Bernhard Ø. Palsson

Also affiliated with University of California San Diego, La Jolla Bioengineering Institute, Joint BioEnergy Institute, Technical University of Denmark

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

8.2Author DataRank

Indexed papers

16in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 16 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

An atlas of human metabolism

Science Signaling(2020)10.1126/scisignal.aaz1482

Top 5%

4.4DataRank

Top 5%483 citations

Pınar Kocabaş, Hao Wang, Pierre‐Etienne Cholley, Daniel Cook, Avlant Nilsson +15 more

Papers

Driven by 100 papers — median percentile 34. Top paper: “Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae”.

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

Genome Research(2006)10.1101/gr.4083206

N/A

8.8DataRank · unranked

227 citations

Baek-Seok Lee, Vasiliy Portnoy, Bernhard Ø. Palsson, Markus J. Herrgård

An atlas of human metabolism

Science Signaling(2020)10.1126/scisignal.aaz1482

Top 5%

4.4DataRank

Top 5%483 citations

Pınar Kocabaş, Hao Wang, Pierre‐Etienne Cholley, Daniel Cook, Avlant Nilsson +15 more

Redefining fundamental concepts of transcription initiation in bacteria

Nature Reviews Genetics(2020)10.1038/s41576-020-0254-8

N/A

3.5DataRank · unranked

157 citations

Stephen Busby, Joseph T. Wade, Jacques van Helden, Adam P. Arkin, Gary D. Stormo +5 more

Systems biology of the structural proteome

BMC Systems Biology(2016)10.1186/s12918-016-0271-6

N/A

1.9DataRank · unranked

60 citations

Nathan Mih, Zhen Zhang, Edward J. O’Brien, Ke Chen, Roger L. Chang +5 more

Impact of insertion sequences on convergent evolution of Shigella species

PLoS Genetics(2020)10.1371/journal.pgen.1008931

N/A

1.7DataRank · unranked

67 citations

Jonathan M. Monk, Helen Billman‐Jacobe, Bernhard Ø. Palsson, Kathryn E. Holt, Jane Hawkey

Empowering drug off-target discovery with metabolic and structural analysis

Nature Communications(2023)10.1038/s41467-023-38859-x

N/A

1.0DataRank · unranked

28 citations

Daniel C. Zielinski, Christopher Dalldorf, João V. Rodrigues, Bernhard Ø. Palsson, Eugene I. Shakhnovich +1 more

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

BMC Genomics(2020)10.1186/s12864-020-06920-4

N/A

1.0DataRank · unranked

39 citations

James T. Yurkovich, David Heckmann, Muyao Wu, Troy E. Sandberg, Zachary A. King +4 more

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Microbial Biotechnology(2023)10.1111/1751-7915.14257

Top 22%

0.930DataRank

Top 22%41 citations

Alexandra Calteau, Antoine Danchin, Colin R. Harwood, John D. Helmann, Claudine Médigue +6 more

SBML Level 3: an extensible format for the exchange and reuse of biological models

Molecular Systems Biology(2020)10.15252/msb.20199110

N/A

0.861DataRank · unranked

311 citations

Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya +95 more

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

UNC Libraries(2020)10.17615/dd92-mf79

N/A

0.745DataRank · unranked

143 citations

Peng Yao, Kerry L. McPhail, Lixin Zhang, Kathleen Dorrestein, Wenyuan Shi +95 more

Large-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae

OMICS: A Journal of Integrative Biology(2003)10.1089/153623103322246584

N/A

0.743DataRank · unranked

141 citations

Iman Famili, Bernhard Ø. Palsson, Jens Nielsen, Jochen Förster

Antibacterial mechanisms identified through structural systems pharmacology

BMC Systems Biology(2013)10.1186/1752-0509-7-102

N/A

0.718DataRank · unranked

25 citations

Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson, Roger L. Chang

iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets

Nucleic Acids Research(2024)10.1093/nar/gkae1009

Top 31%

0.650DataRank

Top 31%30 citations

Jayanth Krishnan, Gaoyuan Li, Xuwen A Lou, Kevin Rychel, Yuan Yuan +9 more

Optimal dimensionality selection for independent component analysis of transcriptomic data

BMC Bioinformatics(2021)10.1186/s12859-021-04497-7

N/A

0.633DataRank · unranked

67 citations

Cameron Lamoureux, Saugat Poudel, Bernhard Ø. Palsson, Anand V. Sastry, John Luke McConn

Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2218835120

Top 33%

0.601DataRank

Top 33%22 citations

Patrick V. Phaneuf, Jonathan M. Monk, Bernhard Ø. Palsson, Edward Catoiu

Machine learning fromPseudomonas aeruginosatranscriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Nucleic Acids Research(2022)10.1093/nar/gkac187

N/A

0.568DataRank · unranked

43 citations

Hannah Tsunemoto, Anand V. Sastry, Richard Szubin, Kevin Rychel, Joseph Sugie +3 more

Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media

GigaScience(2021)10.1093/gigascience/giaa156

N/A

0.548DataRank · unranked

15 citations

Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson +14 more

Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

ACS Synthetic Biology(2021)10.1021/acssynbio.1c00337

Top 39%

0.489DataRank

Top 39%15 citations

Daniel C. Zielinski, James T. Yurkovich, Josefin Johnsen, Richard Szubin, Lei Yang +9 more

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

mSystems(2024)10.1128/msystems.00305-24

N/A

0.484DataRank · unranked

20 citations

Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C. Zielinski +2 more

The quantitative metabolome is shaped by abiotic constraints

Nature Communications(2021)10.1038/s41467-021-23214-9

N/A

0.470DataRank · unranked

22 citations

James T. Yurkovich, Daniel C. Zielinski, Bernhard Ø. Palsson, Amir Akbari

Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii

mSystems(2024)10.1128/msystems.00606-23

N/A

0.343DataRank · unranked

7 citations

Saugat Poudel, Anand V. Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon +7 more

Revealing 29 sets of independently modulated genes in Staphylococcus aureus , their regulators and role in key physiological responses

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.18.997296

N/A

0.330DataRank · unranked

8 citations

Hannah Tsunemoto, Yara Seif, Anand V. Sastry, Richard Szubin, Sibei Xu +7 more

High-resolution temporal profiling of E. coli transcriptional response

Nature Communications(2023)10.1038/s41467-023-43173-7

Top 55%

0.297DataRank

Top 55%6 citations

Kevin Rychel, Andrew Lezia, Anand V. Sastry, Bernhard Ø. Palsson, Jeff Hasty +1 more

Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.28.454220

Top 56%

0.292DataRank

Top 56%4 citations

Hannah Tsunemoto, Anand V. Sastry, Richard Szubin, Kevin Rychel, Joseph Sugie +3 more

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.07.138933

N/A

0.269DataRank · unranked

5 citations

Yara Seif, George Sakoulas, Connor A. Olson, Richard Szubin, Bernhard Ø. Palsson +3 more

Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Current Research in Microbial Sciences(2023)10.1016/j.crmicr.2023.100180

N/A

0.241DataRank · unranked

4 citations

Alison Coady, Richard Szubin, Thomas Martin, Bernhard Ø. Palsson, Victor Nizet +2 more

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.23.003236

N/A

0.208DataRank · unranked

3 citations

Jonathan M. Monk, Laurence Yang, Ali Ebrahim, Bernhard Ø. Palsson, Colton J. Lloyd

Empowering systems-guided drug target discovery with metabolic and structural analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.17.444532

N/A

0.208DataRank · unranked

3 citations

Daniel C. Zielinski, Christopher Dalldorf, João V. Rodrigues, Bernhard Ø. Palsson, Eugene I. Shakhnovich +1 more

CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli

Communications Biology(2024)10.1038/s42003-024-06831-0

N/A

0.184DataRank · unranked

2 citations

Hyun Gyu Lim, Ye Gao, Dmitry A. Rodionov, Ying Hutchison, Richard Szubin +4 more

QSProteome: a community-driven interactive platform for large-scale exploration and evaluation of predicted protein complex structures

Nucleic Acids Research(2025)10.1093/nar/gkaf1099

Top 66%

0.179DataRank

Top 66%2 citations

Delina Kambo, Brianna Rodriguez, Krista Vear, Ziheng Wang, June Akpata +13 more

Establishing comprehensive quaternary structural proteomes from genome sequence

Research Square(2023)10.21203/rs.3.rs-2923626/v1

Top 70%

0.165DataRank

Top 70%2 citations

Maxwell Lu, Bernhard Ø. Palsson, Edward Catoiu, Nathan Mih

Establishing comprehensive quaternary structural proteomes from genome sequence

eLife(2024)10.7554/elife.100485.1

Top 70%

0.165DataRank

Top 70%2 citations

Nathan Mih, Maxwell Lu, Bernhard Ø. Palsson, Edward Catoiu

QSProteome: A Community-Driven Interactive Platform for Large-Scale Exploration and Evaluation of Predicted Protein Complex Structures

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.10.675416

Top 72%

0.111DataRank

Top 72%1 citations

Delina Kambo, Brianna Rodriguez, Krista Vear, Ziheng Wang, June Akpata +13 more

The quantitative metabolome is shaped by abiotic constraints

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.26.315135

N/A

0.104DataRank · unranked

1 citations

James T. Yurkovich, Daniel C. Zielinski, Bernhard Ø. Palsson, Amir Akbari

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.16.541025

N/A

0.104DataRank · unranked

1 citations

Hyun Gyu Lim, Dmitry A. Rodionov, Ying Hutchison, Christopher Dalldorf, Ye Gao +3 more

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

Communications Biology(2021)10.1038/s42003-021-02516-0

N/A

0DataRank · unranked

25 citations

Ye Gao, Anand V. Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov +3 more

Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.06.079640

N/A

0DataRank · unranked

0 citations

Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson +14 more

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

mSphere(2021)10.1128/msphere.00443-21

N/A

0DataRank · unranked

21 citations

Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu +5 more

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008596

N/A

0DataRank · unranked

19 citations

Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih +2 more

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.25.061994

N/A

0DataRank · unranked

0 citations

Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk +2 more

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

PLoS Computational Biology(2021)10.1371/journal.pcbi.1007817

N/A

0DataRank · unranked

11 citations

Jonathan M. Monk, Laurence Yang, Ali Ebrahim, Bernhard Ø. Palsson, Colton J. Lloyd

Optimal dimensionality selection for independent component analysis of transcriptomic data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.26.445885

N/A

0DataRank · unranked

11 citations

Cameron Lamoureux, Saugat Poudel, Bernhard Ø. Palsson, Anand V. Sastry, John Luke McConn

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.08.426013

N/A

0DataRank · unranked

4 citations

Saugat Poudel, Yara Seif, Zeyang Shen, Bernhard Ø. Palsson, Ye Gao

Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.19.079962

N/A

0DataRank · unranked

2 citations

Yara Seif, Hannah Tsunemoto, Saugat Poudel, Michael J. Meehan, Richard Szubin +15 more

Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.30.070904

N/A

0DataRank · unranked

3 citations

Saugat Poudel, Hannah Tsunemoto, Richard Szubin, Michael J. Meehan, Connor A. Olson +15 more

A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

Research Square(2021)10.21203/rs.3.rs-146218/v1

N/A

0DataRank · unranked

3 citations

Ye Gao, Anand V. Sastry, Ying Hefner, Reo Yoo, Dmitry A. Rodionov +3 more

Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.19.452699

Top 100%

0DataRank

Top 100%0 citations

Daniel C. Zielinski, James T. Yurkovich, Josefin Johnsen, Richard Szubin, Lei Yang +8 more

Origin of electroneutrality in living system

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.21.461264

N/A

0DataRank · unranked

0 citations

Bernhard Ø. Palsson, Amir Akbari

Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.20.473592

N/A

0DataRank · unranked

0 citations

Henrik Westh, Michael Kemp, Svend Ellermann‐Eriksen, Bernhard Ø. Palsson, Helle Krogh Johansen +2 more

Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

BMC Genomics(2022)10.1186/s12864-021-08223-8

N/A

0DataRank · unranked

87 citations

Jonathan M. Monk, Bernhard Ø. Palsson, Jason C. Hyun

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Nature Communications(2022)10.1038/s41467-022-30877-5

N/A

0DataRank · unranked

31 citations

Arjun Patel, Ke Chen, Connor A. Olson, Patrick V. Phaneuf, Cameron Lamoureux +5 more

PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.27.065417

N/A

0DataRank · unranked

7 citations

Ye Gao, Anand V. Sastry, Jonathan M. Monk, Nicholas Wong, Richard Szubin +5 more

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Nucleic Acids Research(2022)10.1093/nar/gkac743

N/A

0DataRank · unranked

36 citations

Hannah Tsunemoto, Anand V. Sastry, Richard Szubin, Kevin Rychel, Siddharth Chauhan +3 more

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Scientific Reports(2022)10.1038/s41598-022-11134-7

N/A

0DataRank · unranked

22 citations

Ye Gao, Jonathan M. Monk, Ying Hefner, Nicholas Wong, Richard Szubin +6 more

Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010377

N/A

0DataRank · unranked

9 citations

Bernhard Ø. Palsson, Amir Akbari

Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.487056

N/A

0DataRank · unranked

4 citations

Patrick V. Phaneuf, Jonathan M. Monk, Bernhard Ø. Palsson, Edward Catoiu

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.487013

N/A

0DataRank · unranked

1 citations

Arjun Patel, Ke Chen, Connor A. Olson, Patrick V. Phaneuf, Cameron Lamoureux +5 more

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.487074

N/A

0DataRank · unranked

0 citations

Hannah Tsunemoto, Anand V. Sastry, Richard Szubin, Kevin Rychel, Siddharth Chauhan +3 more

Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.04.077271

N/A

0DataRank · unranked

7 citations

Nick Dillon, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin +4 more

Blood donor exposome and impact of common drugs on red blood cell metabolism

medRxiv(2020)10.1101/2020.08.17.20176891

N/A

0DataRank · unranked

8 citations

Davide Stefanoni, Aarash Bordbar, Aaron Issaian, Bernhard Ø. Palsson, Larry J. Dumont +12 more

Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

Nature Communications(2023)10.1038/s41467-023-43549-9

N/A

0DataRank · unranked

20 citations

Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard Ø. Palsson, Jason C. Hyun

Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

Cell Reports(2023)10.1016/j.celrep.2023.113105

N/A

0DataRank · unranked

24 citations

Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner, Richard Szubin +11 more

Comparison of metal‐bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis

Protein Science(2020)10.1002/pro.3876

N/A

0DataRank · unranked

4 citations

Matthew R. Lam, Mónica Rosas‐Lemus, Joanna Sławek, M. Woińska, Ivan G. Shabalin +6 more

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC

mSystems(2023)10.1128/msystems.00279-23

N/A

0DataRank · unranked

14 citations

Saugat Poudel, Yara Seif, Zeyang Shen, Bernhard Ø. Palsson, Ye Gao

E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding

Scientific Reports(2023)10.1038/s41598-023-31812-4

N/A

0DataRank · unranked

12 citations

Ali Hosseinnia, Sunyoung Kim, Norman Goodacre, Li Zhang, Zhongge Zhang +5 more

Metabolic homeostasis and growth in abiotic cells

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2300687120

N/A

0DataRank · unranked

9 citations

Bernhard Ø. Palsson, Amir Akbari

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

Genome biology(2023)10.1186/s13059-023-03028-2

N/A

0DataRank · unranked

9 citations

Bernhard Ø. Palsson, Jason C. Hyun

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

Frontiers in Microbiology(2020)10.3389/fmicb.2020.596626

N/A

0DataRank · unranked

4 citations

Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard Ø. Palsson, Mary N. Parenteau +1 more

Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

NAR Genomics and Bioinformatics(2023)10.1093/nargab/lqad006

N/A

0DataRank · unranked

6 citations

Sang‐Mok Lee, Ali Ebrahim, Zoe K. Scott-Nevros, Bernhard Ø. Palsson, Laurence Yang +4 more

Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

npj Systems Biology and Applications(2020)10.1038/s41540-020-00151-9

N/A

0DataRank · unranked

30 citations

Heather A. Danhof, Colleen K. Brand, Numan Oezguen, Firas S. Midani, Bernhard Ø. Palsson +5 more

Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557250

N/A

0DataRank · unranked

10 citations

Daniel Stephenson, Eric J. Earley, Gregory R. Keele, Ariel Hay, Alicia Key +21 more

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

Research Square(2023)10.21203/rs.3.rs-2729651/v1

N/A

0DataRank · unranked

9 citations

Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C. Zielinski +2 more

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.20.529291

N/A

0DataRank · unranked

4 citations

Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V. Sastry, Svetlana Maurya +4 more

Alleleomes characterize the survivors of 3.5 billion years of bacterial evolution

Research Square(2023)10.21203/rs.3.rs-3168663/v1

N/A

0DataRank · unranked

3 citations

Edward Catoiu, Jason C. Hyun, Bernhard Ø. Palsson

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

mSystems(2020)10.1128/msystems.00828-19

N/A

0DataRank · unranked

12 citations

Henrique Machado, Nicholas Dillon, Hannah Tsunemoto, Richard Szubin, Samira Dahesh +6 more

StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.26.542519

N/A

0DataRank · unranked

2 citations

Ke Chen, Bernhard Ø. Palsson, Laurence Yang, Jiao Zhao

A data-driven approach for timescale decomposition of biochemical reaction networks

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.21.554230

N/A

0DataRank · unranked

2 citations

Zachary B. Haiman, Bernhard Ø. Palsson, Amir Akbari

Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.26.542542

N/A

0DataRank · unranked

1 citations

Jonathan M. Monk, Richard Szubin, Ying Hefner, Bernhard Ø. Palsson, Jason C. Hyun

Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes

Cell Metabolism(2024)10.1016/j.cmet.2024.06.007

N/A

0DataRank · unranked

43 citations

Daniel Stephenson, Eric J. Earley, Gregory R Keele, Ariel Hay, Alicia Key +21 more

Metabolic and genetic basis for auxotrophies in Gram-negative species

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1910499117

N/A

0DataRank · unranked

65 citations

Kumari Sonal Choudhary, Ying Hefner, Amitesh Anand, Laurence Yang, Bernhard Ø. Palsson +1 more

Blood donor exposome and impact of common drugs on red blood cell metabolism

JCI Insight(2020)10.1172/jci.insight.146175

N/A

0DataRank · unranked

81 citations

Davide Stefanoni, Aarash Bordbar, Aaron Issaian, Bernhard Ø. Palsson, Larry J. Dumont +12 more

StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

PLoS Computational Biology(2024)10.1371/journal.pcbi.1011865

N/A

0DataRank · unranked

17 citations

Ke Chen, Bernhard Ø. Palsson, Laurence Yang, Jiao Zhao

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

Nature Communications(2024)10.1038/s41467-024-49231-y

N/A

0DataRank · unranked

16 citations

Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V. Sastry, Svetlana Maurya +4 more

Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2410492121

N/A

0DataRank · unranked

12 citations

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0DataRank · unranked

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N/A

0DataRank · unranked

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N/A

0DataRank · unranked

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0DataRank · unranked

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Nature Biotechnology(2020)10.1038/s41587-020-0446-y

N/A

0DataRank · unranked

558 citations

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Additional File 2: Database S2:

Figshare(2016)10.6084/m9.figshare.c.3634922_d2

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.28.610213

N/A

0DataRank · unranked

0 citations

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eLife(2024)10.7554/elife.100485

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0DataRank

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N/A

0DataRank · unranked

7 citations

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N/A

0DataRank · unranked

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Figshare(2016)10.6084/m9.figshare.c.3634922_d3

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N/A

0DataRank · unranked

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N/A

0DataRank · unranked

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N/A

0DataRank · unranked

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N/A

0DataRank · unranked

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N/A

0DataRank · unranked

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