Hello Rav,
Q. The kitzur Shulchan Aruch (5:11) says that after flatulating, its forbidden to utter any holy words until the odor is gone. Would the same apply to thinking Torah thoughts or reading Torah without speaking out the words, or can we be lenient to continue learning out of a sefer silently while the odor is still present?
Thanks

A. Talmud Brochos 24b and Shulchan Aruch (O.H. 79: 9 and 103: 1) rule that one should stop praying the amida, reading shema or learning Torah after himself passing gasses, until the odor is gone.
For the flatulence of others, he should also halt tefila and shema, but not the learning of Torah. Mishna Berura (79: 30) explains that since bad odor that has no open existing source, prohibits words of kedusha only on the Rabbinical level, when bitul Torah (the annulment of Torah learning) of many may be involved, our Sages were lenient.
Horav Shlomo Miller’s opinion in regards to just thinking in learning after one’s own gas discharge is that one should avoid thinking in learning and concentrate on Shivisi Hashem (see question 1627 above) or on divrei musar on good midos and plans for performing mitzvos.

Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit’a