GTax: improving de novo transcriptome assembly by removing foreign RNA contamination von Alvarez, Roberto Vera, Landsman, David

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TPMCalculator: one-step software to quantify mRNA abundance of genomic features von Vera Alvarez, Roberto, Pongor, Lorinc Sandor, Mariño-Ramírez, Leonardo, Landsman, David

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COG database update: focus on microbial diversity, model organisms, and widespread pathogens von Galperin, Michael Y, Wolf, Yuri I, Makarova, Kira S, Vera Alvarez, Roberto, Landsman, David, Koonin, Eugene V

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Database resources of the National Center for Biotechnology Information von Agarwala, Richa, Barrett, Tanya, Beck, Jeff, Benson, Dennis A, Bollin, Colleen, Bolton, Evan, Bourexis, Devon, Brister, J Rodney, Bryant, Stephen H, Canese, Kathi, Cavanaugh, Mark, Charowhas, Chad, Clark, Karen, Dondoshansky, Ilya, Feolo, Michael, Fitzpatrick, Lawrence, Funk, Kathryn, Geer, Lewis Y, Gorelenkov, Viatcheslav, Graeff, Alan, Hlavina, Wratko, Holmes, Brad, Johnson, Mark, Kattman, Brandi, Khotomlianski, Viatcheslav, Kimchi, Avi, Kimelman, Michael, Kimura, Masato, Kitts, Paul, Klimke, William, Kotliarov, Alex, Krasnov, Sergey, Kuznetsov, Anatoliy, Landrum, Melissa J, Landsman, David, Lathrop, Stacy, Lee, Jennifer M, Leubsdorf, Carl, Lu, Zhiyong, Madden, Thomas L, Marchler-Bauer, Aron, Malheiro, Adriana, Meric, Peter, Karsch-Mizrachi, Ilene, Mnev, Anatoly, Murphy, Terence, Orris, Rebecca, Ostell, James, O'Sullivan, Christopher, Palanigobu, Vasuki, Panchenko, Anna R, Phan, Lon, Pierov, Borys, Pruitt, Kim D, Rodarmer, Kurt, Sayers, Eric W, Schneider, Valerie, Schoch, Conrad L, Schuler, Gregory D, Sherry, Stephen T, Siyan, Karanjit, Soboleva, Alexandra, Soussov, Vladimir, Starchenko, Grigory, Tatusova, Tatiana A, Thibaud-Nissen, Francoise, Todorov, Kamen, Trawick, Bart W, Vakatov, Denis, Ward, Minghong, Yaschenko, Eugene, Zasypkin, Aleksandr, Zbicz, Kerry

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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails von Peng, Yunhui, Li, Shuxiang, Onufriev, Alexey, Landsman, David, Panchenko, Anna R.

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DNA methylation cues in nucleosome geometry, stability and unwrapping von Li, Shuxiang, Peng, Yunhui, Landsman, David, Panchenko, Anna R

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Nucleosome adaptability conferred by sequence and structural variations in histone H2A–H2B dimers von Shaytan, Alexey K, Landsman, David, Panchenko, Anna R

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A unified phylogeny-based nomenclature for histone variants von Talbert, Paul B, Ahmad, Kami, Almouzni, Geneviève, Ausió, Juan, Berger, Frederic, Bhalla, Prem L, Bonner, William M, Cande, W Zacheus, Chadwick, Brian P, Chan, Simon W L, Cross, George A M, Cui, Liwang, Dimitrov, Stefan I, Doenecke, Detlef, Eirin-López, José M, Gorovsky, Martin A, Hake, Sandra B, Hamkalo, Barbara A, Holec, Sarah, Jacobsen, Steven E, Kamieniarz, Kinga, Khochbin, Saadi, Ladurner, Andreas G, Landsman, David, Latham, John A, Loppin, Benjamin, Malik, Harmit S, Marzluff, William F, Pehrson, John R, Postberg, Jan, Schneider, Robert, Singh, Mohan B, Smith, M Mitchell, Thompson, Eric, Torres-Padilla, Maria-Elena, Tremethick, David John, Turner, Bryan M, Waterborg, Jakob Harm, Wollmann, Heike, Yelagandula, Ramesh, Zhu, Bing, Henikoff, Steven

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Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006 von Gamez, Rocío M, Rodríguez, Fernando, Vidal, Newton Medeiros, Ramirez, Sandra, Vera Alvarez, Roberto, Landsman, David, Mariño-Ramírez, Leonardo

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Detection of new pioneer transcription factors as cell-type-specific nucleosome binders von Peng, Yunhui, Song, Wei, Teif, Vladimir B, Ovcharenko, Ivan, Landsman, David, Panchenko, Anna R

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Database resources of the National Center for Biotechnology Information von Sayers, Eric W, Barrett, Tanya, Benson, Dennis A, Bolton, Evan, Bryant, Stephen H, Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M, DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Geer, Lewis Y, Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J, Lu, Zhiyong, Madden, Thomas L, Madej, Tom, Maglott, Donna R, Marchler-Bauer, Aron, Miller, Vadim, Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Pruitt, Kim D, Schuler, Gregory D, Sequeira, Edwin, Sherry, Stephen T, Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A, Wagner, Lukas, Wang, Yanli, John Wilbur, W, Yaschenko, Eugene, Ye, Jian

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Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways von Yu, Weishi, McIntosh, Carl, Lister, Ryan, Zhu, Iris, Han, Yixing, Ren, Jianke, Landsman, David, Lee, Eunice, Briones, Victorino, Terashima, Minoru, Leighty, Robert, Ecker, Joseph R, Muegge, Kathrin

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Binding of HMGN proteins to cell specific enhancers stabilizes cell identity von He, Bing, Deng, Tao, Zhu, Iris, Furusawa, Takashi, Zhang, Shaofei, Tang, Wei, Postnikov, Yuri, Ambs, Stefan, Li, Caiyi Cherry, Livak, Ferenc, Landsman, David, Bustin, Michael

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Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes von Zhu, Iris, Landsman, David

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Role of the pre-initiation complex in Mediator recruitment and dynamics von Knoll, Elisabeth R, Zhu, Z Iris, Sarkar, Debasish, Landsman, David, Morse, Randall H

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Cohort profile: St. Michael's Hospital Tuberculosis Database (SMH-TB), a retrospective cohort of electronic health record data and variables extracted using natural language proces... von Landsman, David, Abdelbasit, Ahmed, Wang, Christine, Guerzhoy, Michael, Joshi, Ujash, Mathew, Shaun, Pou-Prom, Chloe, Dai, David, Pequegnat, Victoria, Murray, Joshua, Chokar, Kamalprit, Banning, Michaelia, Mamdani, Muhammad, Mishra, Sharmistha, Batt, Jane

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A standardized nomenclature for mammalian histone genes von Seal, Ruth L, Denny, Paul, Bruford, Elspeth A, Gribkova, Anna K, Landsman, David, Marzluff, William F, McAndrews, Monica, Panchenko, Anna R, Shaytan, Alexey K, Talbert, Paul B

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Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin von He, Bing, Zhu, Iris, Postnikov, Yuri, Furusawa, Takashi, Jenkins, Lisa, Nanduri, Ravikanth, Bustin, Michael, Landsman, David

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BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks von Pongor, Lorinc S, Gross, Jacob M, Vera Alvarez, Roberto, Murai, Junko, Jang, Sang-Min, Zhang, Hongliang, Redon, Christophe, Fu, Haiqing, Huang, Shar-Yin, Thakur, Bhushan, Baris, Adrian, Marino-Ramirez, Leonardo, Landsman, David, Aladjem, Mirit I, Pommier, Yves

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The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction von Garzón-Martínez, Gina A, Zhu, Z Iris, Landsman, David, Barrero, Luz S, Mariño-Ramírez, Leonardo

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