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Education and qualifications (2)

University of California, Santa Cruz: Santa Cruz, CA, US

1995-09-01 to 2000-08-31 | PhD (Molecular, Cellular and Developmental Biology)
Education
Source: Self-asserted source
Steven Hallam

Sarah Lawrence College: Bronxville, New York, US

1988-09-01 to 1992-05-31 | BA
Education
Source: Self-asserted source
Steven Hallam

Research resources (4)

Resolving carbon fluxes within microbial communities inhabiting full-scale bioenergy facilities

Tracking carbon flow through syntrophic interspecies interactions in methanogenic microbiomes

Expanding the functional metagenomics toolkit with CRAGE and CRISPR-Cas9 in taxonomically diverse microbial host chassis

Engineering enzyme networks for biomass deconstruction in synthetic microbial communities

Works (37)

An automated high-throughput lighting system for screening photosynthetic microorganisms in plate-based formats

Communications Biology
2025-03-14 | Journal article
DOI: 10.1038/s42003-025-07853-y
Contributors: Avery J. C. Noonan; Paula M. N. Cameron; Kalen Dofher; Nannaphat Sukkasam; Tony Liu; Lucas Rönn; Tanakarn Monshupanee; Steven J. Hallam
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Crossref

Marine Heatwaves Modulate Food Webs and Carbon Transport Processes

2024-10-30 | Preprint
DOI: 10.21203/rs.3.rs-5256564/v1
Contributors: Mariana Bif; Colleen Kellogg; Yibin Huang; Julia Anstett; Sachia Traving; Angelica Pena; Steven Hallam; Kenneth Johnson
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MetaPathways v3.5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes

2024-06-06 | Preprint
DOI: 10.1101/2024.06.04.597460
Contributors: Ryan J. McLaughlin; Tony X. Liu; Tomer Altman; Aditi N. Nallan; Aria S. Hahn; Julia Anstett; Connor Morgan-Lang; Kishori M. Konwar; Steven J. Hallam
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3D Bioprinting of Food Grade Hydrogel Infused with Living Pleurotus ostreatus Mycelium in Non-sterile Conditions

ACS Applied Bio Materials
2024-05-20 | Journal article
DOI: 10.1021/acsabm.4c00048
Contributors: Nicholas Lin; Alireza Taghizadehmakoei; Lorena Polovina; Isobel McLean; Juan C. Santana-Martínez; Chloe Naese; Christopher Moraes; Steven James Hallam; Joseph Dahmen
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Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Nature Communications
2023-09-04 | Journal article
DOI: 10.1038/s41467-023-40907-5
Contributors: Brandon Kieft; Niko Finke; Ryan J. McLaughlin; Aditi N. Nallan; Martin Krzywinski; Sean A. Crowe; Steven J. Hallam
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Crossref

Emerging enzyme surface display systems for waste resource recovery

Environmental Microbiology
2023-02 | Journal article
DOI: 10.1111/1462-2920.16284
Contributors: Beth Davenport; Steven J. Hallam
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Crossref

Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment

Microbiology Resource Announcements
2023-02-16 | Journal article
DOI: 10.1128/mra.00759-22
Contributors: Yilin Qiu; Avery J. C. Noonan; Kalen Dofher; Moritz Koch; Brandon Kieft; Xuan Lin; Ryan M. Ziels; Steven J. Hallam; J. Cameron Thrash
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Crossref

Relabeling Metabolic Pathway Data with Groups to Improve Prediction Outcomes

2022 | Book chapter
DOI: 10.1007/978-3-031-17531-2_4
Contributors: Abdur Rahman M. A. Basher; Steven J. Hallam
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Metagenome-Assembled Genomes for “ Candidatus Phormidium sp. Strain AB48” and Co-occurring Microorganisms from an Industrial Photobioreactor Environment

Microbiology Resource Announcements
2022-12-15 | Journal article
DOI: 10.1128/mra.00447-22
Contributors: Avery J. C. Noonan; Yilin Qiu; Brandon Kieft; Sean Formby; Tony Liu; Kalen Dofher; Moritz Koch; Steven J. Hallam; Irene L. G. Newton
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Fractional factorial experimental design for optimizing volatile fatty acids from anaerobic fermentation of municipal sludge: Microbial community and activity investigation

Renewable Energy
2022-11 | Journal article
DOI: 10.1016/j.renene.2022.08.145
Contributors: Resty Nabaterega; Brandon Kieft; Steven J. Hallam; Cigdem Eskicioglu
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Crossref

Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis

The ISME Journal
2022-10-01 | Journal article
DOI: 10.1038/s41396-022-01281-0
Contributors: Ya-Fei Ou; Hong-Po Dong; Simon J McIlroy; Sean A Crowe; Steven J Hallam; Ping Han; Jens Kallmeyer; Rachel L Simister; Aurele Vuillemin; Andy O Leu et al.
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Crossref

Metabolic Pathway Prediction using Non-negative Matrix Factorization with Improved Precision

2021 | Book chapter
DOI: 10.1007/978-3-030-79290-9_4
Contributors: Abdur Rahman Mohd Abul Basher; Ryan J. McLaughlin; Steven J. Hallam
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Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters

Communications Biology
2021-10-22 | Journal article
DOI: 10.1038/s42003-021-02731-9
Contributors: Sachia J. Traving; Colleen T. E. Kellogg; Tetjana Ross; Ryan McLaughlin; Brandon Kieft; Grace Y. Ho; Angelica Peña; Martin Krzywinski; Marie Robert; Steven J. Hallam
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The abundance of mRNA transcripts of bacteroidetal polyethylene terephthalate (PET) esterase genes may indicate a role in marine plastic degradation

2021-08-11 | Preprint
DOI: 10.21203/rs.3.rs-567691/v2
Contributors: Hongli Zhang; Robert Dierkes; Pablo Pérez-García; Sebastian Weigert; Stefanie Sternagel; Steven Hallam; Thomas Schott; Klaus Juergens; Christel Vollstedt; Cynthia Chibani et al.
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Crossref

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Nature Communications
2021-06-09 | Journal article
DOI: 10.1038/s41467-021-23698-5
Contributors: Kristopher Kieft; Zhichao Zhou; Rika E. Anderson; Alison Buchan; Barbara J. Campbell; Steven J. Hallam; Matthias Hess; Matthew B. Sullivan; David A. Walsh; Simon Roux et al.
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Bacteroidetal cold-active and promiscuous esterases play a significant role in global polyethylene terephthalate (PET) degradation

2021-06-04 | Preprint
DOI: 10.21203/rs.3.rs-567691/v1
Contributors: Hongli Zhang; Robert Dierkes; Pablo Pérez-García; Sebastian Weigert; Stefanie Sternagel; Steven Hallam; Thomas Schott; Klaus Juergens; Christel Vollstedt; Cynthia Chibani et al.
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Crossref

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

The ISME Journal
2021-06-01 | Journal article
DOI: 10.1038/s41396-020-00889-4
Contributors: Heyu Lin; David B Ascher; Yoochan Myung; Carl H Lamborg; Steven J Hallam; Caitlin M Gionfriddo; Kathryn E Holt; John W Moreau
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Ecology and molecular targets of hypermutation in the global microbiome

Nature Communications
2021-05-24 | Journal article
DOI: 10.1038/s41467-021-23402-7
Contributors: Simon Roux; Blair G. Paul; Sarah C. Bagby; Stephen Nayfach; Michelle A. Allen; Graeme Attwood; Ricardo Cavicchioli; Ludmila Chistoserdova; Robert J. Gruninger; Steven J. Hallam et al.
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Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

The ISME Journal
2021-04-01 | Journal article
DOI: 10.1038/s41396-020-00825-6
Contributors: M Consuelo Gazitúa; Dean R Vik; Simon Roux; Ann C Gregory; Benjamin Bolduc; Brittany Widner; Margaret R Mulholland; Steven J Hallam; Osvaldo Ulloa; Matthew B Sullivan
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Crossref

Insights into the controls on metabolite distributions along a latitudinal transect of the western Atlantic Ocean

2021-03-09 | Preprint
DOI: 10.1101/2021.03.09.434501
Contributors: Winifred M. Johnson; Melissa C. Kido Soule; Krista Longnecker; Maya P. Bhatia; Steven J. Hallam; Michael W. Lomas; Elizabeth B. Kujawinski
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An integrated, modular approach to data science education in microbiology

PLOS Computational Biology
2021-02-25 | Journal article
DOI: 10.1371/journal.pcbi.1008661
Contributors: Kimberly A. Dill-McFarland; Patricia M. Palagi; Stephan G. König; Florent Mazel; David C. Oliver; Lisa M. McEwen; Kris Y. Hong; Steven J. Hallam
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Crossref

Metabolic pathway inference using multi-label classification with rich pathway features

PLOS Computational Biology
2020-10-01 | Journal article
DOI: 10.1371/journal.pcbi.1008174
Contributors: Abdur Rahman M. A. Basher; William Cannon; Ryan J. McLaughlin; Steven J. Hallam
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Crossref

leADS: improved metabolic pathway inference based on active dataset subsampling

2020-09-16 | Preprint
DOI: 10.1101/2020.09.14.297424
Contributors: Abdur Rahman M. A. Basher; Aditi N. Nallan; Ryan J. McLaughlin; Julia Anstett; Steven J. Hallam
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Crossref

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

2020-09-08 | Preprint
DOI: 10.21203/rs.3.rs-68034/v1
Contributors: Kristopher Kieft; Zhichao Zhou; Rika Anderson; Alison Buchan; Barbara Campbell; Steven Hallam; Matthias Hess; Matthew Sullivan; David Walsh; Simon Roux et al.
Source: check_circle
Crossref

Relabeling metabolic pathway data with groups to improve prediction outcomes

2020-08-24 | Preprint
DOI: 10.1101/2020.08.21.260109
Contributors: Abdur Rahman M. A. Basher; Steven J. Hallam
Source: check_circle
Crossref

An integrated, modular approach to data science education in the life sciences

2020-07-26 | Preprint
DOI: 10.1101/2020.07.25.218453
Contributors: Kimberly A Dill-McFarland; Stephan G König; Florent Mazel; David Oliver; Lisa M McEwen; Kris Y Hong; Steven J Hallam
Source: check_circle
Crossref

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

2020-06-04 | Preprint
DOI: 10.1101/2020.06.03.132969
Contributors: Heyu Lin; David B. Ascher; Yoochan Myung; Carl H. Lamborg; Steven J. Hallam; Caitlin M. Gionfriddo; Kathryn E. Holt; John W. Moreau
Source: check_circle
Crossref

Metabolic pathway prediction using non-negative matrix factorization with improved precision

2020-05-30 | Preprint
DOI: 10.1101/2020.05.27.119826
Contributors: Abdur Rahman M. A. Basher; Ryan J. McLaughlin; Steven J. Hallam
Source: check_circle
Crossref

Ecology and molecular targets of hypermutation in the global microbiome

2020-04-02 | Preprint
DOI: 10.1101/2020.04.01.020958
Contributors: Simon Roux; Blair G. Paul; Sarah C. Bagby; Michelle A. Allen; Graeme Attwood; Ricardo Cavicchioli; Ludmila Chistoserdova; Steven J. Hallam; Maria E. Hernandez; Matthias Hess et al.
Source: check_circle
Crossref

Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction

2020-02-23 | Preprint
DOI: 10.1101/2020.02.20.940205
Contributors: Abdur Rahman M. A. Basher; Steven J. Hallam
Source: check_circle
Crossref

Metabolic pathway inference using multi-label classification with rich pathway features

2020-02-03 | Preprint
DOI: 10.1101/2020.02.02.919944
Contributors: Abdur Rahman M. A. Basher; Ryan J. McLaughlin; Steven J. Hallam
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Crossref

Metabolite composition of sinking particles differs from surface suspended particles across a latitudinal transect in the South Atlantic

Limnology and Oceanography
2020-01 | Journal article
DOI: 10.1002/lno.11255
Contributors: Winifred M. Johnson; Krista Longnecker; Melissa C. Kido Soule; William A. Arnold; Maya P. Bhatia; Steven J. Hallam; Benjamin A. S. Van Mooy; Elizabeth B. Kujawinski
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An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

Nature Microbiology
2019-06-10 | Journal article
DOI: 10.1038/s41564-019-0469-7
Contributors: Peter Rahfeld; Lyann Sim; Haisle Moon; Iren Constantinescu; Connor Morgan-Lang; Steven J. Hallam; Jayachandran N. Kizhakkedathu; Stephen G. Withers
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Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil

The ISME Journal
2019-04-01 | Journal article
DOI: 10.1038/s41396-018-0334-3
Contributors: David J Levy-Booth; Ian J W Giesbrecht; Colleen T E Kellogg; Thierry J Heger; David V D’Amore; Patrick J Keeling; Steven J Hallam; William W Mohn
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Crossref

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome

The ISME Journal
2018-11-01 | Journal article
DOI: 10.1038/s41396-018-0215-9
Contributors: Zachary Armstrong; Keith Mewis; Feng Liu; Connor Morgan-Lang; Melanie Scofield; Evan Durno; Hong Ming Chen; Kevin Mehr; Stephen G Withers; Steven J Hallam
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Crossref

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients

Nature Communications
2017-12 | Journal article
DOI: 10.1038/s41467-017-01376-9
Contributors: Alyse K. Hawley; Masaru K. Nobu; Jody J. Wright; W. Evan Durno; Connor Morgan-Lang; Brent Sage; Patrick Schwientek; Brandon K. Swan; Christian Rinke; Monica Torres-Beltrán et al.
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Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

Science
2017-11-24 | Journal article
DOI: 10.1126/science.aan8260
Contributors: Maria G. Pachiadaki; Eva Sintes; Kristin Bergauer; Julia M. Brown; Nicholas R. Record; Brandon K. Swan; Mary Elizabeth Mathyer; Steven J. Hallam; Purificacion Lopez-Garcia; Yoshihiro Takaki et al.
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