Biochemistry and Molecular Biology
Penn State Science
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BMMB 502: Critical Analysis of the Biochemical, Microbial, and Molecular Biology Scientific Literature

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Critical Analysis of the Biochemical, Microbial, and Molecular Biology Scientific Literature

BMMB 502

Spring 2017

Tuesdays        8:00-9:15 am                                      307 Bouke Building
Instructor: Ross Hardison                                           Office: 304 Wartik Laboratory
Telephone: 814-863-0113                                          E-mail:
Office hours: by appointment

Course Description and Objectives

This course is designed to improve the student’s ability to read and interpret the primary scientific literature in biochemistry, microbiology, and molecular biology (BMMB). The immediate aim is to help the students prepare for the candidacy exam, and it is expected that skills acquired or honed during this course will be used for the rest of their careers. The scientific method requires the assilimation of prior knowledge and the application of appropriate methods to generate new data that provide robust insights into important problems. Critical reading of the literature is essential to those endeavors. New techniques, new data, and new insights are natural outcomes of scientific pursuits, and one learns about them through critical reading of the literature.

The course begins with the common characteristics of good papers, including a guide to reading papers. Two classic papers in RNA splicing mechanisms serve as exemplars of excellent papers. Then we will read and critically discuss papers that examine several different themes. Of course, any topics in BMMB would be appropriate for honing one’s skills in critical analysis of papers. I have selected papers that illustrate a range of types of papers and topics.

Expectations of the students

After the introductory class, the classes will be devoted to the critical discussion of papers, usually as a short series of papers on a topic. The papers are listed in the schedule. All students should read each paper and come to class prepared to discuss it. One student (or two if needed to match the numbers of students and papers) will be the discussion leader for each paper. The leader will present a brief background summarizing the question(s) addressed and how these questions fit into a larger context. Thus the leader will be expected to read more extensively on the topic than is expected of the rest of the class. The goal is not for the leader to cover the paper while everyone else listens, but rather the leader should engage the class in a discussion of key topics. The leader should ask questions of the students, and student answers will serve as the mode for discussion. A good way for the leader to prepare for the class is to make a presentation (e.g. PowerPoint) with a few slides on the background, and then slides with the key figures or tables for discussion. Also the leader should have questions ready to ask. Other students can also ask questions. The instructor can help point questions to individual students to insure that everyone participates. The goal for each class is to critically evaluate the strengths and weaknesses of each paper.


Grades will be assigned by the instructor based on each student’s work as the discussion leader (50%) and participation in discussions when not a leader (50%).


Date Theme Topic Papers
10-Jan Examples of excellent, influential papers What makes a good paper? How to read a paper. Hardison presentation
17-Jan Discovery of self splicing RNA Cech et al. 1981; Cech Nobel Lecture 1989
24-Jan A branched splicing intermediate Ruskin et al. 1984
31-Jan Transcriptomes and controversies in interpreting them RNA-seq for transcriptome determination: the method Mortazavi et al. 2008
7-Feb Global analyses of transcriptomes; PCAs Hardison presentation
14-Feb Mammalian transcriptomes differ mainly by species, not tissue Lin et al. 2014
21-Feb Mammalian transcriptomes differ mainly by tissue, not species Gilad & Mizrahi-Man 2015
28-Feb Meta-analysis of RNA-seq expression data across species, tissues, studies Sudmant et al. 2015
7-Mar Spring Break
14-Mar Insights from 3-D structures of chromosomes 3-D chromosomal conformation capture: method Dekker et al. 2002
21-Mar High resolution HiC for inferring loops Rao et al. 2014
28-Mar Induction of Pluripotency Nobel lecture from Shinya Yamanaka Yamanaka 2012
4-Apr Induction of pluripotency by defined factors Takahashi and Yamanaka 2006
11-Apr Utilizing epigenomic information to better understand the genetic basis of complex phenotypes Genetic variants in regulatory regions and their role in complex phenotypes Maurano et al. 2012
18-Apr Obesity associated variants in FTO target a distal gene Smemo et al. 2014
25-Apr Summary How will this course help your own writing?
2-May Finals week, no  final exam


The Eberly College of Science Code of Mutual Respect and Cooperation ( embodies the values that we hope our faculty, staff, and students possess and will endorse to make The Eberly College of Science a place where every individual feels respected and valued, as well as challenged and rewarded.

The Eberly College of Science is committed to the academic success of students enrolled in the College's courses and undergraduate programs. When in need of help, students can utilize various College and University wide resources for learning assistance.

Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at

In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.”

Academic Integrity

All Penn State policies regarding ethics and honorable behavior apply to this course (see links below for policy statements). Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. All University policies regarding academic integrity apply to this course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such. All exam answers must be your own, and you must not provide any assistance to other students during exams. Any instances of academic dishonesty WILL be pursued under the University and Eberly College of Science regulations concerning academic integrity.