResearchGate, request it through ResearchGate. The authors can send you a private pdf copy even if the publisher keeps it behind a paywall.
Institutional VPNs - how to get past paywalls
Universities, public libraries, and other research-focused employers (like Cedars-Sinai) often pay for licenses to access journals. If an article is behind a paywall to you at home, you may be able to access it by searching when connected to your institution's internet or by connecting through an institutional virtual private network (VPN).
For university students - contact your university library staff to learn more.
- Cal State LA: Off Campus Access to Library Resources
- UCLA: Connecting from Off-Campus
- UC Berkeley: Connect from off campus
- University of Southern California: Remote Access to Electronic Resources
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