Visualizations

UCSF’s top 15 departments for clinical trials

/ Anirvan Chatterjee
Photo: Thomas Hawk

UCSF is a top institution for clinical trials. Here are UCSF’s departments, sorted by the number of open clinical trials from principal investigators who have a primary association to that department. (This list is based on open trials listed in UCSF’s new Clinical Trials website, in cases where trials are associated with one or more principal investigators’ UCSF Profiles pages. If a trial’s PIs span multiple departments, the trial will be counted once for each department.)

  1. Medicine is running 370 trials from 133 PIs/co-PIs
  2. Pediatrics is running 97 trials from 35 PIs/co-PIs
  3. Neurology is running 96 trials from 29 PIs/co-PIs
  4. Surgery is running 41 trials from 28 PIs/co-PIs
  5. Psychiatry is running 40 trials from 28 PIs/co-PIs
  6. Ob/Gyn, Reproductive Sciences is running 35 trials from 13 PIs/co-PIs
  7. Neurological Surgery is running 26 trials from 9 PIs/co-PIs
  8. Radiology is running 24 trials from 14 PIs/co-PIs
  9. Radiation Oncology is running 23 trials from 4 PIs/co-PIs
  10. Anesthesia is running 19 trials from 15 PIs/co-PIs
  11. Dermatology is running 13 trials from 8 PIs/co-PIs
  12. Ophthalmology is running 13 trials from 7 PIs/co-PIs
  13. Proctor Foundation is running 12 trials from 4 PIs/co-PIs
  14. Orthopaedic Surgery is running 11 trials from 8 PIs/co-PIs
  15. Dean’s Office is running 11 trials from 11 PIs/co-PIs
  16. Urology is running 9 trials from 6 PIs/co-PIs

Photo: Thomas Hawk, CC-BY-NC 2.0

Top 20 UCSF departments for junior/senior faculty collaboration

/ Anirvan Chatterjee

Some UCSF departments do a better job of fostering collaboration between junior and senior faculty members. Using UCSF Profiles data, I looked at co-authorship patterns among current faculty at departments across UCSF, to see which departments have the highest rate of junior-senior collaborations. (Caveat: Departments can have different sizes, faculty experience mixes, and field-specific publishing patterns, so comparisons are always imperfect.)

Method

  1. I used UCSF Profiles to identity current UCSF faculty (title includes the words “Professor,” “Dean,” or “Chancellor”) with at least 5 publications, and at least 3 years of publishing experience (i.e. time between the earliest and latest publications). I assigned faculty to departments using their current primary departmental affiliation, and considered only those departments with 20 such faculty members.
  2. In each department, I sorted the faculty by seniority using, in order, title (e.g. “Professor” outranks “Assistant Professor”), number of publications, and length of publishing experience. I then selected the 25% most junior and 25% most senior faculty from each department, and considered every possible junior-senior pair. (So for a department of 40 people, I’d pick out 10 junior, and 10 senior faculty, for a total of 100 junior-senior combinations).
  3. For each of these combinations, I checked if there exists at least one publication where both the junior and senior faculty members are listed as co-authors. For example, if there was a department of 12 faculty members, I’d pick the 3 most junior (A, B, C) and 3 most senior (X, Y, Z); if A and X have been co-authors on 1 publication, and B and Y on 3 publications, then there have been 2 unique junior/senior co-authorship pairs, of 9 possible.

The top 20 departments

  1. Urology • 43%
    the 10 most junior and 10 most senior faculty have 43 unique junior/senior co-authorship pairs, of 100 possible
  2. Physiological Nursing • 35%
    the 7 most junior and 7 most senior faculty have 17 unique junior/senior co-authorship pairs, of 49 possible
  3. Radiation Oncology • 34%
    the 8 most junior and 8 most senior faculty have 22 unique junior/senior co-authorship pairs, of 64 possible
  4. Neurological Surgery • 30%
    the 15 most junior and 15 most senior faculty have 67 unique junior/senior co-authorship pairs, of 225 possible
  5. Orofacial Sciences • 22%
    the 8 most junior and 8 most senior faculty have 14 unique junior/senior co-authorship pairs, of 64 possible
  6. Preventive & Restorative Dental Sciences • 20%
    the 12 most junior and 12 most senior faculty have 29 unique junior/senior co-authorship pairs, of 144 possible
  7. Cellular Molecular Pharmacology • 19%
    the 6 most junior and 6 most senior faculty have 7 unique junior/senior co-authorship pairs, of 36 possible
  8. Orthopaedic Surgery • 18%
    the 16 most junior and 16 most senior faculty have 46 unique junior/senior co-authorship pairs, of 256 possible
  9. Family Community Medicine • 16%
    the 10 most junior and 10 most senior faculty have 16 unique junior/senior co-authorship pairs, of 100 possible
  10. Pathology • 15%
    the 16 most junior and 16 most senior faculty have 39 unique junior/senior co-authorship pairs, of 256 possible
  11. Family Health Care Nursing • 14%
    the 7 most junior and 7 most senior faculty have 7 unique junior/senior co-authorship pairs, of 49 possible
  12. Laboratory Medicine • 14%
    the 13 most junior and 13 most senior faculty have 24 unique junior/senior co-authorship pairs, of 169 possible
  13. Cardiovascular Research Institute • 14%
    the 6 most junior and 6 most senior faculty have 5 unique junior/senior co-authorship pairs, of 36 possible
  14. Radiology • 13%
    the 35 most junior and 35 most senior faculty have 157 unique junior/senior co-authorship pairs, of 1225 possible
  15. Bioengineering • 12%
    the 8 most junior and 8 most senior faculty have 8 unique junior/senior co-authorship pairs, of 64 possible
  16. Institute for Health Aging • 12%
    the 8 most junior and 8 most senior faculty have 8 unique junior/senior co-authorship pairs, of 64 possible
  17. Otolaryngology • 12%
    the 11 most junior and 11 most senior faculty have 15 unique junior/senior co-authorship pairs, of 121 possible
  18. Pharmaceutical Chemistry • 11%
    the 8 most junior and 8 most senior faculty have 7 unique junior/senior co-authorship pairs, of 64 possible
  19. Neurology • 10%
    the 42 most junior and 42 most senior faculty have 173 unique junior/senior co-authorship pairs, of 1764 possible
  20. Dermatology • 10%
    the 12 most junior and 12 most senior faculty have 14 unique junior/senior co-authorship pairs, of 144 possible

Photo: CTSI at UCSF

UCSF Profiles coauthorship networks, by degree

/ Anirvan Chatterjee / 1 Comment

We’re using UCSF Profiles data to explore whether co-authorship networks are a good way to show the connections between researchers at UCSF.

We can start off by looking at immediate co-authorship connections. I was surprised at how few current UCSF co-authors most users have. The flip side of co-authoring widely outside of one’s institution is that there are fewer internal co-authors:

Avg # contacts, 1 degree away

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UCSF dentistry co-authorships, internal vs. external (by institutions)

/ Anirvan Chatterjee

What does a typical UCSF publication look like, in terms of the number of internal co-authors vs. the number of external co-authoring institutions? Here’s a breakdown among dentistry-related publications by UCSF researchers published in 2013. (This is the same analysis as yesterday, but looking at the number of external institutions, vs. the number of external people.)

Again, I was surprised to see so many co-authorships between a single UCSF researcher and one or researchers from one or more external institutions (the very top row of results), which accounts for 52% of the papers we looked at.

UCSF vs External Co-Authoring InstitutionsView as PDF Continue reading →

UCSF dentistry co-authorships, internal vs. external

/ Anirvan Chatterjee

What does a typical UCSF publication look like, in terms of internal vs. external co-authors? Here’s a breakdown of each type of co-author, among dentistry-related publications by UCSF researchers published in 2013.

Three immediate take-aways:

  • I was surprised to see so many co-authorships between a single UCSF researcher and one or more external researchers — the very top row of results. By volume, this accounts for 52% of the papers we looked at.
  • When every author is internal to UCSF, there’s an average of 3.5 UCSF co-authors
  • When there’s an external collaboration, there’s an average of 2.0 UCSF co-authors

UCSF vs External Co-AuthorsView as PDF Continue reading →

UCSF dentistry collaborations, visualized

/ Anirvan Chatterjee

Looking at cross-institutional co-authorship networks is a useful way of seeing not only who we work with, but also where there may be gaps of interest.

I first looked at dentistry-related publications by UCSF researchers published in 2013, breaking out the institutions we co-authored with. And there we are, sitting pretty in the center of our universe, collaborating with major institutions in the US, Korea, Australia, Italy, Denmark, and more.

(Details: Institution node sizes indicate the total volume of dentistry-related articles published. Connecting line widths indicate the number of articles co-authored between two institutions. Distance between nodes indicates the tightness of co-authorship networks, and different sets of node colors help distinguish groups of institutions whose researchers frequently co-author together. Of 462 institutions that collaborated with UCSF researchers, we’re showing only 91 that had 10 or more cross-institutional articles in that time.)

View full-size visualization (PDF)

UCSF dentistry research co-authorships, Jan 1 - Dec 5 2013

Then I looked at the total universe of dentistry-related publications published in 2013 (see below). Notice a difference? I have to admit that it took me a while to find UCSF in the mess of dots. (If you look at the full-size view, we’re in the medium blue section, next to the pinks.) Of course this says more about the sheer volume of research being published by universities all over the world, than about any lack of cross-institutionally collaborative spirit on our part; in fact I hid over 80% of the institutions in the first image to keep it readable, which accounts for a a good chunk of the difference. But the sheer weight of institutions from Europe, East Asia, and Latin America in this second image that aren’t there in the first is intriguing, and something I’m going to try digging into.

(Details: Institution node sizes indicate the total volume of dentistry-related articles published. Connecting line widths indicate the number of articles co-authored between two institutions. Distance between nodes indicates the tightness of co-authorship networks, and different sets of node colors help distinguish groups of institutions whose researchers frequently co-author together. Of 2,575 institutions that we found, we’re showing only 374 that had 10 or more cross-institutional articles in that time.)

View full-size visualization (PDF)

Dentistry research co-authorships, Jan 1-Dec 5 2013

(And yes, I realize fully well that I’m probably looking at the wrong things here, privileging increasing the count of cross-institutional collaborations as an end in itself, avoiding any consideration of research quality, and giving greater visual weight to institutions that publish more, regardless of the size of the institution or the quality of work. Pretty pictures lie can hide lots of flaws. I hope you’ll bear with me as I publicly iterate through these topics, step by step, hopefully getting just a little bit less dumb every time.)

Additional uninteresting details: I searched Web of Science for dentistry-related articles published in 2013 (i.e. from January 1-December 5, 2013). I began by running a search for any articles published in 2013 matching a number of dentistry-related keywords (dental, dentistry, electrogalvanism, endodontics, jaw relation record, mouth rehabilitation, odontometry, oral, orthodontics, periodontics, prosthodontics, teeth, tooth), then filtered only those that matched the “DENTISTRY ORAL SURGERY MEDICINE” Web of Science category.

Every researcher at UCSF — by department

/ Anirvan Chatterjee

Co-authorship networks can help us understand internal research collaboration patterns at UCSF. I used data from UCSF Profiles to create a visualization of (almost) every researcher currently at UCSF, and how their intra-UCSF co-authorship networks break out by department.

This visualization by department bears some more investigation than the previous one by school. Department of Medicine researchers are all over, collaborating with a wide variety of external departments. But an initial visual inspection suggests that almost all major departments have co-authorship relationships with members of other departments; some, like neurology, appear to form large standalone clusters, while others, like radiology, are more enmeshed in the work of others. This visualization flattens complex relationships into two dimensions, but it’s a starting point as we work to understand how UCSF collaborates.

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Every Researcher at UCSF, by department

Every researcher at UCSF — by school

/ Anirvan Chatterjee / 1 Comment

Co-authorship networks can help us understand internal research collaboration patterns at UCSF. I used data from UCSF Profiles to create a visualization of (almost) every researcher currently at UCSF, and how their intra-UCSF co-authorship networks break out by school.

Unsurprisingly, the School of Medicine takes up most of the space, and the visualization is probably most interesting in terms of what it might suggest about the smaller schools. Researchers from the Schools of Nursing and Dentistry form their own visible clusters, who often work with each other, but also have co-authorship relationships with researchers at the School of Medicine. But I was surprised by the School of Pharmacy, whose researchers form a main clusters in the bottom right, as well as additional clusters in the middle and top left, due to strong collaborative relationships with School of Medicine researchers.

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Every Researcher at UCSF, by school

HIV/AIDS research collaborations, visualized

/ Anirvan Chatterjee

Co-authorship networks give us a sense of the strength of research collaborations. We used co-authorship data to visualize how top HIV/AIDS research institutions worked with one another, based on publications from June 2012 to September 2013. UCSF collaborations are indicated via red lines.

Visualization details: Data includes all known publications related to HIV/AIDS between June 2012 and September 2013 that includes co-authors from two or more institutions. We map each author to their institution, and the size of each institution corresponds with the number of HIV/AIDS publications its members co-authored in that time; only the most prolific institutions are shown to ensure readability of the image. The width of the lines connecting institutions corresponds to the number of publications that include co-authors from both of these institutions. Collaborations with UCSF researchers are indicated with red lines. Colors indicate clusters of institutions that often publish collaboratively, based on network modularity.

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HIV-AIDS Collaborations, June 2012 - Sep 2013