Works by Clum, Alicia

Results: 52

Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion.

Published in:

Plant & Soil, 2022, v. 471, n. 1/2, p. 507, doi. 10.1007/s11104-021-05247-7

By:

Martínez-Hidalgo, Pilar;
Humm, Ethan A.;
Still, David W.;
Shi, Baochen;
Pellegrini, Matteo;
de la Roca, Gabriela;
Veliz, Esteban;
Maymon, Maskit;
Bru, Pierrick;
Huntemann, Marcel;
Clum, Alicia;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Ivanova, Natalia N.;
Kyrpides, Nikos C.;
Shapiro, Nicole;
Eloe-Fadrosh, Emiley A.

Publication type:

Article

High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698).

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0236-4

By:

Patil, Yogita;
Müller, Nicolai;
Schink, Bernhard;
Whitman, William B.;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Daum, Chris;
Shapiro, Nicole;
Ivanova, Natalia;
Kyrpides, Nikos;
Woyke, Tanja;
Junghare, Madan

Publication type:

Article

Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0229-3

By:

Hutt, Lee P.;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, Tatiparthi;
Daum, Chris;
Shapiro, Nicole;
Ivanova, Natalia;
Kyrpides, Nikos;
Woyke, Tanja;
Boden, Rich

Publication type:

Article

Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.

Published in:

Standards in Genomic Sciences, 2016, p. 1, doi. 10.1186/s40793-016-0188-0

By:

Boden, Rich;
Hutt, Lee P.;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, Tatiparthi;
Chew Yee Ngan;
Daum, Chris;
Shapiro, Nicole;
Markowitz, Victor;
Ivanova, Natalia;
Woyke, Tanja;
Kyrpides, Nikos

Publication type:

Article

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T.

Published in:

Standards in Genomic Sciences, 2016, v. 11, p. 1, doi. 10.1186/s40793-016-0193-3

By:

Nicholson, Wayne L.;
Davis, Christina L.;
Shapiro, Nicole;
Huntemann, Marcel;
Clum, Alicia;
Reddy, T. B. K.;
Pillay, Manoj;
Markowitz, Victor;
Varghese, Neha;
Pati, Amrita;
Ivanova, Natalia;
Kyrpides, Nikos;
Woyke, Tanja

Publication type:

Article

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.

Published in:

Standards in Genomic Sciences, 2016, v. 11, p. 1, doi. 10.1186/s40793-016-0184-4

By:

Melton, Emily Denise;
Sorokin, Dimitry Y.;
Overmars, Lex;
Chertkov, Olga;
Clum, Alicia;
Pillay, Manoj;
Ivanova, Natalia;
Shapiro, Nicole;
Kyrpides, Nikos C.;
Woyke, Tanja;
Lapidus, Alla L.;
Muyzer, Gerard

Publication type:

Article

Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

Published in:

Standards in Genomic Sciences, 2016, v. 11, p. 1, doi. 10.1186/s40793-016-0168-4

By:

Rice, Marlen C.;
Norton, Jeanette M.;
Valois, Frederica;
Bollmann, Annette;
Bottomley, Peter J.;
Klotz, Martin G.;
Laanbroek, Hendrikus J.;
Suwa, Yuichi;
Stein, Lisa Y.;
Sayavedra-Soto, Luis;
Woyke, Tanja;
Shapiro, Nicole;
Goodwin, Lynne A.;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Kyrpides, Nikos;
Varghese, Neha;
Mikhailova, Natalia;
Markowitz, Victor

Publication type:

Article

High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409 with an incomplete denitrification pathway.

Published in:

Standards in Genomic Sciences, 2016, v. 11, n. 1, p. 1, doi. 10.1186/s40793-016-0140-3

By:

Zhou, En-Min;
Murugapiran, Senthil;
Mefferd, Chrisabelle;
Liu, Lan;
Xian, Wen-Dong;
Yin, Yi-Rui;
Ming, Hong;
Yu, Tian-Tian;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T.;
Ngan, Chew;
Daum, Chris;
Shapiro, Nicole;
Markowitz, Victor

Publication type:

Article

Terabase-scale metagenome coassembly with MetaHipMer.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-67416-5

By:

Hofmeyr, Steven;
Egan, Rob;
Georganas, Evangelos;
Copeland, Alex C.;
Riley, Robert;
Clum, Alicia;
Eloe-Fadrosh, Emiley;
Roux, Simon;
Goltsman, Eugene;
Buluç, Aydın;
Rokhsar, Daniel;
Oliker, Leonid;
Yelick, Katherine

Publication type:

Article

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.

Published in:

Genome Biology & Evolution, 2015, v. 7, n. 6, p. 1590, doi. 10.1093/gbe/evv090

By:

Ying Chang;
Sishuo Wang;
Satoshi Sekimoto;
Aerts, Andrea L.;
Choi, Cindy;
Clum, Alicia;
LaButti, Kurt M.;
Lindquist, Erika A.;
Chew Yee Ngan;
Ohm, Robin A.;
Salamov, Asaf A.;
Grigoriev, Igor V.;
Spatafora, Joseph W.;
Berbee, Mary L.

Publication type:

Article

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2063-6

By:

Bowers, Robert M.;
Clum, Alicia;
Tice, Hope;
Lim, Joanne;
Singh, Kanwar;
Ciobanu, Doina;
Chew Yee Ngan;
Jan-Fang Cheng;
Tringe, Susannah G.;
Woyke, Tanja

Publication type:

Article

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06681-w

By:

Steindorff, Andrei S.;
Aguilar-Pontes, Maria Victoria;
Robinson, Aaron J.;
Andreopoulos, Bill;
LaButti, Kurt;
Kuo, Alan;
Mondo, Stephen;
Riley, Robert;
Otillar, Robert;
Haridas, Sajeet;
Lipzen, Anna;
Grimwood, Jane;
Schmutz, Jeremy;
Clum, Alicia;
Reid, Ian D.;
Moisan, Marie-Claude;
Butler, Gregory;
Nguyen, Thi Truc Minh;
Dewar, Ken;
Conant, Gavin

Publication type:

Article

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03069-7

By:

Schadt, Christopher;
Martin, Stanton;
Carrell, Alyssa;
Fortner, Allison;
Hopp, Dan;
Jacobson, Dan;
Klingeman, Dawn;
Kristy, Brandon;
Phillips, Jana;
Piatkowski, Bryan;
Miller, Mark A.;
Smith, Montana;
Patil, Sujay;
Flynn, Mark;
Canon, Shane;
Clum, Alicia;
Mungall, Christopher J.;
Pennacchio, Christa;
Bowen, Benjamin;
Louie, Katherine

Publication type:

Article

Quantifying the impact of workshops promoting microbiome data standards and data stewardship.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-89991-1

By:

Kelliher, Julia M.;
Rodriguez, Francisca E.;
Johnson, Leah Y. D.;
Roux, Simon;
Smith, Montana;
Clum, Alicia;
Lynch, Wendi;
Bias, Candace Hope;
Finks, Sarai S.;
Keenum, Ishi;
Kiledal, E. Anders;
Lin, Heng-An;
Longley, Reid;
McDonald, Ryan;
Pitot, Thomas M.;
Rodríguez-Ramos, Josué;
Shen, Jiaxian;
Sprockett, Daniel D.;
Swift, Joel;
Yadav, Archana

Publication type:

Article

Development of a common peroneal nerve injury model in domestic swine for the study of translational neuropathic pain treatments.

Published in:

Journal of Neurosurgery, 2021, v. 135, n. 5, p. 1516, doi. 10.3171/2020.9.JNS202961

By:

Hellman, Abigail;
Maietta, Teresa;
Clum, Alicia;
Byraju, Kanakaharini;
Raviv, Nataly;
Staudt, Michael D.;
Jeannotte, Erin;
Nalwalk, Julia;
Belin, Sophie;
Poitelon, Yannick;
Pilitsis, Julie G.

Publication type:

Article

Pilot study on the effects of low intensity focused ultrasound in a swine model of neuropathic pain.

Published in:

Journal of Neurosurgery, 2021, v. 135, n. 5, p. 1508, doi. 10.3171/2020.9.JNS202962

By:

Hellman, Abigail;
Maietta, Teresa;
Clum, Alicia;
Byraju, Kanakaharini;
Raviv, Nataly;
Staudt, Michael D.;
Jeannotte, Erin;
Ghoshal, Goutam;
Shin, Damian;
Neubauer, Paul;
Williams, Emery;
Heffter, Tamas;
Burdette, Clif;
Jiang Qian;
Nalwalk, Julia;
Pilitsis, Julie G.

Publication type:

Article

Draft genome of Paraburkholderia caballeronis TNe-841T, a free-living, nitrogen-fixing, tomato plant-associated bacterium.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0294-7

By:

Rojas-Rojas, Fernando Uriel;
Tapia-García, Erika Yanet;
Maymon, Maskit;
Humm, Ethan;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Markowitz, Victor;
Ivanova, Natalia;
Kyrpides, Nikos;
Woyke, Tanja;
Shapiro, Nicole;
Hirsch, Ann M.;
Estrada-de los Santos, Paulina

Publication type:

Article

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0258-y

By:

Matrosova, Vera Y.;
Gaidamakova, Elena K.;
Makarova, Kira S.;
Grichenko, Olga;
Klimenkova, Polina;
Volpe, Robert P.;
Tkavc, Rok;
Ertem, Gözen;
Conze, Isabel H.;
Brambilla, Evelyne;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Daum, Chris;
Shapiro, Nicole

Publication type:

Article

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0242-6

By:

Laviad-Shitrit, Sivan;
Göker, Markus;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Daum, Chris;
Shapiro, Nicole;
Markowitz, Victor;
Ivanova, Natalia;
Woyke, Tanja;
Klenk, Hans-Peter;
Kyrpides, Nikos C.;
Halpern, Malka

Publication type:

Article

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence.

Published in:

PLoS ONE, 2017, v. 12, n. 12, p. 1, doi. 10.1371/journal.pone.0188914

By:

Yassin, Atteyet F.;
Langenberg, Stefan;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Shapiro, Nicole;
Ivanova, Natalia;
Woyke, Tanja;
Kyrpides, Nikos C.

Publication type:

Article

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Published in:

Nature Methods, 2013, v. 10, n. 6, p. 563, doi. 10.1038/nmeth.2474

By:

Chin, Chen-Shan;
Alexander, David H;
Marks, Patrick;
Klammer, Aaron A;
Drake, James;
Heiner, Cheryl;
Clum, Alicia;
Copeland, Alex;
Huddleston, John;
Eichler, Evan E;
Turner, Stephen W;
Korlach, Jonas

Publication type:

Article

Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation.

Published in:

Journal of Fungi, 2024, v. 10, n. 7, p. 507, doi. 10.3390/jof10070507

By:

Theobald, Sebastian;
Vesth, Tammi C.;
Geib, Elena;
Nybo, Jane L.;
Frisvad, Jens C.;
Larsen, Thomas O.;
Kuo, Alan;
LaButti, Kurt;
Lyhne, Ellen K.;
Kjærbølling, Inge;
Ledsgaard, Line;
Barry, Kerrie;
Clum, Alicia;
Chen, Cindy;
Nolan, Matt;
Sandor, Laura;
Lipzen, Anna;
Mondo, Stephen;
Pangilinan, Jasmyn;
Salamov, Asaf

Publication type:

Article

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Published in:

Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0287-z

By:

Sevim, Volkan;
Lee, Juna;
Egan, Robert;
Clum, Alicia;
Hundley, Hope;
Lee, Janey;
Everroad, R. Craig;
Detweiler, Angela M.;
Bebout, Brad M.;
Pett-Ridge, Jennifer;
Göker, Markus;
Murray, Alison E.;
Lindemann, Stephen R.;
Klenk, Hans-Peter;
O'Malley, Ronan;
Zane, Matthew;
Cheng, Jan-Fang;
Copeland, Alex;
Daum, Christopher;
Singer, Esther

Publication type:

Article

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.

Published in:

Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0222-3

By:

Högfors-Rönnholm, Eva;
Lopez-Fernandez, Margarita;
Christel, Stephan;
Brambilla, Diego;
Huntemann, Marcel;
Clum, Alicia;
Foster, Brian;
Foster, Bryce;
Roux, Simon;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Copeland, Alex;
Chen, I-Min A.;
Ivanova, Natalia N.;
Kyrpides, Nikos C.;
Harmon-Smith, Miranda;
Eloe-Fadrosh, Emiley A.

Publication type:

Article

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.

Published in:

Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0141-3

By:

Camargo, Antonio Pedro;
de Souza, Rafael Soares Correa;
de Britto Costa, Patrícia;
Gerhardt, Isabel Rodrigues;
Dante, Ricardo Augusto;
Teodoro, Grazielle Sales;
Abrahão, Anna;
Lambers, Hans;
Carazzolle, Marcelo Falsarella;
Huntemann, Marcel;
Clum, Alicia;
Foster, Brian;
Foster, Bryce;
Roux, Simon;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Copeland, Alex

Publication type:

Article

Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.

Published in:

Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0132-4

By:

Nowinski, Brent;
Smith, Christa B.;
Thomas, Courtney M.;
Esson, Kaitlin;
Marin, Roman;
Preston, Christina M.;
Birch, James M.;
Scholin, Christopher A.;
Huntemann, Marcel;
Clum, Alicia;
Foster, Brian;
Foster, Bryce;
Roux, Simon;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Copeland, Alex;
Chen, I.-Min A.

Publication type:

Article

Reconstructing each cell's genome within complex microbial communities--dream or reality?

Published in:

Frontiers in Microbiology, 2015, v. 5, p. 1, doi. 10.3389/fmicb.2014.00771

By:

Clingenpeel, Scott;
Clum, Alicia;
Schwientek, Patrick;
Rinke, Christian;
Woyke, Tanja

Publication type:

Article

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Published in:

Nature Biotechnology, 2018, v. 36, n. 7, p. 660, doi. 10.1038/nbt0718-660a

By:

Bowers, Robert M;
Kyrpides, Nikos C;
Stepanauskas, Ramunas;
Harmon-Smith, Miranda;
Doud, Devin;
Reddy, T B K;
Schulz, Frederik;
Jarett, Jessica;
Rivers, Adam R;
Eloe-Fadrosh, Emiley A;
Tringe, Susannah G;
Ivanova, Natalia N;
Copeland, Alex;
Clum, Alicia;
Becraft, Eric D;
Malmstrom, Rex R;
Birren, Bruce;
Podar, Mircea;
Bork, Peer;
Weinstock, George M

Publication type:

Article

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Published in:

Nature Biotechnology, 2018, v. 36, n. 2, p. 196, doi. 10.1038/nbt0218-196a

By:

Bowers, Robert M;
Kyrpides, Nikos C;
Stepanauskas, Ramunas;
Harmon-Smith, Miranda;
Doud, Devin;
Reddy, T B K;
Schulz, Frederik;
Jarett, Jessica;
Rivers, Adam R;
Eloe-Fadrosh, Emiley A;
Tringe, Susannah G;
Ivanova, Natalia N;
Copeland, Alex;
Clum, Alicia;
Becraft, Eric D;
Malmstrom, Rex R;
Birren, Bruce;
Podar, Mircea;
Bork, Peer;
Weinstock, George M

Publication type:

Article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Published in:

Nature Biotechnology, 2017, v. 35, n. 8, p. 725, doi. 10.1038/nbt.3893

By:

Bowers, Robert M;
Kyrpides, Nikos C;
Stepanauskas, Ramunas;
Harmon-Smith, Miranda;
Doud, Devin;
Reddy, T B K;
Schulz, Frederik;
Jarett, Jessica;
Rivers, Adam R;
Eloe-Fadrosh, Emiley A;
Tringe, Susannah G;
Ivanova, Natalia N;
Copeland, Alex;
Clum, Alicia;
Becraft, Eric D;
Malmstrom, Rex R;
Birren, Bruce;
Podar, Mircea;
Bork, Peer;
Weinstock, George M

Publication type:

Article

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.

Published in:

2024

By:

Anthony, Winston E.;
Allison, Steven D.;
Broderick, Caitlin M.;
Chavez Rodriguez, Luciana;
Clum, Alicia;
Cross, Hugh;
Eloe-Fadrosh, Emiley;
Evans, Sarah;
Fairbanks, Dawson;
Gallery, Rachel;
Gontijo, Júlia Brandão;
Jones, Jennifer;
McDermott, Jason;
Pett-Ridge, Jennifer;
Record, Sydne;
Rodrigues, Jorge Luiz Mazza;
Rodriguez-Reillo, William;
Shek, Katherine L.;
Takacs-Vesbach, Tina;
Blanchard, Jeffrey L.

Publication type:

Letter

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-04013-5

By:

Nunn, Brook L.;
Timmins-Schiffman, Emma;
Mudge, Miranda C.;
Plubell, Deanna L.;
Chebli, Gabriella;
Kubanek, Julia;
Riffle, Michael;
Noble, William S.;
Harvey, Elizabeth;
Nunn, Tasman A.;
Huntemann, Marcel;
Clum, Alicia;
Foster, Brian;
Foster, Bryce;
Roux, Simon;
Palaniappan, Krishnaveni;
Mukherjee, Supratim;
Reddy, T. B. K.;
Daum, Chris;
Copeland, Alex

Publication type:

Article

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03826-8

By:

Oliver, Tiffany;
Varghese, Neha;
Roux, Simon;
Schulz, Frederik;
Huntemann, Marcel;
Clum, Alicia;
Foster, Brian;
Foster, Bryce;
Riley, Robert;
LaButti, Kurt;
Egan, Robert;
Hajek, Patrick;
Mukherjee, Supratim;
Ovchinnikova, Galina;
Reddy, T. B. K.;
Calhoun, Sara;
Hayes, Richard D.;
Rohwer, Robin R.;
Zhou, Zhichao;
Daum, Chris

Publication type:

Article

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 3, p. e17, doi. 10.1093/nar/gkab1115

By:

Andreopoulos, William B;
Geller, Alexander M;
Lucke, Miriam;
Balewski, Jan;
Clum, Alicia;
Ivanova, Natalia N;
Levy, Asaf

Publication type:

Article

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.

Published in:

Nature Communications, 2016, v. 7, n. 9, p. 12662, doi. 10.1038/ncomms12662

By:

Peter, Martina;
Kohler, Annegret;
Ohm, Robin A.;
Kuo, Alan;
Krützmann, Jennifer;
Morin, Emmanuelle;
Arend, Matthias;
Barry, Kerrie W.;
Binder, Manfred;
Choi, Cindy;
Clum, Alicia;
Copeland, Alex;
Grisel, Nadine;
Haridas, Sajeet;
Kipfer, Tabea;
LaButti, Kurt;
Lindquist, Erika;
Lipzen, Anna;
Maire, Renaud;
Meier, Barbara

Publication type:

Article

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-18795-w

By:

Miyauchi, Shingo;
Kiss, Enikő;
Kuo, Alan;
Drula, Elodie;
Kohler, Annegret;
Sánchez-García, Marisol;
Morin, Emmanuelle;
Andreopoulos, Bill;
Barry, Kerrie W.;
Bonito, Gregory;
Buée, Marc;
Carver, Akiko;
Chen, Cindy;
Cichocki, Nicolas;
Clum, Alicia;
Culley, David;
Crous, Pedro W.;
Fauchery, Laure;
Girlanda, Mariangela;
Hayes, Richard D.

Publication type:

Article

A comparative genomics study of 23 Aspergillus species from section Flavi.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-14051-y

By:

Kjærbølling, Inge;
Vesth, Tammi;
Frisvad, Jens C.;
Nybo, Jane L.;
Theobald, Sebastian;
Kildgaard, Sara;
Petersen, Thomas Isbrandt;
Kuo, Alan;
Sato, Atsushi;
Lyhne, Ellen K.;
Kogle, Martin E.;
Wiebenga, Ad;
Kun, Roland S.;
Lubbers, Ronnie J. M.;
Mäkelä, Miia R.;
Barry, Kerrie;
Chovatia, Mansi;
Clum, Alicia;
Daum, Chris;
Haridas, Sajeet

Publication type:

Article

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0048837

By:

Mavromatis, Konstantinos;
Land, Miriam L.;
Brettin, Thomas S.;
Quest, Daniel J.;
Copeland, Alex;
Clum, Alicia;
Goodwin, Lynne;
Woyke, Tanja;
Lapidus, Alla;
Klenk, Hans Peter;
Cottingham, Robert W.;
Kyrpides, Nikos C.

Publication type:

Article

Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach.

Published in:

PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0029437

By:

Ze Peng;
Zhiying Zhao;
Nandita Nath;
Froula, Jeff L.;
Alicia Clum;
Tao Zhang;
Jan-fang Cheng;
Copeland, Alex C.;
Pennacchio, Len A.;
Feng Chen

Publication type:

Article

One Bacterial Cell, One Complete Genome.

Published in:

PLoS ONE, 2010, v. 5, n. 4, p. 1, doi. 10.1371/journal.pone.0010314

By:

Woyke, Tanja;
Tighe, Damon;
Mavromatis, Konstantinos;
Clum, Alicia;
Copeland, Alex;
Schackwitz, Wendy;
Lapidus, Alla;
Dongying Wu;
McCutcheon, John P.;
McDonald, Bradon R.;
Moran, Nancy A.;
Bristow, James;
Jan-Fang Cheng

Publication type:

Article

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1288-y

By:

Lam, Ka-Kit;
Hall, Richard;
Clum, Alicia;
Rao, Satish

Publication type:

Article

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems.

Published in:

New Phytologist, 2024, v. 242, n. 4, p. 1676, doi. 10.1111/nph.19471

By:

Auer, Lucas;
Buée, Marc;
Fauchery, Laure;
Lombard, Vincent;
Barry, Kerry W.;
Clum, Alicia;
Copeland, Alex;
Daum, Chris;
Foster, Brian;
LaButti, Kurt;
Singan, Vasanth;
Yoshinaga, Yuko;
Martineau, Christine;
Alfaro, Manuel;
Castillo, Federico J.;
Imbert, J. Bosco;
Ramírez, Lucia;
Castanera, Raúl;
Pisabarro, Antonio G.;
Finlay, Roger

Publication type:

Article

Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk‐cap (Lactarius) mushrooms.

Published in:

New Phytologist, 2022, v. 235, n. 1, p. 306, doi. 10.1111/nph.18143

By:

Lebreton, Annie;
Tang, Nianwu;
Kuo, Alan;
LaButti, Kurt;
Andreopoulos, William;
Drula, Elodie;
Miyauchi, Shingo;
Barry, Kerrie;
Clum, Alicia;
Lipzen, Anna;
Mousain, Daniel;
Ng, Vivian;
Wang, Ran;
Dai, Yucheng;
Henrissat, Bernard;
Grigoriev, Igor V.;
Guerin‐Laguette, Alexis;
Yu, Fuqiang;
Martin, Francis M.

Publication type:

Article

Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.

Published in:

New Phytologist, 2019, v. 222, n. 1, p. 511, doi. 10.1111/nph.15613

By:

Chang, Ying;
Desirò, Alessandro;
Na, Hyunsoo;
Sandor, Laura;
Lipzen, Anna;
Clum, Alicia;
Barry, Kerrie;
Grigoriev, Igor V.;
Martin, Francis M.;
Stajich, Jason E.;
Smith, Matthew E.;
Bonito, Gregory;
Spatafora, Joseph W.

Publication type:

Article

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.

Published in:

New Phytologist, 2018, v. 217, n. 3, p. 1213, doi. 10.1111/nph.14974

By:

Martino, Elena;
Morin, Emmanuelle;
Grelet, Gwen‐Aëlle;
Kuo, Alan;
Kohler, Annegret;
Daghino, Stefania;
Barry, Kerrie W.;
Cichocki, Nicolas;
Clum, Alicia;
Dockter, Rhyan B.;
Hainaut, Matthieu;
Kuo, Rita C.;
LaButti, Kurt;
Lindahl, Björn D.;
Lindquist, Erika A.;
Lipzen, Anna;
Khouja, Hassine‐Radhouane;
Magnuson, Jon;
Murat, Claude;
Ohm, Robin A.

Publication type:

Article

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae.

Published in:

New Phytologist, 2014, v. 202, n. 2, p. 554, doi. 10.1111/nph.12653

By:

Toome, Merje;
Ohm, Robin A.;
Riley, Robert W.;
James, Timothy Y.;
Lazarus, Katherine L.;
Henrissat, Bernard;
Albu, Sebastian;
Boyd, Alexander;
Chow, Julianna;
Clum, Alicia;
Heller, Gregory;
Lipzen, Anna;
Nolan, Matt;
Sandor, Laura;
Zvenigorodsky, Natasha;
Grigoriev, Igor V.;
Spatafora, Joseph W.;
Aime, M. Catherine

Publication type:

Article

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan.

Published in:

Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2021.632731

By:

Thomas, Scott C.;
Payne, Devon;
Tamadonfar, Kevin O.;
Seymour, Cale O.;
Jiao, Jian-Yu;
Murugapiran, Senthil K.;
Lai, Dengxun;
Lau, Rebecca;
Bowen, Benjamin P.;
Silva, Leslie P.;
Louie, Katherine B.;
Huntemann, Marcel;
Clum, Alicia;
Spunde, Alex;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Chen, I-Min;
Stamatis, Dimitrios

Publication type:

Article

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

Published in:

BMC Genomics, 2010, v. 11, p. 680, doi. 10.1186/1471-2164-11-680

By:

McKinlay, James B.;
Laivenieks, Maris;
Schindler, Bryan D.;
McKinlay, Anastasia A.;
Siddaramappa, Shivakumara;
Challacombe, Jean F.;
Lowry, Stephen R.;
Clum, Alicia;
Lapidus, Alla L.;
Burkhart, Kirk B.;
Harkins, Victoria;
Vieille, Claire

Publication type:

Article

Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources.

Published in:

Current Microbiology, 2019, v. 76, n. 5, p. 566, doi. 10.1007/s00284-019-01657-0

By:

Rojas-Rojas, Fernando Uriel;
Sánchez-López, David;
Tapia-García, Erika Yanet;
Arroyo-Herrera, Ivan;
Maymon, Maskit;
Humm, Ethan;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Ivanova, Natalia;
Kyrpides, Nikos;
Woyke, Tanja;
Shapiro, Nicole;
Hirsch, Ann M.;
Ibarra, J. Antonio

Publication type:

Article

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02809-4

By:

Van Goethem, Marc W.;
Osborn, Andrew R.;
Bowen, Benjamin P.;
Andeer, Peter F.;
Swenson, Tami L.;
Clum, Alicia;
Riley, Robert;
He, Guifen;
Koriabine, Maxim;
Sandor, Laura;
Yan, Mi;
Daum, Chris G.;
Yoshinaga, Yuko;
Makhalanyane, Thulani P.;
Garcia-Pichel, Ferran;
Visel, Axel;
Pennacchio, Len A.;
O'Malley, Ronan C.;
Northen, Trent R.

Publication type:

Article