FIVE YEAR REVIEW, 07/01/2006
Professor, Step IX
CRAIG BENHAM
LIST OF CONTRIBUTIONS TO JOINTLY AUTHORED WORKS
PUBLISHED:
1. Kozak, J. and Benham, C.J. This paper was the result of a joint collaboration in which the
mathematical expertise was provided by Dr. Benham and the chemistry expertise by Dr. Kozak.
Their shares in the project were approximately coequal.
2. Benham, C.J. and Kozak, J. This paper and the following one again were approximately
coequally authored
3. Benham, C.J. and Kozak, J. See 2 above.
6. Benham, C.J. and Kozak, J. This paper was primarily the idea, and the work, of Benham, with
some assistance from Dr. Kozak in the editing stage.
9. Benham, C.J., Brady, G. and Fein, D. This paper presents theoretical calculations of scattering
profiles that were performed by Benham. They are compared with experimental DNA
scattering curves that were determined in Brady’s lab. The paper was written primarily by
Benham.
15 Crowley, P., Benham, C.J., Lenhart, S. and Morgan, J. This paper resulted from a project
undertaken in a graduate math/biology course. The mathematics was contributed primarily by
Lenhart and secondarily by Benham, and the biological component was provided by Crowley
and Morgan.
18 Grassian, V., Brady, G. and Benham, C.J. This is a joint experimental/theoretical study of
solution scattering from DNA superhelices. The theory was contributed by Benham, and the
experiments were performed by Brady and Grassian. The paper was jointly written.
19 Brady, G., Fein, D., Lambertson, H., Grassian, V., Foos, D. and Benham, C.J. This paper was a
joint theoretical/experimental collaboration. The theory was contributed by Dr. Benham, and
the other authors collaborated in performing the experiments. The paper was jointly written by
Drs. Brady and Benham.
22 Brady, G., Foos, D. and Benham, C.J. This paper also was a joint experimental/theoretical
collaboration, in which the theory was developed by Benham and the experiments were
performed by Brady and Foos. The paper was jointly written by Drs. Benham and Brady.
24 Brady, G., Satkowski, D., Foos, D. and Benham, C.J. This paper and the next one (27) were
joint theoretical/experimental studies of the influences of various environmental parameters on
the structure of DNA supercoils in solution. The theory was the responsibility of Benham, and
the other authors performed the experiments. In these two studies little new theory needed to be
developed
27 Brady, G., Foos, D., Satkowski, D. and Benham, C.J. See above remarks for paper 24.
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FIVE YEAR REVIEW, 07/01/2006
Professor, Step IX
CRAIG BENHAM
Since Appointment to Professor 7-1-88
32 Miller, J., Nelson, J., Ye, M., Swenberg, C., Speicher, J. and Benham, C.J. This paper proposed
an explanation for the increased sensitivity of supercoiled DNA to strand breaks that was based
on Benham’s idea that this stress could cause strand separations. The theoretical analysis of the
DNA sequence was performed by Benham, and the experiments were performed by the other
authors. Most of the work was experimental, but the paper was founded on Benham’s theory.
The paper was primarily written by Miller, with revisions by Benham.
33 Enami, M., Sharma, G., Benham, C.J. and Palese, P. This paper shows that influenza
encapsidates its “chromosomes” in a way that is consistent with random packing. Benham
performed the theoretical calculations of the random case, and the other authors, all of whom
worked with Dr. Palese at the time, performed the experiments. The paper was written by Dr.
Palese.
35 Magarshak, Y. and Benham, C.J. This paper presents a mathematical approach to analyzing
RNA structures. The problem was proposed by Benham, and the algebra was developed
primarily by him. Dr. Magarshak developed the geometric and dynamical components. The
paper was written jointly.
36 Magarshak, Y. Benham, C.J., Malinsky, J. and Blumenfeld, I. This paper is a further
development of the methods and ideas presented in #35, with most of the extensions contributed
by Malinsky and Blumenfeld.
37 Benham, C.J. and Jafri, M.S. This paper analyzes the topology of protein structures. The
ideas and methods were contributed by Benham, and their computational implementation was
performed by Jafri, who was a graduate student at the time. The paper was written primarily by
Benham.
39 Bauer, W.R. and Benham, C.J. This is a joint theoretical/experimental study in which the theory
was performed by Benham and the experiments by Bauer. The paper was jointly written.
40 Sioud, M., Opstad, A., Zhao, J.-Q., Levitz, R., Benham, C.J. and Drlica, K. Benham performed
a theoretical analysis of the experiments of the other authors. On that basis Benham developed
and analyzed a model for the mechanism involved. The paper was written primarily by Drs.
Sioud and Drlica.
41 Benham, C.J., Kannan, S. and Warnow, T. This paper and #44 were both motivated by Benham
and based on his ideas. But virtually all proofs were contributed by the other authors. Benham
wrote individual sections of these two papers, but the primary author of both papers was
Warnow.
42 Bauer, W.R., Ohtsubo, H., Ohstubo, E and Benham, C.J. This paper extends and confirms the
work done in #39 above. The Ohtsubos sequenced the DNA used in this study. Bauer did all
other experimental work and Benham performed all theoretical analyses. The paper was written
by Benham and Bauer.
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Professor, Step IX
CRAIG BENHAM
43 Sun, H., Mezei, M., Fye, R. and Benham, C.J. The Monte Carlo methods developed in this
paper were primarily the work of Sun, who was a graduate student at the time working under the
supervision of Benham. Mezei made a minor contribution, and Fye lent his general expertise in
Monte Carlo methods. The paper was written by Sun and Benham.
44 Benham, C.J., Kannan, S., Paterson, M. and Warnow, T. See remarks for #41 above.
47 Miller, D. and Benham, C.J. This paper solves a problem that was formulated by Benham. The
technique of proof was also contributed primarily by Benham, with substantial help from Miller.
The paper was jointly written.
49 Miller, J., Nelson, J., Fleck, E., and Benham, C.J. This paper extends the ideas presented in
#32. Benham contributed the theoretical analyses and the basic model was his. The other
authors performed the experiments and wrote the paper.
50 Aranda, A., Perez-Ortin, J., Benham, C.J. and del Olmo, M. This paper experimentally tested a
model of transcription termination suggested by Benham’s calculations that was reported in
paper #45. All the experimental work was performed in Dr. Perez-Ortin’s lab by the other
authors. The paper was written by them, and revised by Benham.
51 Hristescu, G., Benham, C.J. and Farach, M. This paper presents a parallel implementation of
the algorithm designed by Benham to compute stressed destabilization properties of DNA
sequences. All of the parallelization and optimization were done by Hristescu and Farach, with
some supervision by Benham. The paper was written by Hristescu, and revised by Farach and
then by Benham.
52 Benham, C.J., Kohwi-Shigematsu, T. and Bode, J. This paper reports that matrix attached sites
have characteristic predicted destabilization properties. The calculations were performed by
Benham, and the experiments by the other two authors. This collaboration was initiated by
Bode. A draft of the paper was written by Bode, and revised by Benham.
53 Bode, J., Bartsch, J., Boulikas, T., Iber, M., Mielke, C., Schuebler, D., Seibler, J. and Benham,
C.J. This paper reviews and presents new information regarding the mechanisms and functions
of the architectural components governing chromosome structure. This includes Benham’s
model of the function of destabilized sites, which was originally presented in #52 above.
Benham performed a few new calculations for this paper, and extensively revised it. The
experimental work was performed by the other authors.
54 Sheridan, S., Benham, C.J. and Hatfield, G.W. This paper presented and proved a new model of
gene regulation, which had originally been suggested by calculations of Benham. All the
experimental proof was provided by the other authors, who also were primarily responsible for
writing the paper.
55 Fye, R.M. and Benham, C.J. This paper and the next (#57) present a new theoretical method to
calculate structural properties of DNA. The original idea was Fye’s, but both authors
contributed coequally to its development, and to writing these papers.
57 Fye, R.M. and Benham, C.J. See #55 above.
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Professor, Step IX
CRAIG BENHAM
58 Sheridan, S., Benham, C.J. and Hatfield, G.W. This paper uses an experimental design
proposed by Benham in paper #45 (Benham sole author) to further prove the correctness of the
model presented in #54. The experiments were performed by Sheridan under the supervision of
Hatfield. The paper was written by those authors, and revised by Benham.
59 Messmer, B., Benham, C.J. and Thaler, D. This paper develops a new technique for iteratively
isolating ligand binding components from a heterogeneous mixture. The idea was Messmer’s,
and this was his doctoral thesis work. Benham developed a mathematical analysis of the
phenomenon, and helped revise the paper.
60 He, L., Liu, J., Collins, I., Sanford, S., O’Connell, B., Benham, C.J. and Levens, D. This paper
proves a model of gene regulation that was originally suggested by calculations of Benham.
The experiments were performed in Levens’ lab by the other authors. The paper was written by
Levens and revised by Benham.
61 Baiker, A., Maercker, C., Piechaczek, C., Schmidt, S., Bode, J., Benham, C.J. and Lipps, H.L.
The calculations presented in this paper were performed by Benham. All other parts, which is
most of it, are the work of the other authors. The paper was written primarily by Bode and
Lipps.
62 Bode, J., Benham, C.J., Knopp, A., and Mielke, C. This paper gives additional support for the
destabilization model of scaffold attachment that was originally presented in #52. Benham only
contributed a few additional calculations. Most of the work reported was experimental, and was
done by the other authors.
63 Benham, C.J. and Miller, D. The work presented in this paper was originated by Miller, who
also developed the central ideas for the proofs. These ideas were refined collaboratively by both
authors.
64 Leblanc, B., Benham, C.J., and Clark, D. This paper presents and proves a model of minimal
gene expression. Benham’s theoretical calculations were crucial in developing and refining this
model, and in designing experimental tests for it. The other authors performed the experiments.
The paper was written primarily by Clark.
65 Bode, J., Benham, C.J., Ernst, E., Knopp, A., Marschalek, R., Strick, R. and P. Strissel. This
paper develops a new model for how double strand break repair may be activated. The
experimental part was the work of the Bode lab, and the theoretical part was done by Benham.
The paper was written mostly by Bode.
67 Benham, C.J., Lin, X.-S. and D. Miller. This paper extends the method developed in #47 to a
new context. Dr. Lin first proposed that this could be done; he and Dr. Miller completed the
analysis and wrote the paper. Benham's contributions were minimal, but the other authors
requested that his name appear because it extends a line of research that he originated.
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FIVE YEAR REVIEW, 07/01/2006
Professor, Step IX
CRAIG BENHAM
Since Appointment 3-1-01
68 Engel, H., Ruehl, H., Benham, C.J., Bode, J., and S. Weiss. This paper proves and presents a
new mechanism for the regulation of specific mouse genes. The mechanism was developed by
Drs. Engel and Weiss from ideas presented by Benham. The experiments were done in the
Weiss lab, and the calculations were done by Benham. The paper was jointly written.
69 Bode, J., Fetzer, C., Nehlsen, K., Scinteie, M., Hinrichs, B.-H., Baiker, A., Piechaczek, C.,
Benham, C.J. and H.J. Lipps. This paper extends the work in #61 on designing vectors for gene
therapy. The required property of incorporating an attachment site is shown to be predicted by
Benham's methods. All experiments were performed by the Lipps and Bode labs. The paper
was jointly written.
70 Woynarowski, J.M., Trevino, A., Rodriguez, K., Hardies, S.C. and C.J. Benham. This paper
shows that an anti-tumor drug targets sites that Benham's computational methods predict. All
experiments were done by the Woynarowski lab. The SIDD calculations were performed by
Benham; other calculations by Woynarowski. The paper was written primarily by
Woynarowski.
71 Mielke, C., Christensen, M., Westergaard, O., Bode, J., Benham, C.J. and M. Breindl. This
paper proposes and documents a gene regulation mechanism involving stress-induced
destabilization. The idea was proposed by Breindl. All experiment s were performed in that
lab; all calcyulations were by Benham. The paper was jointly written.
72 Benham, C.J., Savitt, A. and W.R.Bauer. This paper documents a new transition property of
DNA, and develops and implements a method to determine its energetics. The ideas developed
were primarily Benham's. The experiments were performed in the Bauer lab, mostly by Savitt.
All theoretical analysis was by Benham. The paper was written jointly by Benham and Bauer.
73 Hatfield, G.W. and C.J. Benham. This article reviews the roles of topology in bacterial gene
regulation. Much of the work described was collaborative between the authors, with the
Hatfield lab doing all experiments, and Benham performing all theoretical analyses. The paper
was jointly written.
74 Goetze, S., Gluch, A., Benham, C.J., and J. Bode. This paper reports the PhD thesis work of Dr.
Goetze, who did all the experiments and investigated most of the associations reported.
Benham provided extensive computational analyses on which these investigations were based.
The paper was written primarily by Goetze.
75 Potaman, V., Bissler, J., Hashem, V., Oussatcheva, E., Lu, L., Shlyakhtenko, L., Lyubchenko,
Y., Matsuura, T., Ashizawa, T., Leffak, M, Benham, C.J., and R.R. Sinden. This paper is a
collaboration between the Sinden lab and Benham. It reports how stress-driven unwinding of
DNA provides unintended replication origins, which are implicated in a specific disease. All
calculations are Benham's; all experiments are Sinden's. The paper was written mostly in the
Sinden lab.
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FIVE YEAR REVIEW, 07/01/2006
Professor, Step IX
CRAIG BENHAM
76 Bode, J., Goetze, S., Heng, H., Krawetz, S.A. and C.J. Benham. This paper develops the
approach originated in #52 to understand large-scale chromosomal structure. The work was
mostly by the Bode lab, with calculations by Benham. Most writing was by Bode.
77 Opel, M. L., Aeling, K.A., Holmes, W.M., Johnson, R., Benham, C.J., and G.W. Hatfield. This
paper shows that the regulatory mechanism proposed and proved in # 54 and #58 occurs more
generally. The idea of looking at tRNA genes was proposed by Benham on the basis of his
calculations. The experiments were done in the Hatfield and Holmes labs. The paper was
jointly written.
78 Benham, C.J. and C.-P Bi. This paper presents a full description of the computational method
for evaluating the transition behavior of topologically stressed complete chromosomes. Benham
developed this method and designed the algorithm to analyze it. Dr. Bi, who was a postdoc in
Benham's lab at the time, wrote a program that efficiently implemented this calculation. This
method has been extensively used to analyze many complete genomes to date. The paper was
written by Benham.
79 Bi, C.-P. and C.J. Benham. This paper announces a Web site where users can submit short
DNA sequences for Benham's SIDD analysis. The site and the programs that it uses were all
developed by Dr. Bi at Benham's suggestion. Most of the work involved was done by Dr. Bi,
who also wrote the paper.
80 Wang, H., Noordewier, M. and C.J Benham. This paper reports a strong association between
sites that open under topological deformation and specific classes of DNA regulatory regions in
bacteria. This is the first paper to apply the methods developed in #78, and demonstrates their
usefulness in flagging regulatory regions. The ideas developed were primarily Benham's, and
the analyses were performed by Wang, a postdoc in the Benham lab. Dr, Noordewier provided
some intellectual input, and his company provided initial funding and computational resources
for this project.
81 Mielke, S.P., Fink, W.H., Krishnan, V.V., Gronbech-Jensen, N. and C.J. Benham. This paper
develops the first computational method to analyze the effects of dynamically changing
torsional stresses on DNA. It is some of the doctoral work of the first author, Steve Mielke,
who is in the Biophysics GG. Benham suggested the general problem, but Mielke develop the
reported approach entirely on his own. The paper was written primarily by Mielke.
82 Polonskaya, Z., Benham, C.J., and J. Hearing. This paper proposes and documents how
topologically destabilized DNA is involved in the initiation of replication in a virus. The project
was proposed by Dr. Hearing, in whose lab all experiments were performed. Benham
performed all calculations. The paper was jointly written.
83 AK, Prashanth and C.J. Benham. This paper was joint work by both coauthors. Dr. AK, who is
a postdoctoral fellow with Benham, performed all calculations. The paper was jointly written.
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Professor, Step IX
CRAIG BENHAM
84 Benham, C.J. and S.P. Mielke. This review article was written coequally by both authors.
85 Mielke, S.P., Gronbech-Jensen, N., Krishnan, V.V., Fink, W.H. and C.J. Benham. This paper,
together with #81, are two components of S. Mielke's doctoral research program. It presents the
first computational method to analyze stress-driven transitions in a dynamical context. The
general problem was presented to Mielke by Benham, but the specific approach that is
developed here is essentially entirely Mielke's. The paper was written largely by Mielke, with
contributions from the other authors. The research and the writing were overseen by Benham.
86 Wang, H., Kaloper, M and C.J. Benham. This paper presents a database that provides access to
the SIDD analyses of more than 125 microbial genomes. These analyses are done using the
method reported in #78. Wang oversaw the analyses of all these genomes, Kaloper developed
the database and its interface, and Benham directed the project. The paper was written by Wang
and Benham.
87 Bode, J., Winkelmann, S., Goetze, S., Spiker, S., Tsutsui, K., Bi, C., AK, Prashanth and
Benham, C.J. This paper was the result of a long research program. The experimental
components were performed in the Bode lab, and the extensive calculations were performed by
Benham. The paper was written by Benham, with input and revisions by Bode and AK.
88 Wang, H.Q. and Benham, C.J. The idea of developing a promoter prediction was Benham’s.
The actual development process was performed by Wang, with Benham supervising the project.
The paper was jointly written.
89 Benham, C.J. and Singh, R. The need for making this comment was noted by Singh, and the
paper was jointly coauthored. The scientific poiunts made in this paper were primarily the work
of Benham.
90 Kang, Y., Moressi, C., Scheetz, T., Xie, L., Tran, D., Casavant, T., AK, Prashanth, Benham,
C.J., Davidson, B. and McCray, P.B. This paper was primarily the work of the McCray lab.
The investigation of how SIDD properties correlate with integration sites was performed in the
Benham lab. This work was done primarily by AK, with oversight by Benham. Benham and
AK jointly cowrote the portion of the paper reporting these results.
91 Nieduszynski, C., Hiraga, S-I., AK, P., Benham, C. J. and Donaldson, A. This paper develops a
database of replication origins. As one of the essenial attributes of these sites is propensity for
SIDD, this attribute was included in the database. The analysis of SIDD properties was
performed by AK as overseen by Benham. The paper and the database were constructed
primarily in the Donaldson lab.
92 Wang, H.Q. and Benham, C.J. The idea behind this project was due to Wang, who also
performed most of the computational analyses required. Benham’s role was limited to
oversight, and to extensively revising the paper.
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FIVE YEAR REVIEW, 07/01/2006
Professor, Step IX
CRAIG BENHAM
93 Mielke, S.P., Gronbach-Jensen, N. and Benham, C.J. This paper extends the Brownian
dynamics approach for analyzing DNA to include explicit salt. The programs required were all
written by Mielke with technical advice from Gronbach-Jensen. The project was overseen by
Benham. The paper was written primarily by Mielke, with revisions by the other authors.
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