The major journals in bioinformatics are (for algorithms, methods and software):

• Bioinformatics (former CABIOS)
• Journal of Computational Biology
• BMC Bioinformatics

There are a lot of papers also in:

• Nucleic Acids Research (database and software issues)

And then there are all the genomics, phylogenetics, evolution-related journals. What I suggest is that you follow the journals where you have the most articles on your research topic.

Hi,

This webpage lists most of the journals in Bioinformatics and Computational Biology.

Link to the webpage

Top 10 in that list are:

1. BIOINFORMATICS - Bioinformatics/computer Applications in The Biosciences
2. JCB - Journal of Computational Biology
3. BMC Bioinformatics
4. TITB - IEEE Transactions on Information Technology in Biomedicine
5. PLOS COMPUT BIOL - Plos Computational Biology
6. CMPB - Computer Methods and Programs in Biomedicine
7. BIB - Briefings in Bioinformatics
8. CANDC - Computational Biology and Chemistry / Computers & Chemistry
9. JBI - Journal of Biomedical Informatics
10. TCBB - IEEE/ACM Transactions on Computational Biology and Bioinformatics

Also you can follow their twitter feeds for more updates.

I hope this helps.

I post this question even before I start my PhD in computational biology.

After 3 years of my PhD study, I try to give a proper answer:

Short Answer : Not only journals but also conferences.

Long Answer The most thing you should focus on, if you want to design software or algorithms, is the following top conferences:

1. ISMB

2. RECOMB

3. WABI

These conferences publish state-of-the-art ideas of algorithms and software.

Then it comes journals:

1. Bioinformatics

2. Genome Research (software)

3. Nature Methods (software)

4. Nature Genetics

5. Nature Review Genetics

6. Journal of Computational Biology

7. BMC Bioinformatics

8. Nucleic Acids Research

You may wonder: so many journals, how could I handle them.

Again, you need to firstly focus on those top conferences, and there are only three. Try to read all papers on them.

Then, try to follow some new research ideas in Nature series.

Finally, follow articles on these journals for the specific topics you are interested in.

That is my understanding, hope it helps.