Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns by Tang, Alison D., Soulette, Cameron M., van Baren, Marijke J., Hart, Kevyn, Hrabeta-Robinson, Eva, Wu, Catherine J., Brooks, Angela N.

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation by Pachter, Lior, Trapnell, Cole, Williams, Brian A, Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J, Salzberg, Steven L, Wold, Barbara J

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Marine algae and land plants share conserved phytochrome signaling systems by Duanmu, Deqiang, Bachy, Charles, Sudek, Sebastian, Wong, Chee-Hong, Jiménez, Valeria, Rockwell, Nathan C., Martin, Shelley S., Ngan, Chew Yee, Reistetter, Emily N., van Baren, Marijke J., Price, Dana C., Wei, Chia-Lin, Reyes-Prieto, Adrian, Lagarias, J. Clark, Worden, Alexandra Z.

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The UCSC Genome Browser database: 2025 update by Perez, Gerardo, Barber, Galt P, Benet-Pages, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Christopher M, Nassar, Luis R, Raney, Brian J, Speir, Matthew L, van Baren, Marijke J, Vaske, Charles J, Haussler, David, Kent, W James, Haeussler, Maximilian

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The transcriptional diversity of 25 Drosophila cell lines by Cherbas, Lucy, Willingham, Aarron, Zhang, Dayu, Yang, Li, Zou, Yi, Eads, Brian D, Carlson, Joseph W, Landolin, Jane M, Kapranov, Philipp, Dumais, Jacqueline, Samsonova, Anastasia, Choi, Jeong-Hyeon, Roberts, Johnny, Davis, Carrie A, Tang, Haixu, van Baren, Marijke J, Ghosh, Srinka, Dobin, Alexander, Bell, Kim, Lin, Wei, Langton, Laura, Duff, Michael O, Tenney, Aaron E, Zaleski, Chris, Brent, Michael R, Hoskins, Roger A, Kaufman, Thomas C, Andrews, Justen, Graveley, Brenton R, Perrimon, Norbert, Celniker, Susan E, Gingeras, Thomas R, Cherbas, Peter

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Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress by Cuvelier, Marie L, Guo, Jian, Ortiz, Alejandra C, van Baren, Marijke J, Tariq, Muhammad Akram, Partensky, Frédéric, Worden, Alexandra Z

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Disruption of a Long-Range Cis-Acting Regulator for Shh Causes Preaxial Polydactyly by Lettice, Laura A., Horikoshi, Taizo, Simon J. H. Heaney, van Baren, Marijke J., van der Linde, Herma C., Breedveld, Guido J., Joosse, Marijke, Akarsu, Nurten, Oostra, Ben A., Endo, Naoto, Shibata, Minoru, Suzuki, Mikio, Takahashi, Eiichi, Shinka, Toshikatsu, Nakahori, Yutaka, Ayusawa, Dai, Nakabayashi, Kazuhiko, Scherer, Stephen W., Heutink, Peter, Hill, Robert E., Noji, Sumihare

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Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla by Waltman, Peter H, Guo, Jian, Reistetter, Emily Nahas, Purvine, Samuel, Ansong, Charles K, van Baren, Marijke J, Wong, Chee-Hong, Wei, Chia-Lin, Smith, Richard D, Callister, Stephen J, Stuart, Joshua M, Worden, Alexandra Z

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Estimating the Nucleotide Diversity in Ceratodon purpureus (Ditrichaceae) from 218 Conserved Exon-Primed, Intron-Spanning Nuclear Loci by McDaniel, Stuart F, Baren, Marijke J. van, Jones, Kelly S, Payton, Adam C, Quatrano, Ralph S

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Iterative gene prediction and pseudogene removal improves genome annotation by van Baren, Marijke J, Brent, Michael R

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The developmental transcriptome of Drosophila melanogaster by Graveley, Brenton R, Celniker, Susan E, Brooks, Angela N, Carlson, Joseph W, Duff, Michael O, Landolin, Jane M, Yang, Li, Artieri, Carlo G, van Baren, Marijke J, Boley, Nathan, Booth, Benjamin W, Brown, James B, Cherbas, Lucy, Davis, Carrie A, Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H, Mattiuzzo, Nicolas R, Miller, David, Sturgill, David, Tuch, Brian B, Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E, Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E, Wan, Kenneth H, Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J, Brenner, Steven E, Brent, Michael R, Cherbas, Peter, Gingeras, Thomas R, Hoskins, Roger A, Kaufman, Thomas C, Oliver, Brian

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Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations by Simmons, Melinda P, Bachy, Charles, Sudek, Sebastian, van Baren, Marijke J, Sudek, Lisa, Ares, Jr, Manuel, Worden, Alexandra Z

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Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants by van Baren, Marijke J, Bachy, Charles, Reistetter, Emily Nahas, Purvine, Samuel O, Grimwood, Jane, Sudek, Sebastian, Yu, Hang, Poirier, Camille, Deerinck, Thomas J, Kuo, Alan, Grigoriev, Igor V, Wong, Chee-Hong, Smith, Richard D, Callister, Stephen J, Wei, Chia-Lin, Schmutz, Jeremy, Worden, Alexandra Z

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Mutations in the DJ-1 Gene Associated with Autosomal Recessive Early-Onset Parkinsonism by Bonifati, Vincenzo, Rizzu, Patrizia, van Baren, Marijke J., Schaap, Onno, Breedveld, Guido J., Krieger, Elmar, Marieke C. J. Dekker, Squitieri, Ferdinando, Ibanez, Pablo, Joosse, Marijke, van Dongen, Jeroen W., Vanacore, Nicola, van Swieten, John C., Brice, Alexis, Meco, Giuseppe, van Duijn, Cornelia M., Oostra, Ben A., Heutink, Peter

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The PCR Suite by van Baren, Marijke J., Heutink, Peter

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A Double RING-H2 Domain in RNF32, a Gene Expressed during Sperm Formation by van Baren, Marijke J., van der Linde, Herma C., Breedveld, Guido J., Baarends, Willy M., Rizzu, Patrizia, de Graaff, Esther, Oostra, Ben A., Heutink, Peter

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The completion of the Mammalian Gene Collection (MGC) by Temple, Gary, Gerhard, Daniela S, Rasooly, Rebekah, Feingold, Elise A, Good, Peter J, Robinson, Cristen, Mandich, Allison, Derge, Jeffrey G, Lewis, Jeanne, Shoaf, Debonny, Collins, Francis S, Jang, Wonhee, Wagner, Lukas, Shenmen, Carolyn M, Misquitta, Leonie, Schaefer, Carl F, Buetow, Kenneth H, Bonner, Tom I, Yankie, Linda, Ward, Ming, Phan, Lon, Astashyn, Alex, Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maidak, Bonnie L, Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Riddick, Lillian, Webb, David, Weber, Janet, Wu, Wendy, Pruitt, Kim D, Maglott, Donna, Siepel, Adam, Brejova, Brona, Diekhans, Mark, Harte, Rachel, Baertsch, Robert, Kent, Jim, Haussler, David, Brent, Michael, Langton, Laura, Comstock, Charles L G, Stevens, Michael, Wei, Chaochun, van Baren, Marijke J, Salehi-Ashtiani, Kourosh, Murray, Ryan R, Ghamsari, Lila, Mello, Elizabeth, Lin, Chenwei, Pennacchio, Christa, Schreiber, Kirsten, Shapiro, Nicole, Marsh, Amber, Pardes, Elizabeth, Moore, Troy, Lebeau, Anita, Muratet, Mike, Simmons, Blake, Kloske, David, Sieja, Stephanie, Hudson, James, Sethupathy, Praveen, Brownstein, Michael, Bhat, Narayan, Lazar, Joseph, Jacob, Howard, Gruber, Chris E, Smith, Mark R, McPherson, John, Garcia, Angela M, Gunaratne, Preethi H, Wu, Jiaqian, Muzny, Donna, Gibbs, Richard A, Young, Alice C, Bouffard, Gerard G, Blakesley, Robert W, Mullikin, Jim, Green, Eric D, Dickson, Mark C, Rodriguez, Alex C, Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M, Hirst, Martin, Zeng, Thomas, Tse, Kane, Moksa, Michelle, Deng, Merinda, Ma, Kevin, Mah, Diana, Pang, Johnson, Taylor, Greg, Chuah, Eric, Deng, Athena

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Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants by van Baren, Marijke J., Bachy, Charles, Reistetter, Emily Nahas, Purvine, Samuel O., Grimwood, Jane, Sudek, Sebastian, Yu, Hang, Poirier, Camille, Deerinck, Thomas J., Kuo, Alan, Grigoriev, Igor V., Wong, Chee-Hong, Smith, Richard D., Callister, Stephen J., Wei, Chia-Lin, Schmutz, Jeremy, Worden, Alexandra Z.

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Hemimelic extra toes and Hammer toe are distinct mutations that show a genetic interaction by Heus, H C, Luijsterburg, A J, van Baren, M J, Breedveld, G J, Joosse, M N, Nieuwenhuizen, I M, Vermeij-Keers, C, Oostra, B A, Heutink, P

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Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms by Trapnell, Cole, Williams, Brian A., Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J., Salzberg, Steven L., Wold, Barbara J., Pachter, Lior

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