Paramvir Dehal - Publications, H-index & Citations

Paramvir Dehal

e.o. lawrence berkeley national laboratory

28H指数

73论文数

3.4W被引数

收录论文 25

发表时间

Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation 推动FAIR数据向可比、组织化、可预测的AI就绪数据发展，以供社区验证

Communications Biology

IF5.1

2026-07-18

OAAI

Elisha M. Wood-Charlson; Wolmar N. Åkerström; Lindsey Anderson; Mikayla A. Borton; Stephen K. Burley; Neil Byers; Ishwar Chandramouliswaran; Sylvain V. Costes; Paramvir S. Dehal; Mitchel Doktycz; Emiley Eloe-Fadrosh; Christopher Henry; Kjiersten Fagnan; Oliver Fiehn; Mahantesh Halappanavar; Bonnie Hurwitz; Marcin P. Joachimiak; Sean Jungbluth; Julia Koblitz; Gazi Mahmud; Lee Ann McCue; Thomas O. Metz; Nigel Mouncey; Christopher J. Mungall; Tiffanie M. Nelson; Valerie Skye; Amanda M. Saravia-Butler; V. Ratna Saripalli; Susannah G. Tringe; Tim Van Den Bossche; Adam P. Arkin

KBase: Open-source platform for collaborative biological data analysis and publication

Journal of Molecular Biology

IF4.5

2026-02-05

OAAI

Elisha M. Wood-Charlson; Christopher Henry; Paramvir Dehal; Gazi Mahmud; Ben Allen; Kathleen Bielsmith; D.Dakota Blair; Shane Canon; Mikaela Cashman; Dylan Chivian; Robert Cottingham; Zach Crocket; Ellen Dow; Meghan Drake; Janaka N. Edirisinghe; José P. Faria; Andrew Freiburger; Tianhao Gu; Prachi Gupta; AJ Ireland

A bacterial sensor taxonomy across earth ecosystems for machine learning applications 用于机器学习应用的跨地球生态系统的细菌传感器分类法

MSYSTEMS

IF4.6

2024-01-23

OAAI

Park, Helen; Joachimiak, Marcin P.; Jungbluth, Sean P.; Yang, Ziming; Riehl, William J.; Canon, R. Shane; Arkin, Adam P.; Dehal, Paramvir S.

Metagenome-assembled genome extraction and analysis from microbiomes using KBase (vol 1350, pg 32, 2022)

NATURE PROTOCOLS

IF16

2022-11-30

OAAI

Chivian, Dylan; Jungbluth, Sean P.; Dehal, Paramvir S.; Wood-Charlson, Elisha M.; Canon, Richard S.; Allen, Benjamin H.; Clark, Mikayla M.; Gu, Tianhao; Land, Miriam L.; Price, Gavin A.; Riehl, William J.; Sneddon, Michael W.; Sutormin, Roman; Zhang, Qizhi; Cottingham, Robert W.; Henry, Chris S.; Arkin, Adam P.

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

NATURE PROTOCOLS

IF16

2022-11-14

OAAI

A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum

current opinion in plant biology

IF4.5

2021-12-01

OAAI

Kumari, Sunita; Kumar, Vivek; Beilsmith, Kathleen; Seaver, Samuel M. D.; Canon, Shane; Dehal, Paramvir; Gu, Tian; Joachimiak, Marcin; Lerma-Ortiz, Claudia; Liu, Filipe; Lu, Zhenyuan; Pearson, Eric; Ranjan, Priya; Riel, William; Henry, Christopher S.; Arkin, Adam P.; Ware, Doreen

A genomic catalog of Earth's microbiomes (Nov, 10.1038/s41587-020-0718-6, 2020)地球微生物组的基因组目录 (11月，10.1038/s41587-020-0718-6，2020)

NATURE BIOTECHNOLOGY

IF41.7

2021-04-01

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I- Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

A genomic catalog of Earth's microbiomes (November, 10.1038/s41587-020-0718-6, 2020)地球微生物组的基因组目录 (11月，10.1038/s41587-020-0718-6，2020)

NATURE BIOTECHNOLOGY

IF41.7

2020-11-18

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

A genomic catalog of Earth's microbiomes 地球微生物组的基因组目录

NATURE BIOTECHNOLOGY

IF41.7

2020-11-09

458

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

KBase: The United States Department of Energy Systems Biology Knowledgebase

NATURE BIOTECHNOLOGY

IF41.7

2018-07-06

928

OAAI

Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.; Harris, Nomi L.; Stevens, Rick L.; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W.; Henderson, Matthew L.; Riehl, William J.; Murphy-Olson, Dan; Chan, Stephen Y.; Kamimura, Roy T.; Kumari, Sunita; Drake, Meghan M.; Brettin, Thomas S.; Glass, Elizabeth M.; Chivian, Dylan; Gunter, Dan; Weston, David J.; Allen, Benjamin H.; Baumohl, Jason; Best, Aaron A.; Bowen, Ben; Brenner, Steven E.; Bun, Christopher C.; Chandonia, John-Marc; Chia, Jer-Ming; Colasanti, Ric; Conrad, Neal; Davis, James J.; Davison, Brian H.; DeJongh, Matthew; Devoid, Scott; Dietrich, Emily; Dubchak, Inna; Edirisinghe, Janaka N.; Fang, Gang; Faria, Jose P.; Frybarger, Paul M.; Gerlach, Wolfgang; Gerstein, Mark; Greiner, Annette; Gurtowski, James; Haun, Holly L.; He, Fei; Jain, Rashmi; Joachimiak, Marcin P.; Keegan, Kevin P.; Kondo, Shinnosuke; Kumar, Vivek; Land, Miriam L.; Meyer, Folker; Mills, Marissa; Novichkov, Pavel S.; Oh, Taeyun; Olsen, Gary J.; Olson, Robert; Parrello, Bruce; Pasternak, Shiran; Pearson, Erik; Poon, Sarah S.; Price, Gavin A.; Ramakrishnan, Srividya; Ranjan, Priya; Ronald, Pamela C.; Schatz, Michael C.; Seaver, Samuel M. D.; Shukla, Maulik; Sutormin, Roman A.; Syed, Mustafa H.; Thomason, James; Tintle, Nathan L.; Wang, Daifeng; Xia, Fangfang; Yoo, Hyunseung; Yoo, Shinjae; Yu, Dantong

metaMicrobesOnline: phylogenomic analysis of microbial communities

NUCLEIC ACIDS RESEARCH

IF13.1

2012-11-30

OAAI

Chivian, Dylan; Dehal, Paramvir S.; Keller, Keith; Arkin, Adam P.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

NUCLEIC ACIDS RESEARCH

IF13.1

2012-06-14

OAAI

Novichkov, Pavel S.; Brettin, Thomas S.; Novichkova, Elena S.; Dehal, Paramvir S.; Arkin, Adam P.; Dubchak, Inna; Rodionov, Dmitry A.

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

GENOME BIOLOGY

IF9.4

2011-10-12

OAAI

Rajeev, Lara; Luning, Eric G.; Dehal, Paramvir S.; Price, Morgan N.; Arkin, Adam P.; Mukhopadhyay, Aindrila

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

PLOS GENETICS

IF3.7

2011-06-09

497

OAAI

Goodwin, Stephen B.; Ben M'Barek, Sarrah; Dhillon, Braham; Wittenberg, Alexander H. J.; Crane, Charles F.; Hane, James K.; Foster, Andrew J.; Van der Lee, Theo A. J.; Grimwood, Jane; Aerts, Andrea; Antoniw, John; Bailey, Andy; Bluhm, Burt; Bowler, Judith; Bristow, Jim; van der Burgt, Ate; Canto-Canche, Blondy; Churchill, Alice C. L.; Conde-Ferraez, Laura; Cools, Hans J.; Coutinho, Pedro M.; Csukai, Michael; Dehal, Paramvir; De Wit, Pierre; Donzelli, Bruno; van de Geest, Henri C.; van Ham, Roeland C. H. J.; Hammond-Kosack, Kim E.; Henrissat, Bernard; Kilian, Andrzej; Kobayashi, Adilson K.; Koopmann, Edda; Kourmpetis, Yiannis; Kuzniar, Arnold; Lindquist, Erika; Lombard, Vincent; Maliepaard, Chris; Martins, Natalia; Mehrabi, Rahim; Nap, Jan P. H.; Ponomarenko, Alisa; Rudd, Jason J.; Salamov, Asaf; Schmutz, Jeremy; Schouten, Henk J.; Shapiro, Harris; Stergiopoulos, Ioannis; Torriani, Stefano F. F.; Tu, Hank; de Vries, Ronald P.; Waalwijk, Cees; Ware, Sarah B.; Wiebenga, Ad; Zwiers, Lute-Harm; Oliver, Richard P.; Grigoriev, Igor V.; Kema, Gert H. J.

A universal TagModule collection for parallel genetic analysis of microorganisms

NUCLEIC ACIDS RESEARCH

IF13.1

2010-05-21

OAAI

Oh, Julia; Fung, Eula; Price, Morgan N.; Dehal, Paramvir S.; Davis, Ronald W.; Giaever, Guri; Nislow, Corey; Arkin, Adam P.; Deutschbauer, Adam

MicrobesOnline: an integrated portal for comparative and functional genomics

NUCLEIC ACIDS RESEARCH

IF13.1

2009-11-11

407

OAAI

Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan; Friedland, Greg D.; Huang, Katherine H.; Keller, Keith; Novichkov, Pavel S.; Dubchak, Inna L.; Alm, Eric J.; Arkin, Adam P.

Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity

ENVIRONMENTAL MICROBIOLOGY

IF4

2009-09-04

294

OAAI

Walker, Christopher B.; Stolyar, Sergey; Chivian, Dylan; Pinel, Nicolas; Gabster, Jeffrey A.; Dehal, Paramvir S.; He, Zhili; Yang, Zamin Koo; Yen, Huei-Che B.; Zhou, Jizhong; Wall, Judy D.; Hazen, Terry C.; Arkin, Adam P.; Stahl, David A.

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix FastTree: 用剖面代替距离矩阵计算大型最小进化树

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2009-04-17

4.1K

OAAI

Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

BMC GENOMICS

IF3.7

2009-01-01

OAAI

Yang, Yunfeng; Harris, Daniel P.; Luo, Feng; Xiong, Wenlu; Joachimiak, Marcin; Wu, Liyou; Dehal, Paramvir; Jacobsen, Janet; Yang, Zamin; Palumbo, Anthony V.; Arkin, Adam P.; Zhou, Jizhong

Metabolic Flux Analysis of Shewanella spp. Reveals Evolutionary Robustness in Central Carbon Metabolism

BIOTECHNOLOGY AND BIOENGINEERING

IF3.6

2008-11-13

PREAI

Tan, Yinjie J.; Martin, Hector Garcia; Dehal, Paramvir S.; Deutschbauer, Adam; Llora, Xavier; Meadows, Adam; Arkin, Adam; Keasling, Jay D.

研究方向