|
Publication List
Journals (* Authors
initials are explained at bottom of page)
|
Authors
|
Year |
Title |
Journal |
Volume |
Pages |
Abstract / Full Text |
| SP, APA |
2007 |
Efficient stochastic sensitivity analysis of discrete
event systems |
Journal of Computational Physics |
221 |
724-738 |
PDF |
| AEK, MJC, PSN, SM, DVV, APA, AAM, MSG, ID |
2006 |
RegTransBase—a database of regulatory sequences
and interactions in a wide range of prokaryotic
genomes |
Nucleic Acids Research |
|
D1-D6 |
PDF |
|
HK, CJM,
MS, NAB, APA
|
2006 |
Automated Abstraction Methodology for
Genetic Regulatory Networks |
Trans. on Comput. Syst. Biol. |
VI, LNBI 4220 |
150–175 |
PDF |
| EJA, KHH, APA |
2006 |
The Evolution of Two-Component Systems
in Bacteria Reveals Different Strategies
for Niche Adaptation |
PLoS Computational Biology |
2(11) |
1-13 |
PDF |
| MS, APA |
2006 |
Deviant effects in molecular reaction
pathways |
Nature Biotechnology |
24(10) |
1235-1240 |
PDF |
| MO, KW, PH, HRB, APA |
2006 |
Morphology matters in immune cell
chemotaxis: membrane asymmetry
affects amplification |
Physical Biology |
3 |
190–199 |
PDF |
| APA, DAF |
2006 |
Fast, cheap and somewhat in control |
Genome Biology |
7(8):114 |
1-6 |
PDF |
| SSA, APA |
2006 |
Simulating cell
biology |
Current Biology |
16(14) |
R523-r527 |
PDF |
| MEC, QH, ZH, KHH, EJA, XFW, TCH, APA, JDW, JZZ and
MWF |
2006 |
Temporal Transcriptomic Analysis as Desulfovibrio
vulgaris Hildenborough
Transitions into Stationary Phase during Electron Donor Depletion |
Applied and Environmental Micorbiology |
72(8) |
5578-5588 |
PDF |
| SRC, QH, KHH, SPG, EJA, ZH, MZH, TCH, JDW, JZ, APA,
AKS |
2006 |
Global Analysis of Heat Shock Response in
Desulfovibrio vulgaris Hildenborough |
Journal of Bacteriology |
188(5) |
1817-1828 |
PDF |
| AM, ZH, EJA, APA, EEB, SCB, WC, TCH, QH, HH, KHH,
RH, DCJ, NK, MK, PO, AR, JS, JDW, JW, ZY, HY, JZ, JDK |
2006 |
Salt stress in Desulfovibrio vulgaris Hildenborough:
An integrated genomics approach. |
Journal of Bacteriology |
188(11) |
4068-4078 |
PDF |
| MNP, EJA, APA |
2006 |
The Histidine Operon Is Ancient. |
Journal of Molecular Evol. |
62(6) |
807-808 |
PDF |
| MNP, APA, EJA |
2006 |
The Life-Cycle of Operons |
PLoS Genetics |
2(6) |
859-0873 |
PDF |
| ABL, DKT, KHH, EJA, XFW, APA, SDB, LW, TY, XL, GSW,
JZ |
2006 |
Transcriptome Profiling of Shewanella oneidensis Gene
Expression
following Exposure to Acidic and Alkaline pH |
Journal of Bacteriology |
188(4) |
1633-1642 |
PDF |
| TSH, SKL, JDK, APA |
2006 |
A tightly regulated inducible expression system utilizing
the fim inversion recombination switch. |
Biotechnology and Bioengineering |
94(1) |
1-4 |
PDF |
| AMD, DC, APA |
2006 |
Genomics for environmental microbiology. |
Current Opinion in Biotechnology |
17(3) |
229-235 |
PDF |
| RF, MF, MO, TR, APA, AP |
2006 |
Model Discrimination Using Data Collaboration |
Journal of Physical Chemistry A |
110 |
6803-6813 |
PDF |
| JCA, EJC, APA, CAV |
2006 |
Environmentally controlled invasion of cancer cells
by engineered bacteria.
|
Journal of Molecular Biology |
355(4) |
619-627 |
PDF |
| PF, MIJ, APA |
2006 |
Robust design of biological experiments |
NIPS |
2005 conference proceedings |
|
PDF |
| MNP, APA, EJA |
2006 |
OpWise: Operons aid the identification of differentially
expressed
genes in bacterial microarray experiments |
BMC Bioinformatics |
7:19 |
1-16 |
PDF |
| SDB, MM, SD, SS, KHH, EJA, YY, LW, TY, XL, APA, KC,
JZ, DKT |
2006 |
Cellular Response of Shewanella oneidensis to Strontium
Stress |
Applied and Environmental Micorbiology |
72(1) |
890–900 |
PDF |
| QH, KHH, ZH, EJA, MWF, TCH, APA, JDW, JZ |
2006 |
Energetic Consequences of Nitrite Stress in Desulfovibrio
vulgaris
Hildenborough, Inferred from Global Transcriptional Analysis |
Applied and Environmental Micorbiology |
72(6) |
4370–4381 |
PDF |
| DAR, ILD, APA, EJA, MSG |
2005 |
Dissimilatory metabolism of nitrogen oxides in bacteria:
comparative reconstruction of transcriptional networks. |
PLoS Computational Biology |
1(5) |
415-431 |
PDF |
| CR, JRK, APA |
2005 |
Phosphatase localization in
bacterial chemotaxis: divergent mechanisms, convergent principles |
Phys. Biol. |
2 |
148–158 |
PDF |
| WL, RPS, MiP, PF, MIJ, APA, RWD, CN, GG |
2005 |
Genome-Wide Requirements for Resistance to Functionally
Distinct DNA-Damaging Agents. |
PLoS Genetics |
1(2)e24 |
235-246 |
PDF |
| PS, DA, PC, APA, MO |
2005 |
Numerical computation of diffusion on a surface. |
PNAS |
102(32) |
11151-11156 |
PDF |
| LW, JCB, JET, APA, DVS |
2005 |
Stochastic gene expression in a lentiviral positive-feedback
loop: HIV-1 Tat fluctuations drive phenotypic diversity. |
Cell |
122(2) |
169-182 |
PDF |
| EJA, KHH, MNP, RPK, KK, ID, APA |
2005 |
The MicrobesOnline Web site
for comparative genomics |
Genome Research |
15(7) |
1015–1022 |
PDF |
| MNP, EJA, APA |
2005 |
Interruptions in gene expression drive highly expressed
operons to the leading strand of DNA replication. |
Nucleic Acids Research |
33(10) |
3224-3234 |
PDF |
| MNP, KHH, APA, EJA |
2005 |
Operon formation is driven by co-regulation and not
by horizontal gene transfer. |
Genome Research |
15(6) |
809-819 |
PDF |
| PF, GG, JK, MIJ, APA |
2005 |
A latent variable model for
chemogenomic profiling. |
Bioinformatics |
21(15) |
3286-3293 |
PDF |
| MNP, KKH, EJA, APA |
2005 |
A novel method for accurate operon predictions in
all
sequenced prokaryotes |
Nucleic Acids Research |
33 (3) |
880–892 |
PDF |
| DMW, VV, APA |
2005 |
A microbial modified prisoner’s dilemma game:
how frequencydependent
selection can lead to random phase variation |
Journal of Theoretcial Biology |
234(2) |
255-262 |
PDF |
| DMW, VV, APA |
2005 |
Diversity in times of adversity: probabilistic strategies
in microbial survival games |
Journal of Theoretcial Biology |
234(2) |
227-253 |
PDF |
| YL,WG,YW, LW, XL, TY, EJA, APA, DKT, MWF, and JZ |
2005 |
Transcriptome Analysis of Shewanella oneidensis
MR-1 in Response to
Elevated Salt Conditions |
Journal of Bacteriology |
187(7) |
2501-2507 |
PDF |
| MS, SP, APA |
2005 |
Stochastic amplification and signaling in enzymatic
futile cycles through noise-induced bistability with oscillations |
PNAS |
102(7) |
2310-2315 |
PDF |
| CAV, DMW and APA |
2005 |
The Bacillus subtilis sin Operon: An Evolvable Network
Motif |
Genetics |
169(3) |
1187–1202 |
PDF |
| CR, MF, APA |
2004 |
An Allosteric Model for Transmembrane Signaling in
Bacterial Chemotaxis |
Journal of Molecular Biology |
|
1–13 |
PDF |
DAR, ID, APA, EJA and
MSG |
2004 |
Reconstruction of regulatory and metabolic pathways
in
metal-reducing ä-proteobacteria |
Genome Biology |
5(11) |
Article R90/1-27 |
PDF |
| HG, YW, XL, TY, LW, EJA, APA, DKT, and JZ |
2004 |
Global Transcriptome Analysis of the Heat Shock Response
of
Shewanella oneidensis |
Journal of Bacteriology |
186(22) |
7796–7803 |
PDF |
| CR, HS, APA |
2004 |
Putting the "Control" in Metabolic Control
Analysis |
DYCOPS |
|
|
PDF |
| MV, APA, JR |
2004 |
Response experiments for nonlinear systems with
application to reaction kinetics and genetics |
PNAS |
101(19) |
7223–7228 |
PDF |
| HHM, BS, APA |
2004 |
The Evolution of Genetic Regulatory Systems in Bacteria |
Nature Reviews |
5 |
169-178 |
PDF |
|
CR, JRK, APA
|
2004 |
Design and Diversity in Bacterial Chemotaxis: A Comparitive
Study in Escherichia coli and Bacillus subtilis |
PLOS |
2 (2) |
239-252 |
PDF |
| GG, PF, ...,APA |
2004 |
Chemogenomic Profiling: Identifying the functional
interactions of small molecules in yeast |
PNAS |
101(3) |
793-798 |
PDF |
|
MH, APA, JLK,
et al.
|
2003 |
The systems biology markup language (SBML): a medium
for representation and exchange of biochemical network models |
Bioinformatics |
19(4) |
524-531 |
[PDF-103kb]
|
| CR, APA |
2003 |
Stochastic Chemical Kinetics and the Quasi-Steady-State
Assumption |
Journal of Chemical Physics |
118(11) |
4999-5010 |
[PDF-157kb]
|
|
DMW, APA
|
2003 |
Motifs, modules and games in bacteria |
Current Opinion in Microbiology |
6(2) |
125-134 |
[PDF-273kb]
|
|
LSW, DVS, APA
|
2003 |
Theoretical Design of a Gene Therapy To Prevent AIDS
but Not Human Immunodeficiency Virus Type 1 Infection |
Journal of Virology |
77(18) |
10028-10036 |
[PDF-906kb]
|
|
MS, APA,
JR
|
2002 |
Signal Processing by Simple Chemical Systems |
Journal of Physical Chemistry A |
106 |
10205-10221 |
[PDF-220kb]
|
|
GG, APA, PF,
et al.
|
2002 |
Functional profiling of the Saccharomyces cerevisiae
genome |
Nature |
418 |
387-391 |
[PDF-317kb]
|
|
AG, APA
|
2002 |
Genetic "Code": Representations and Dynamical Models
of Genetic Components and Networks |
Annu. Rev. Genomics Hum. Genet. |
3 |
341-369 |
[PDF-360kb]
|
| DMW, APA |
2002 |
15 minutes of fim: Control of Phase Variation in E.
coli |
OMICS |
6(1) |
91-114 |
[PDF-783kb]
|
| SP, APA |
2002 |
Motifs and Modules in Cellular Signal Processing |
IEEE International Conference (Cat. No.02CH37334) |
vol.4. |
4032-4035 |
PDF |
|
CR, DMW, APA
|
2002 |
Control, exploitation and tolerance of intracellular
noise |
Nature |
420 |
231-238 |
[PDF-538kb]
|
|
WV, APA,
JR
|
2002 |
Determination of causal connectivities of species
in reaction networks |
PNAS |
99(9) |
5816-5821 |
[Abstract]
[PDF-314kb]
|
| CR, APA |
2001 |
Control motifs for intracellular regulatory networks |
Annual Review of Biomedical Engineering |
3 |
391-419 |
[PubMed]
[PDF-337kb]
|
| APA |
2001 |
Synthetic Cell Biology |
Current Opinion in Biotechnology |
12 |
638-644 |
[PDF-67kb]
|
| MS, APA,JR |
2001 |
On the deduction of chemical reaction pathways from
measurements of time-series of concentrations. |
Chaos |
11(1) |
108-114 |
[PDF-379kb]
|
| HHM, APA |
2000 |
Towards a circuit engineering discipline. |
Current Biology |
10(8) |
318-320 |
[PubMed]
[PDF-94kb]
|
| HHM, APA |
1999 |
It's a noisy business! Genetic regulation at the nanomolar
scale. |
Trends in Genetics |
15(2) |
65-69 |
[PubMed]
[PDF-164kb]
|
| HHM, APA |
1998 |
Simulation of prokaryotic genetic circuits |
Annual Review of Biophysics and Biomolecular Structure |
27 |
199-224 |
[PubMed]
[ARBBS]
[PDF-339kb]
|
| APA, JR, HHM |
1998 |
Stochastic kinetic analysis of pathway bifurcation
in phage lambda-infected Escherichia coli cells. |
Genetics |
149(4) |
1633-1648 |
[PubMed]
[Genetics]
[PDF-347kb]
|
| APA, PDS, JR |
1997 |
A test case of correlation metric construction of
a reaction pathway from measurements |
Science |
77(5330) |
1275-1279 |
[Science]
[PDF-573kb] |
| CAS, APA, JR |
1997 |
An endogenous calcium oscillator may control early
embryonic division |
PNAS |
94(4) |
1194-1199 |
[PubMed]
[PNAS]
[PDF-256kb]
|
| HHM, APA |
1997 |
Stochastic mechanisms in gene expression |
PNAS |
94(3) |
814-819 |
[PubMed]
[PNAS]
[PDF-387kb]
|
| APA, JR |
1995 |
Statistical construction of chemical reaction mechanisms
from measured time series |
Journal of Physical Chemistry |
99(3) |
970-979 |
[PDF-3Mb]
|
| APA, JR |
1994 |
Computational functions in biochemical reaction networks |
Biophysical Journal |
67(2) |
560-578 |
[PubMed] |
| APA, DYC |
1992 |
Optimizing nucleotide mixtures to encode specific
subsets of amino acids for semi-random mutagenesis |
Biotechnology |
10(3) |
297-300 |
[PubMed] |
| APA, DYC |
1992 |
An algorithm for protein engineering |
PNAS |
89(16) |
7811-7815 |
[PubMed]
[PNAS] |
| APA, ..., DYC |
1990 |
Applications of imaging spectroscopy in molecular
biology. II. Colony screening based on absorption spectra. |
Biotechnology |
8(8) |
746-749 |
[PubMed] |
BookChapters (*
Authors initials are explained at bottom of page)
| Authors |
Year |
Title |
Book |
Editors |
ISBN |
Info |
| APA |
2000 |
Signal Processing in Biochemical Reaction Networks |
Self-Organized Biological Dynamics and Nonlinear
Control |
J. Walleczek |
0521-6243-63 |
[Amazon]
[PDF-11Mb] |
| APA, DCY |
1992 |
Digital Imaging Spectroscopy |
The Photosynthetic Reaction Center |
J. Deisenhofer, J.R. Norris |
0122-0866-00 |
[Amazon] |
Conference Proceedings
(* Authors initials are explained at bottom of page)
| Authors |
Year |
Title |
Book |
Editors |
ISBN |
Info |
| APA, ..., DCY |
1992 |
Recursive Ensemble Mutagenesis: A Combinatorial Optimization
Technique For Protein Engineering |
Parallel Problem Solving from Nature II. Proceedings
of the Second International Conference on Parallel Problem Solving
from Nature. |
R. Maenner, B. Manderick |
0521-6243-63 |
[Amazon] |
| Initials |
Author |
|
Initials |
Author |
|
Initials |
Author |
AAM
|
Andrey A. Mironov
|
|
ID |
Inna Dubchak |
|
PH |
Paul Herzmark |
| ABL |
Adam B. Leaphart |
|
JCA |
J. Chris Anderson |
|
PO |
Paul Oeller |
AEK
|
Alexei E. Kazakov
|
|
JCB |
John C. Burnett |
|
PS |
Peter Schwartz |
| AG |
Alex Gilman |
|
JDK |
Jay D. Keasling |
|
PSN |
Pavel S. Novichkov |
| AKS |
A. K. Singh |
|
JDW |
Judy D. Wall |
|
QH |
Qiang He |
| AM |
Aindrilla Mukhopadhyay |
|
JET |
Jared E. Toettcher |
|
RF |
Ryan Feeley |
| AMD |
Adam M. Deutschbauer |
|
JK |
Jochen Kumm |
|
RH |
Rick Huang |
| APA |
Adam P. Arkin |
|
JLK |
Jay L. Kasberger |
|
RPK |
Richard P. Koche |
| AP |
Andrew Packard |
|
JR |
John Ross |
|
RPS |
Robert P. St. Onge |
| AR |
Alyssa Redding |
|
JRK |
John R. Kirby |
|
RWD |
Ronald W. Davis |
| BS |
Balaji Srinivasan |
|
JS |
Jun Sun |
|
SCB |
Sharon C. Borglin |
| CAS |
Craig A. Swanson |
|
JW |
Jing Wei |
|
SD |
Sameer Deshpande |
| CAV |
Christopher A. Voigt |
|
JZ |
Jizhong Zhou |
|
SDB |
Steven D. Brown |
| CJM |
Christopher J. Myers |
|
KC |
Karuna Chourey |
|
SKL |
Sung Kuk Lee |
| CN |
Corey Nislow |
|
KHH |
Katherine Huang |
|
SM
|
Simon Minovitsky |
| CR |
Christopher Rao |
|
KK |
Keith Keller |
|
SP |
Sergey Plyasunov |
| DA |
David Adalsteinsson |
|
KW |
Kit Wong |
|
SPG |
S. P. Gaucher |
| DAF |
Daniel A. Fletcher |
|
LW |
Liyou Wu |
|
SRC |
S. R. Chhabra |
| DAR |
Dmitry A Rodionov |
|
LSW |
Leor S. Weinberger |
|
SS |
Sudipta Seal |
| DC |
Dylan Chivian |
|
MF |
Michael Frenklach |
|
SSA |
Steven Andrews |
| DCJ |
Dominque C. Joyner |
|
MH |
Michael Hucka |
|
TCH |
Terry C. Hazen |
| DCY |
Douglas C. Youvan |
|
MIJ |
Michael I. Jordon |
|
TR |
Trent Russi |
| DKT |
Dorothea K. Thompson |
|
MiP |
Michael Proctor |
|
TSH |
Tim S. Ham |
| DMW |
Denise Wolf |
|
MJC
|
Michael J. Cipriano
|
|
TY |
Tinfeng Yan |
| DVS |
David V. Schaffer |
|
MM |
Madhavi Martin |
|
VV |
Vijay V. Vazirani |
DVV
|
Dimitry V. Vinogradov
|
|
MO |
Matthew Onsum |
|
WG |
Weimin Gao |
| EEM |
Edward E. Baidoo |
|
MNP |
Morgan Price |
|
WV |
William Vance |
| EJA |
Eric J. Alm |
|
MSG |
Mikhail S Gelfand |
|
WL |
William Lee |
| EJC |
Elizabeth J. Clarke |
|
MS |
Michael Samoilov |
|
XFW |
Xiu-Feng Wan |
| GG |
Guri Giaever |
|
MV |
Marcel Vlad |
|
XL |
Xueduan Liu |
| GSW |
Gene S. Wickham |
|
MWF |
Matthew W. Fields |
|
YL |
Yongqing Liu, |
| HG |
Haichun Gao |
|
MZH |
M. Z. Hadi |
|
YW |
Yue Wang |
| HH |
Hoi-Ying Holman |
|
NAB |
Nathan A. Barker |
|
YY |
Yunfeng Yang |
| HHM |
Harley H. McAdams |
|
NK |
Natalie Katz |
|
ZH |
Zhili He |
| HK |
Hiroyuki Kuwahara |
|
PC |
Phillip Colella |
|
ZY |
Zamin Yang |
| HRB |
Henry R Bourne |
|
PDS |
Pei-Dong Shen |
|
|
|
| HS |
Herbert Sauro |
|
PF |
Patrick Flaherty |
|
|
|
| |
|
|
|
|
|
|
|
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