Eric J. Alm

Also affiliated with Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Technology

Biochemistry, Genetics and Molecular BiologyMedicineEnvironmental Science

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

19.2Author DataRank

Indexed papers

6in 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 6 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.

A framework for human microbiome research

Nature(2012)10.1038/nature11209

Top 2%

8.4DataRank

Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Papers

Driven by 44 papers — median percentile 97. Top paper: “A framework for human microbiome research”.

A framework for human microbiome research

Nature(2012)10.1038/nature11209

Top 2%

8.4DataRank

Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

Nature Communications(2017)10.1038/s41467-017-01973-8

Top 3%

6.9DataRank

Top 3%1042 citations

Sean M. Gibbons, Thomas Gurry, Rafael A. Irizarry, Eric J. Alm, Claire Duvallet

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Water Research(2022)10.1016/j.watres.2022.118070

N/A

4.4DataRank · unranked

120 citations

Fuqing Wu, Mary Bushman, Jianbo Zhang, Maxim Imakaev, Peter R. Chai +18 more

Daily, oral FMT for long-term maintenance therapy in ulcerative colitis: results of a single-center, prospective, randomized pilot study

BMC Gastroenterology(2021)10.1186/s12876-021-01856-9

N/A

4.0DataRank · unranked

126 citations

Nathaniel D. Chu, Le Thanh Tu Nguyen, Magen Phillips, Cheryl Collins, Karen A. Fortner +16 more

Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States

ACS ES&T Water(2022)10.1021/acsestwater.1c00434

Top 6%

4.0DataRank

Top 6%99 citations

Fuqing Wu, Kyle A. McElroy, Maxim Imakaev, Noriko Endo, Amy Xiao +15 more

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Journal of Computational Biology(2013)10.1089/cmb.2013.0073

N/A

3.0DataRank · unranked

71 citations

Eric J. Alm, Sharon L. R. Kardia, Mukul S. Bansal

Improved gene tree error correction in the presence of horizontal gene transfer

Bioinformatics(2015)10.1093/bioinformatics/btu806

N/A

2.2DataRank · unranked

67 citations

Yi-Chieh Wu, Eric J. Alm, Sharon L. R. Kardia, Mukul S. Bansal

Structure, function and diversity of the healthy human microbiome

Nature(2012)10.1038/nature11234

N/A

1.4DataRank · unranked

10088 citations

Curtis Huttenhower, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger +235 more

Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

Frontiers in Microbiology(2020)10.3389/fmicb.2020.610001

N/A

1.3DataRank · unranked

59 citations

Sarah J. Spencer, Sara Gushgari-Doyle, Mon Oo Yee, Jana Voříšková, Yifan Li +3 more

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

The Science of The Total Environment(2021)10.1016/j.scitotenv.2021.150121

N/A

0.859DataRank · unranked

305 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +23 more

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Bioinformatics(2012)10.1093/bioinformatics/bts225

N/A

0.810DataRank · unranked

221 citations

Eric J. Alm, Sharon L. R. Kardia, Mukul S. Bansal

Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020

Water Research(2021)10.1016/j.watres.2021.117400

N/A

0.781DataRank · unranked

181 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +17 more

Anatomy promotes neutral coexistence of strains in the human skin microbiome

Cell Host & Microbe(2022)10.1016/j.chom.2021.12.007

N/A

0.776DataRank · unranked

175 citations

Anne C. Kuan, Ravalika Damerla, Alexandra J. Poret, Jacob S. Baker, A. Delphine Tripp +3 more

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

medRxiv(2020)10.1101/2020.06.15.20117747

N/A

0.741DataRank · unranked

139 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +23 more

Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss

Lecture Notes in Computer Science(2013)10.1007/978-3-642-37195-0_1

N/A

0.600DataRank · unranked

4 citations

Eric J. Alm, Sharon L. R. Kardia, Mukul S. Bansal

Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states

medRxiv(2021)10.1101/2021.03.10.21253235

N/A

0.529DataRank · unranked

33 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +17 more

Sparse autoencoders uncover biologically interpretable features in protein language model representations

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2506316122

N/A

0.494DataRank · unranked

26 citations

Mihir Bafna, Eric J. Alm, Bonnie Berger, Onkar Singh Gujral

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

medRxiv(2021)10.1101/2021.06.10.21258580

N/A

0.457DataRank · unranked

20 citations

Fuqing Wu, Mary Bushman, Jianbo Zhang, Maxim Imakaev, Peter R. Chai +18 more

Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after fecal microbiota transplant in inflammatory bowel disease

Scientific Reports(2024)10.1038/s41598-024-68619-w

N/A

0.449DataRank · unranked

19 citations

Athos Bousvaros, Michael Docktor, Abby L. Kaplan, Paul A. Rufo, McKenzie Leier +8 more

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

mSystems(2021)10.1128/msystems.00537-21

N/A

0.442DataRank · unranked

18 citations

Simon Roux, Hanqiao Zhang, Anatori Prieto, Drishti Soneja, John‐Marc Chandonia +10 more

Anatomy promotes neutral coexistence of strains in the human skin microbiome

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.12.443817

N/A

0.406DataRank · unranked

14 citations

Anne C. Kuan, Ravalika Damerla, Alexandra J. Poret, Jacob S. Baker, Arielle D. Tripp +3 more

Nationwide trends in COVID-19 cases and SARS-CoV-2 wastewater concentrations in the United States

medRxiv(2021)10.1101/2021.09.08.21263283

N/A

0.312DataRank · unranked

7 citations

Fuqing Wu, Kyle A. McElroy, Maxim Imakaev, Noriko Endo, Amy Xiao +15 more

Microbe-seq : high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.14.422699

N/A

0.292DataRank · unranked

6 citations

Shijie Zhao, Yehang Yin, Huidan Zhang, David M. Needham, Ethan D. Evans +5 more

Industrialization drives convergent microbial and physiological shifts in the human metaorganism

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.20.683358

N/A

0.241DataRank · unranked

4 citations

Malte Rühlemann, Ana Paula Schaan, Yue Ma, Lucas Moitinho‐Silva, Eike Matthias Wacker +61 more

An immune-competent human gut microphysiological system enables inflammation-modulation of Faecalibacterium prausnitzii

Research Square(2023)10.21203/rs.3.rs-3373576/v1

N/A

0.241DataRank · unranked

4 citations

Yu-Ja Huang, Martin Trapečar, Charles Wright, Kirsten Schneider, John Kemmit +7 more

Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.03.597175

N/A

0.241DataRank · unranked

4 citations

Michael S. DeMott, Shane R. Byrne, K. Flores, Mathilde Poyet, Mathieu Groussin +6 more

Antigen-specific induction of CD4 + CD8αα + intraepithelial T lymphocytes by Bacteroidetes species

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.05.236513

N/A

0.241DataRank · unranked

4 citations

Preksha Bhagchandani, Mariya London, Mark Mimee, Scott W. Olesen, Mathilde Poyet +11 more

Daily, Oral FMT for Long-Term Maintenance Therapy in Ulcerative Colitis: Results of a Single-Center, Prospective, Randomized Pilot Study.

Research Square(2020)10.21203/rs.3.rs-62372/v1

N/A

0.208DataRank · unranked

3 citations

Nathaniel D. Chu, Le Thanh Tu Nguyen, Magen Phillips, Cheryl Collins, Karen A. Fortner +16 more

Convergent genomic responses of human gut bacteria to variations in industrialization

10.1101/2025.10.20.683395

N/A

0.208DataRank · unranked

3 citations

Lénárd L. Szánthó, Silvio Waschina, Lucas Moitinho-Silva, Laura K. Mews, Joan F. Camarena +24 more

Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.29.596306

N/A

0.165DataRank · unranked

2 citations

Michael S. DeMott, Yifeng Yuan, Farzan Ghanegolmohammadi, Stefanie Kaiser, James G. Fox +3 more

Lectin-Seq: a method to profile lectin-microbe interactions in native communities

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.14.520458

N/A

0.165DataRank · unranked

2 citations

Christine R. Isabella, Rebecca L. Walker, Dallis Sergio, Tony Gaca, Smrithi Raman +13 more

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.14.203604

N/A

0DataRank · unranked

0 citations

Simon Roux, Hanqiao Zhang, Anatori Prieto, Drishti Soneja, John‐Marc Chandonia +10 more

The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study

Reproductive Sciences(2020)10.1007/s43032-019-00113-5

N/A

0DataRank · unranked

95 citations

Giuliano Moysés Borrelli, Carlo Martins, Esper G. Kallás, Sabri Saeed Sanabani, Linda G. Griffith +3 more

“Waste Not, Want Not” — Leveraging Sewer Systems and Wastewater-Based Epidemiology for Drug Use Trends and Pharmaceutical Monitoring

Journal of Medical Toxicology(2021)10.1007/s13181-021-00853-4

N/A

0DataRank · unranked

53 citations

Noriko Endo, Claire Duvallet, Newsha Ghaeli, Kaitlyn Hess, Eric J. Alm +3 more

Wastewater network infrastructure in public health: Applications and learnings from the COVID-19 pandemic

PLOS Global Public Health(2021)10.1371/journal.pgph.0000061

N/A

0DataRank · unranked

49 citations

Noriko Endo, Claire Duvallet, Newsha Ghaeli, Mariana Matus, Jennings Heussner +5 more

Daily, Oral FMT for Longterm Maintenance Therapy in Ulcerative Colitis: Results of a single-center, prospective, randomized pilot study.

Research Square(2021)10.21203/rs.3.rs-62372/v2

N/A

0DataRank · unranked

3 citations

Nathaniel D. Chu, Le Thanh Tu Nguyen, Magen Phillips, Cheryl Collins, Karen A. Fortner +16 more

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Science(2022)10.1126/science.abm1483

N/A

0DataRank · unranked

284 citations

Shijie Zhao, Yehang Yin, Huidan Zhang, David M. Needham, Ethan D. Evans +5 more

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.01.073353

N/A

0DataRank · unranked

7 citations

Sarah J. Spencer, Sara Gushgari-Doyle, Mon Oo Yee, Jana Voříšková, Yifan Li +3 more

Maternal Microbiota Modulate a Fragile X-like Syndrome in Offspring Mice

Genes(2022)10.3390/genes13081409

N/A

0DataRank · unranked

10 citations

Katherine T. Weber, Lily J. Kim, Tony E. Chavarria, Sebastian E. Carrasco, Sureshkumar Muthupalani +11 more

An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii

npj Biofilms and Microbiomes(2024)10.1038/s41522-024-00501-z

N/A

0DataRank · unranked

26 citations

Yu-Ja Huang, Martin Trapečar, Charles Wright, Kirsten Schneider, John Kemmitt +8 more

Structured community transitions explain the switching capacity of microbial systems

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2312521121

N/A

0DataRank · unranked

24 citations

Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J. Alm, Ricard V. Solé +2 more

The impact of gastrointestinal dysmotility on the aerodigestive microbiome of pediatric lung transplant recipients

The Journal of Heart and Lung Transplantation(2020)10.1016/j.healun.2020.11.013

N/A

0DataRank · unranked

6 citations

Debra Boyer, Gary Visner, Dawn Freiberger, Margot Lurie, Madeline Kane +7 more

Host transcriptional responses to gut microbiome variation arising from urbanism

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.26.683539

N/A

0DataRank · unranked

0 citations

Shreya Nirmalan, Adnan Alazizi, Henriette Mair-Meijers, Adwoa Agyei, Mary Afihene +19 more

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria

The ISME Journal(2020)10.1038/s41396-020-0696-1

N/A

0DataRank · unranked

25 citations

Nathan I Johns, Anthony Yang, Florencia Velez‐Cortes, Christopher S. Smillie, Mark Smith +3 more

Eric J. Alm

Indexed papers

Top data-sharing exemplar

Papers