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Christian Louboutin Appoints Jaden Smith as Men’s Creative Director

“I found him very interesting, very kind, and very, very humble, and above all, very interesting: The way he is, the way he dresses, the way he thinks.”

That’s Christian Louboutin talking about Jaden Smith, whom he tapped to become his first men’s creative director — roughly 15 years after he first extended his red-soled universe into men’s.

The American rapper and actor is moving to Paris to take up the role and is to present his first designs in January during men’s fashion week in the French capital. He is to oversee the creation of four collections a year across shoes, leather goods and accessories, along with developing campaigns, events and immersive experiences.

“This is the one of the biggest honors of my life, and I feel a lot of pressure to be able to live up to everything that Christian has done for the house, and also stepping into such a serious role,” Smith told WWD over Teams from Los Angeles. “When he reached out to me, I was just blown away, because of how similar we are and how much we like to do things in a similar manner.

“I can’t wait to show the world what we’ve been working on,” he added. “I think that the universe of Christian Louboutin men’s has so much potential.”

In a separate interview at his new Paris offices a stone’s throw from the Louvre, Louboutin said the appointment will allow him to focus more on his fast-growing women’s business — and leverage the creative and communication prowess of Smith to rev up the men’s category, which accounts for 24 percent of the business, but has recently been logging single-digit declines.

What might seem like a sudden handover has actually been percolating inside Louboutin’s head for several years.

On one side, Louboutin realized he was becoming overstretched given his hands-on approach to design, prototype development and manufacturing, spending many days each month tinkering at his Italian factories. On the other loomed Smith, whom he met in 2019, realizing with each subsequent encounter how much the American creative reminded him of his younger self — not to mention their shared love of color, fun and joyful self-expression.

“Dressing for him is an adventure,” he said of Smith. “It’s a form of communication. It’s thoughtful, but it’s playful. There are very few people that I find as surprising, the way he puts things together.”

In fact, Louboutin said he did not launch any formal search for a men’s creative director, settling on Smith as the organic result of his ruminations.

“He arrived before the idea of a creative director,” the shoe guru related. “It’s not because I needed the creative director, it’s because of him, in fact. And so it happened like that.

“The day I said to myself, ‘He’d be a great person to work with’ was the day I realized I had been studying him without realizing it. I saw him interacting with people.…He’s very well-mannered, super respectful and curious. And those, for me, are values or qualities that are important.”

Smith, 27, said he and Louboutin, 62, share a passion for ancient architecture, a deep affinity for music, and a love of dancing.

(In fact, among Louboutin’s first steps into men’s was creating shoes for Mika so the Lebanese pop star could comfortably dance while performing.)

As for fashion, “we both have our own unique style of dressing that is very particular to us,” Smith said, also describing similar creative methods. “We have a very similar workflow where we go into the office, and then maybe, if there’s a dinner party or something, we go there, and we continue the same conversation that we were having in the office with the same people, and we are just constantly in this bubble of creativity.”

Jaden Smith

Courtesy of Christian Louboutin

During the interview, Smith discussed his passion for footwear, reflected in his large archive of shoes that he doesn’t actually wear, but keeps for reference.

“Just so that I can look at the materials, different lasts, different cuts, different internal shaping, different foot beds, different insoles, laces, shoe boxes,” he said. “Shoes are definitely a passion of mine.”

Cofounder of MSFTSrep — a streetwear label he launched with sister Willow Smith and friends in 2012 — Smith has also frequently collaborated with New Balance and acted as its ambassador.

He disclosed plans to launch a new version of the brand called MSFTSRep Infinity — hinged on retrospective elements, “art and movement” — that will allow him to devote himself to the Louboutin project.

Asked if he picks the shoes first or last when he gets dressed, Smith replied: “First I go with the emotion of how I’m feeling on that day.…Once I gauge whether it’s an all-black day or a colorful day, I start trying on the shoes.

“If I have new shoes, then I’ll put them on first. If I don’t, then I’ll just go based on how I’m feeling in a top-down kind of way.”

Smith said Louboutins came onto his radar when he was extremely young thanks to famous and stylish parents: actors Jada Pinkett Smith and Will Smith.

“I would be in my mom’s closet, hanging out with her as she got ready for an event and she had a row of shoes with red bottoms. I became bewildered by the shoes at a very young age,” he related. “And then I realized that my dad also had shoes with red bottoms. And then my sister got older and started wearing them. And the first girlfriend that I ever had was like, ‘I need you to buy me some red bottoms.’ So it was something that was a part of my life forever since I was extremely, extremely young. And then I got my first pair around the time I started doing premieres for the first time.”

Louboutin said he would continue to oversee the men’s category, while letting Smith take the lead on design, image making and social media. “Because of his generation…there is a kind of mentality that is very different.”

And a different reach: Smith counts 19.1 million followers on Instagram.

“When I design shoes, I don’t think about a campaign at all,” Louboutin related. “I think about the colors, the materials, but I don’t think about the narrative.…(Jaden) is going to show the brand’s vision in a much more visible way.”

The designer also lauded Smith’s “richer universe that goes beyond the fashion perimeter” given that his creative tentacles stretch into music, photography, film and activism.

“He’s someone who’s very curious, who’s very panoramic, who does a lot of things, who’s interested and who connects all the things he does,” Louboutin said. “One of the first questions he had was about our sustainability efforts, because it’s important to him. And that is very, very, very good because we have started to do a lot of important work around sustainability.”

But mostly Louboutin marveled at their similarities. “He has the same enthusiasm that I have,” he said, also describing a similar appreciation for objects and an incredible attention to detail, likely sharpened over years of collaboration with New Balance, and his other creative pursuits. “We have very different backgrounds, but we have a very similar mentality.

“He has a way of seeing things, of digesting things, of transforming that really connects with my way of functioning.”

The star of “The Pursuit of Happyness” and “The Karate Kid” — and the singer of such songs as “Icon” and “Still in Love” — Smith said fashion has long been an attraction.

“I feel like fashion is just one of the most artistically expressive communities of people in the world, and that’s what brought me to fashion, because of my wanting to feel accepted in an artistic way and to be able to express myself creatively without feeling judged by everybody else in the community,” he said.

Smith arrives amid healthy business for the privately held company, with double-digit growth at present fueled largely by innovation in women’s footwear, including its “everlasting sole,” more low-heel options, substantial comfort enhancements, and price increases limited to cost of goods, according to Alexis Mourot, chief executive officer of Louboutin.

Emblematic of its momentum is its bestselling Miss Z pump, which features an expanded toe box and a padded insole.

“In women’s shoes, we are gaining market share,” Mourot said in an interview, noting that 70 percent of its business today is with heels below 10 centimeters, whereas two years ago it was above 10 centimeters.

The executive attributed softness in its men’s shoes to market conditions, but said Smith’s arrival should ignite the business.

“I think we can double the (men’s) business in the next couple of years,” said Mourot, citing opportunities in retail and wholesale channels. At present, men’s products are sold in about 125 points of sale globally.

Today, Louboutin operates dedicated men’s stores in Paris and New York “and we look to have more in the future,” Mourot said.

Sneakers represent about half of Louboutin’s men’s offering, and the other half is made with leather soles. The Louis and Chambeliss lines are among bestsellers, the executive noted.

An “avant-premiere capsule” by Smith will be available in January at select boutiques worldwide and on Christianlouboutin.com, with his debut fall 2026 collection will hit stores next May.

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September 17, 2025
Countries that’ll boycott if Israel competes – DW – 09/17/2025

Following announcements from Ireland, Slovenia, the Netherlands and Iceland, Spain became on Wednesday the first country among the “Big Five,” the five largest contributors to the Eurovision Song Contest, to officially declare its decision to boycott the 2026 event to be held in Vienna from May 12-16, if Israel’s participation goes ahead as planned.

The country’s withdrawal was approved by a majority of the board of directors of Spanish state broadcaster RTVE, with 10 votes in favour, four against, and one abstention. The vote came after Spanish Minister for Culture, Ernest Urtasun, stated last week that Spain should withdraw from the event if Israel remained on the list of participating countries.

Dutch public broadcaster, AVROTROS, also stated that it could “no longer justify Israel’s participation in the current situation, given the ongoing and severe human suffering in Gaza.”

A decision on Israel’s participation is expected in December.

JJ from Austria won the contest in 2025, which is why the next event will be held in ViennaImage: Baden Roth/IMAGO/ZUMA Press Wire

Why is Israel in the Eurovision Song Contest?

Israel made its debut at Eurovision in 1973, when it was still called the “Grand Prix d’Eurovision de la Chanson.” That was when the country became a member of the European Broadcasting Union (EBU), an association including 73 active members of broadcasters from 56 countries and 35 associate members from 21 countries in Europe, North Africa and the Middle East.

Israel is not the only non-European participant in the contest. There’s also Armenia and Azerbaijan — and since 2015, Australia has become the “most exotic” Eurovision competitor. The show has a huge fan base there, and Australia was accepted into the EBU as an associate member.

The inclusion of broadcasters and countries beyond the borders of Europe is also the reason why the event is called the “Eurovision Song Contest” and not the “European Song Contest.”

With four first places, Israel is one of the most successful participants. But the Middle East conflict has impacted the contest several times over the past five decades.

Israeli Netta Barzilai won the 2018 Eurovision Song Contest, bringing the event to Tel Aviv a year laterImage: Vyacheslav Prokofyev/TASS/dpa/picture alliance

Security for Israeli contestants

In 1973, Ilanit was the first artist to compete for Israel. Strict security measures were implemented because, only a few months earlier, Palestinian terrorists had killed 11 Israeli athletes in the Olympic Village in Munich. Ilanit was supposedly wearing a bulletproof vest, the audience had to remain seated throughout her performance and photographers had to take a picture pointing at the ceiling to prove that their cameras were not disguised firearms.

In 2024, Israeli contestant Eden Golan also performed under special protection. Several participating countries had called on the EBU to exclude Israel from the contest. The EBU considered it, but not because of the Gaza war itself. EBU officials feared the original title of Israel’s entry, “October Rain,” was too explicit a reference to the event that triggered the Gaza war: the Hamas terrorist attack on Israel on October 7, 2023, in which around 1,200 Israelis were killed and 240 were taken hostage in Gaza. Once the lyrics of the song were changed, Golan’s participation was allowed to go ahead.

There were already calls for Israel’s withdrawal in 2024, the year Eden Golan (center) represented the countryImage: Jessica Gow/TT News Agency/AP/picture alliance

Fines for pro-Palestinian protests

The repeated use of protest symbols and slogans by the audience or by artists has not gone unpunished. This became particularly clear in Tel Aviv in 2019.

On the evening of the Eurovision final, the Icelandic band Hatari held up scarves with Palestinian flags to the camera, causing controversy. The EBU fined the Icelandic broadcaster RUV €5,000.

During a performance by global superstar Madonna that same evening a male dancer and a female dancer — one carrying the Israeli flag and the other carrying the Palestinian flag — walked up the stairs arm in arm. The US singer later said that this was a “message of peace and unity.” But the EBU was less enthusiastic about it. Though there was no fine in this case, the contest organizers released a statement saying the act was not cleared with them and that Madonna was aware the contest was non-political.

The competitions in Malmö in 2024 and Basel in 2025 were tainted by protests critical of Israel. In the hall, audience members whistled and booed the Israeli performers.

This article was originally written in German.

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September 17, 2025
Criminal damage or critical commentary? Legal reflections on Banksy’s short-lived judge mural – The Art Newspaper

Two big art law stories have made global headlines over the past month and it would be remiss not to cover at least one of them in this column. So let’s begin with the Banksy that arrived overnight on the wall of the Royal Courts of Justice in London on 8 September and was then “removed” two days later.

Like ice sculptures and castles of sand, this Banksy has become an evanescent artwork. And aside from its legal subject matter—a bewigged judge beating down a protestor—what are the legalities of the whole affair?

The first point relates to the illegality of affixing paint on the wall of a building without the owner’s consent, which in most cases constitutes the offence of criminal damage, subject to a maximum penalty in England of ten years behind bars. Because this wasn’t just any old building but a Grade I listed building, the sentencing guidelines would instruct a judge to impose on a convicted offender a longer sentence within this range. Some reporting has said that if the “real Banksy” is found and prosecuted his cherished mask of anonymity would surely fall. Food for thought.

The second legal point relates to the intellectual property (IP) in the image. With copyright, the “author” of a work of visual art benefits from a right to stop others from making unauthorised reproductions. Does Banksy benefit from this right, even though the image might have been created illegally? In principle, yes—provided the work, for the purposes of copyright law, is considered sufficiently “original”. I doubt anyone would question the originality of a Banksy!

However, even if there is copyright in the image, a court might not enforce it on the basis that to do so could be seen as contrary to the public interest (meaning, it might encourage others to break the law by creating more works in this way). But there is no guarantee.

Also, if anyone wants to reproduce images of the work, then the fair dealing exceptions in UK copyright law might protect such activities, provided they’re for purposes such as news reporting or critical commentary. So even if copyright does subsist in a work of street art like this, there appear to be significant workarounds.

It’s likely a moot point: Banksy has stated in print that “copyright is for losers”. That said, anyone who assumes his works are completely free of IP enforcement should think again. His company Pest Control registers his commercial works for Artist’s Resale Right royalties and has also been in a bitter dispute around registered EU trademarks for the past few years.

There is another, more theoretical point about moral rights in a Banksy. Moral rights exist for copyright-protected works, allowing creators to stop any mistreatment of the work that might negatively affect their honour or reputation. Could it be said that painting over his work would harm his honour or reputation? Probably not. On the contrary, the covering up seems to contribute to his aura as a man of mystery who likes to play fast and loose with the law.

The other recent art law story was the discovery of “Contessa Colleoni” in an online sales catalogue of a house, a work that had been looted from a Jewish dealer in Nazi-occupied Amsterdam in 1940. I have run out of words, so you will have to wait until a later issue to read more about this. Besides, the story is developing, with the local police now involved.

So with a disappearing Banksy and a reappearing Contessa, the world of art law has not been short of thought-provoking material.

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September 17, 2025
Vivo V60e 5G mobile expected price in India, leaked images and specifications

Published on: Sept 17, 2025 03:24 pm IST

Vivo V60e could be the next V-series phone in India, positioned below the Vivo V60.

It has only been about a month since Vivo launched the Vivo V60 in the Indian market, and now there are already rumours about the Vivo V60e launching in India. The phone will likely sit below the Vivo V60, come in gold and purple colourways, and offer the MediaTek Dimensity 7300 chipset. This has been spotted by 91mobiles Hindi, which has posted alleged images of the Vivo V60e alongside several details.

Vivo V60e could look a lot like the Vivo T4 Pro.(Vivo)

What we know about the Vivo V60e

91mobiles reports that the phone could feature the MediaTek Dimensity 7300 chipset, with pricing expected to be around ₹28,999 for the base model with 128 GB storage and 8 GB RAM, ₹30,999 for the 256 GB model, and around ₹31,999 for the top-end model with 12 GB RAM and 256 GB storage. Notably, from the images shared by 91mobiles, the phone seems to be missing the Zeiss branding, which has been a highlight of the Vivo V60 so far. Nonetheless, the phone could feature a dual-camera setup, as seen in the images.

The design could be very reminiscent of the Vivo V60, including the ring flash, and it could be offered in two colours: Noble Gold and Elite Purple, and may support IP68 and IP69 dust and water resistance, alongside diamond shield glass protection. For the battery, the device may come with a 6,500 mAh battery, with support for 90W fast charging just like the Vivo V60.

The release date is currently unclear, but it is worth noting that the previous model, the Vivo V50, only launched in April earlier this year, so it has not been very long.

MOBILE FINDER: iPhone 17 LATEST Details

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September 17, 2025
FIH Pro League 2025-26 schedule for Indian hockey team

The Indian men’s hockey team will start its FIH Hockey Pro League 2025-26 campaign at home on February 11 against former Olympic champions Belgium.

The seventh edition of the FIH Pro League, however, begins simultaneously in Ireland and Argentina from December 9, 2025. A total of 144 matches will be staged across 10 countries over seven months.

India, bronze medallists at the Paris 2024 Olympics, will play Argentina and Belgium in its home leg which runs from February 10 to 15.

Harmanpreet Singh’s India, who narrowly avoided relegation last season after finishing eighth, will then travel to Australia before wrapping up the season in Europe with matches scheduled in the Netherlands and UK.

The highly anticipated India vs Pakistan hockey clashes are slated for June 23 and 26, respectively, in London.

Pakistan are making their Pro League debut after New Zealand, the 2024-25 Nations Cup winners, declined their spot. As runners-up, Pakistan accepted the invitation to compete in their place.

The 2025-26 FIH Pro League season also doubles up as a qualification pathway for the LA 2028 Olympics, with the winners of the men’s and women’s competitions earning direct berths to the upcoming Summer Games.

The Indian women, meanwhile, will miss this edition after being relegated to the FIH Nations Cup following their last-place finish in the 2024-25 hockey league.

Since its launch in 2019, the Pro League has been dominated by the Netherlands. The Dutch women have lifted five of the six titles, while the men have won three, with both sides reigning champions coming into this season.

FIH Pro League 2025-26 schedule for Indian hockey team

All in Indian Standard Time (IST)

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September 17, 2025
Millions could benefit from faster biparametric MRI scan for prostate cancer

Original story from UCL

A quicker, cheaper biparametric MRI scan is just as accurate at diagnosing prostate cancer as the current 30–40 minute scan and should be rolled out to make MRI scans more accessible, according to a new clinical trial.

The PRIME trial, funded by the John Black Charitable Foundation and Prostate Cancer UK, and published in JAMA, confirms that a two-part MRI scan is just as effective at diagnosing prostate cancer, whilst cutting scan time to just 15-20 minutes and reducing the need for a doctor to be present.

The investigators, from UCL, UCLH and the University of Birmingham say the results are likely to lead to changes in clinical practice, making MRI accessible to more men in the UK and beyond.

Prostate cancer is the most common cancer in men, with around 56,000 diagnoses and 12,000 deaths each year in the UK. The introduction of MRI scans over the last decade, following work by UCL researchers, has been the biggest change in how prostate cancer is diagnosed for the past 30 years.

Abnormalities seen on the MRI scan allow targeted tissue biopsies to be taken that can improve cancer detection. A normal MRI result, which occurs in around a third of patients, is reassuring and allows men to avoid an unnecessary biopsy.

Despite the clear benefits of the MRI scan, in many healthcare settings around the world, men who need a scan still do not get one. For example, previous research has estimated that 35% of US prostate cancer patients received an MRI in 2022. In England and Wales, only 62% of men who needed a prostate MRI received one in 2019 (the most recent year for when data is available, which can be viewed here).

Veeru Kasivisvanathan, lead researcher and Chief Investigator on the trial from UCL Surgery & Interventional Science and UCLH, said: “Currently around four million MRI scans are needed each year globally to diagnose prostate cancer. This demand is set to rise rapidly with a predicted surge in prostate cancer cases over the next 20 years.”

“Time, cost and staff availability are all limiting factors in how many scans can be offered, which makes the results of the PRIME trial particularly important. If we can do the scan in up to half the time, with fewer staff and at lower cost, that will make a huge difference in allowing every man who needs a scan to be able to get one in a timely fashion.”

In the study, cancer specialists from 22 hospitals in 12 countries across the world recruited 555 patients aged 59–70 to see whether a streamlined two-part ‘biparametric’ MRI could detect cancer at the same rate as a full three-part ‘multiparametric’ MRI, which is currently standard of care in the UK and includes a third stage where a dye is injected into the patient.

All patients underwent the full three-part scan. Radiologists then assessed the two-part scan without the dye, and separately assessed the three-part scan with the dye, for every patient. A prostate biopsy was done when required to confirm whether or not the diagnosis was correct.

Researchers from UCL and UCLH confirmed that the two-part scan was just as effective at diagnosing prostate cancer. In total, 29% of the patients had important prostate cancer diagnosed by the shorter two-part scan, the same percentage as the longer three-part scan.

Francesco Giganti, a lead radiologist on the trial from UCL Surgery & Interventional Science and UCLH, said: “The three-part multiparametric MRI scan has been a game-changer for the diagnosis of prostate cancer, sparing thousands of patients unnecessary biopsies and improving cancer detection.”

“Currently we inject a dye into the patient that highlights the presence of cancer on the MRI scan, but this step requires time and the presence of a clinician, and can on rare occasion cause mild side effects.”

“Being able to make accurate diagnoses without the contrast stage will reduce scan time meaning we can offer scans to more men using the same number of scanners and operators. However, it is vital that the scans are of optimal diagnostic quality and that they are interpreted by a radiologist with dedicated expertise in prostate MRI.”

As well as making the procedure more efficient in terms of time and personnel, a two-stage MRI would generate significant cost savings per scan. In the NHS currently, a three-phase MRI scan costs £273 on average. At £145, a two-phase scan is 47% cheaper. In countries like the US where healthcare costs tend to be much higher, the savings are likely to be even greater.

Prostate Cancer UK’s TRANSFORM trial, the biggest prostate cancer screening trial for 20 years that will include MRI, is due to begin later this year. It will be jointly led by UCL researchers alongside collaborators from Imperial College London, The Institute of Cancer Research and Queen Mary University of London. The trial will find the best way to screen men for prostate cancer, achieving the evidence needed for the introduction of a national screening program. The results of the PRIME trial are an important step towards realizing this ambition.

‘Dual-mode’ tracer enables visual and audio guidance in prostate procedures

A fluorine-18–based tracer could offer surgeons high resolution PET imagesto identify ‘hidden’ cancer.

Matthew Hobbs, Director of Research at Prostate Cancer UK, said: “The results from the PRIME trial, showing that a faster, cheaper, type of prostate MRI is just as good as the current standard MRI at detecting prostate cancer, are a hugely important step in the right direction for making MRIs more efficient.”

“Another trial is already happening in the UK and the results of the two trials together should provide the complete evidence package we need to change practice across the country. We encourage NICE to prepare to review their guidelines as soon as that evidence base is complete, so that we can make MRI quicker, cheaper and less onerous for men.”

“Our funding for PRIME, alongside the John Black Charitable Foundation, also provided recommendations of a few simple ways for hospitals to improve scan quality. So, while we await a review by NICE, hospitals should use guidelines from UCL’s GLIMPSE trial, so that they are ready for the implementation of biparametric MRI if it’s recommended, and so that the men having MRI scans right now get the most accurate scan possible.”

The PRIME study also received funding from the European Association of Urology Research Foundation and the Wolfgang Dieckmann Foundation.

Aqua Asif, co-first author of the study from UCL Surgery & Interventional Science, said: “These findings show that we can deliver faster, more accessible prostate MRI scans without compromising accuracy. That has the potential to transform care, allowing more men to get the scans they need, when they need them, and ultimately improving outcomes worldwide. It has been a privilege to contribute to PRIME at this stage of my career, and I am incredibly proud of what has been achieved through the dedication of our collaborators across so many centers. This trial would not have been possible without the support of our funders, our patients, and the commitment of the entire team.”

Alexander Ng, co-first author of the study from UCL Surgery & Interventional Science, said: “Since we introduced MRI into the prostate cancer pathway, it has been our missions to ensure that every man who requires an MRI can get one. PRIME is a major leap in this direction, allowing men to receive a shorter, cheaper and less invasive scan that is just as good as a longer, more expensive scan that requires an intravenous cannula with an injection. We continue to strive to improve the global equity in access to an accurate and timely prostate cancer diagnosis, to improve the prostate cancer paradigm for patients all around the world.”

This article has been republished from the following materials. Material may have been edited for length and house style. For further information, please contact the cited source. Our press release publishing policy can be accessed here.

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September 17, 2025
How The Morning Show became TV’s most chaotic drama

Apple TV+
The show is headlined by Reese Witherspoon and Jennifer Aniston, both of whose characters have experienced major plot twists and turns (Credit: Apple TV+)

“I like it because it’s pacy and there is always a lot going on,” she adds. “It’s definitely a ‘no-scroll’ show. And this probably makes me a terrible person, but it just looks so nice. Everyone is beautiful and slick and smart and dressed like your dreams, and sometimes that’s exactly what you want in your one hour of free time between getting the kids to bed and passing out.”

Despite the show’s grounding in current affairs, this escapism is definitely key to the series’ appeal. Fans often talk about the Architectural Digest-type joy of seeing Alex’s penthouse (“Just excited for season 2 of The Morning Show to see Alex Levy’s New York apartment AGAIN,” one viewer said on X), while others are drawn to it for its absurdity. “This show is stupid and insane and laughable and I will watch every episode they give me,” one person commented on Reddit.

Fans won’t be disappointed by season four, which continues with the show’s own chaotic brand of entertainment, and boasts even more star faces: Marion Cotillard, Jeremy Irons, William Jackson Harper and Aaron Pierre have all joined, following in the footsteps of Jon Hamm and Greta Lee, who arrived in series three and two, respectively. Following last season’s merger between the UBA and NBN networks, there are more unhinged power grabs for the business, a plane crash unfolding live on air, unbelievable romantic liaisons, and a fantastical story involving false imprisonment, a Russian oligarch and a night at the opera, just to give a taste of some of the many plotlines it lurches between. One surreal episode even opens with presenter Yanko (Néstor Carbonell) doing a song-and-dance number, surrounded by doves, to Rick Astley’s Never Gonna Give You Up.

At points, its melodramatic ludicrousness can jar with its mentions of real-life news events such as the Ukraine war, or the repealing of Roe v Wade. However, Kevin Taft, a US entertainment journalist and previous co-host of The Morning Show After Show podcast, believes it can be both timely and over-the-top all at once: “I actually like that they put in real-life events, because it really is more interesting to see how they work in what’s truly happening, whether it’s an election cycle or the [Covid-19] pandemic. Lots of shows and movies during the pandemic just ignored that it was happening and I’m thinking, ‘This isn’t just a small blip in daily life. This is a moment in history and has changed how we all live.’ When a show or movie ignores it, that just seems false to me.”

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September 17, 2025
A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution
Preissl, S., Gaulton, K. J. & Ren, B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat. Rev. Genet. 24, 21–43 (2023).

Article
CAS
PubMed

Google Scholar
Wittkopp, P. J. & Kalay, G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13, 59–69 (2012).

Article
CAS

Google Scholar
Marand, A. P., Eveland, A. L., Kaufmann, K. & Springer, N. M. cis-Regulatory elements in plant development, adaptation, and evolution. Annu. Rev. Plant Biol. 74, 111–137 (2023).

Article
CAS
PubMed
PubMed Central

Google Scholar
Oka, R. et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18, 1–24 (2017).

Article

Google Scholar
Maher, K. A. et al. Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell 30, 15–36 (2018).

Article
CAS
PubMed

Google Scholar
Lu, Z. et al. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nat. Plants 5, 1250–1259 (2019).

Article
CAS
PubMed

Google Scholar
Reynoso, M. A. et al. Evolutionary flexibility in flooding response circuitry in angiosperms. Science 365, 1291–1295 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Kajala, K. et al. Innovation, conservation, and repurposing of gene function in root cell type development. Cell 184, 3333–3348. e3319 (2021).

Article
CAS
PubMed

Google Scholar
Ricci, W. A. et al. Widespread long-range cis-regulatory elements in the maize genome. Nat. Plants 5, 1237–1249 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Cusanovich, D. A. et al. A single-cell atlas of in vivo mammalian chromatin accessibility. Cell 174, 1309–1324. e1318 (2018).

Article
CAS
PubMed
PubMed Central

Google Scholar
Domcke, S. et al. A human cell atlas of fetal chromatin accessibility. Science 370, eaba7612 (2020).

Article
CAS
PubMed
PubMed Central

Google Scholar
Lu, Z. et al. Tracking cell-type-specific temporal dynamics in human and mouse brains. Cell 186, 4345–4364. e4324 (2023).

Article
CAS
PubMed
PubMed Central

Google Scholar
Javelle, M., Vernoud, V., Rogowsky, P. M. & Ingram, G. C. Epidermis: the formation and functions of a fundamental plant tissue. New Phytol. 189, 17–39 (2011).

Article
CAS
PubMed

Google Scholar
Kadioglu, A., Terzi, R., Saruhan, N. & Saglam, A. Current advances in the investigation of leaf rolling caused by biotic and abiotic stress factors. Plant Sci. 182, 42–48 (2012).

Article
CAS
PubMed

Google Scholar
Xu, Y. et al. Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. Planta 239, 803–816 (2014).

Article
CAS
PubMed

Google Scholar
Dorrity, M. W. et al. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nat. Commun. 12, 3334 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Farmer, A., Thibivilliers, S., Ryu, K. H., Schiefelbein, J. & Libault, M. Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. Mol. Plant 14, 372–383 (2021).

Article
CAS
PubMed

Google Scholar
Tu, X., Marand, A. P., Schmitz, R. J. & Zhong, S. A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells. Plant Commun. 3, 100308 (2022).

Article
CAS
PubMed
PubMed Central

Google Scholar
Nobori, T. et al. A rare PRIMER cell state in plant immunity. Nature 638, 197–205 (2025).

Article
CAS
PubMed
PubMed Central

Google Scholar
Marand, A. P., Chen, Z., Gallavotti, A. & Schmitz, R. J. A cis-regulatory atlas in maize at single-cell resolution. Cell 184, 3041–3055. e3021 (2021).

Article
CAS
PubMed

Google Scholar
Feng, D. et al. Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips. BMC Biol. 20, 274 (2022).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhang, L. et al. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol. 24, 65 (2023).

Article
CAS
PubMed
PubMed Central

Google Scholar
Swift, J. Exaptation of ancestral cell-identity networks enables C₄ photosynthesis. Nature 636, 143–150 (2024).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhang, X. et al. A spatially resolved multi-omic single-cell atlas of soybean development. Cell 188, 550–567. e519 (2025).

Article
CAS
PubMed

Google Scholar
Mendieta, J. P. et al. Investigating the cis-regulatory basis of C₃ and C₄ photosynthesis in grasses at single-cell resolution. Proc. Natl Acad. Sci. USA 121, e2402781121 (2024).

Article
CAS
PubMed
PubMed Central

Google Scholar
Wing, R. A., Purugganan, M. D. & Zhang, Q. The rice genome revolution: from an ancient grain to Green Super Rice. Nat. Rev. Genet. 19, 505–517 (2018).

Article
CAS
PubMed

Google Scholar
Dong, Q. et al. Genome‐wide Hi‐C analysis reveals extensive hierarchical chromatin interactions in rice. Plant J. 94, 1141–1156 (2018).

Article
CAS
PubMed

Google Scholar
Wei, X. et al. A quantitative genomics map of rice provides genetic insights and guides breeding. Nat. Genet. 53, 243–253 (2021).

Article
CAS
PubMed

Google Scholar
Yang, Y. et al. Natural variation of OsGluA2 is involved in grain protein content regulation in rice. Nat. Commun. 10, 1949 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729–18734 (2010).

Article
CAS
PubMed
PubMed Central

Google Scholar
Xu, Q. et al. DNA demethylation affects imprinted gene expression in maize endosperm. Genome Biol. 23, 77 (2022).

Article
CAS
PubMed
PubMed Central

Google Scholar
Ohashi-Ito, K. & Fukuda, H. HD-Zip III homeobox genes that include a novel member, ZeHB-13 (Zinnia)/ATHB-15 (Arabidopsis), are involved in procambium and xylem cell differentiation. Plant Cell Physiol. 44, 1350–1358 (2003).

Article
CAS
PubMed

Google Scholar
Wu, R. et al. CFL1, a WW domain protein, regulates cuticle development by modulating the function of HDG1, a class IV homeodomain transcription factor, in rice and Arabidopsis. Plant Cell 23, 3392–3411 (2011).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhong, R., Richardson, E. A. & Ye, Z.-H. The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell 19, 2776–2792 (2007).

Article
CAS
PubMed
PubMed Central

Google Scholar
Wang, Z. et al. Salicylic acid promotes quiescent center cell division through ROS accumulation and down‐regulation of PLT1, PLT2, and WOX5. J. Integr. Plant Biol. 63, 583–596 (2021).

Article
CAS
PubMed

Google Scholar
Gontarek, B. C., Neelakandan, A. K., Wu, H. & Becraft, P. W. NKD transcription factors are central regulators of maize endosperm development. Plant Cell 28, 2916–2936 (2016).

Article
CAS
PubMed
PubMed Central

Google Scholar
Sun, X. et al. Activation of secondary cell wall biosynthesis by miR319‐targeted TCP 4 transcription factor. Plant Biotechnol. J. 15, 1284–1294 (2017).

Article
CAS
PubMed
PubMed Central

Google Scholar
Kamiya, N., Nagasaki, H., Morikami, A., Sato, Y. & Matsuoka, M. Isolation and characterization of a rice WUSCHEL‐type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem. Plant J. 35, 429–441 (2003).

Article
CAS
PubMed

Google Scholar
Cui, H. et al. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316, 421–425 (2007).

Article
CAS
PubMed

Google Scholar
Zhang, T.-Q., Chen, Y., Liu, Y., Lin, W.-H. & Wang, J.-W. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root. Nat. Commun. 12, 2053 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Ortiz-Ramírez, C. et al. Ground tissue circuitry regulates organ complexity in maize and Setaria. Science 374, 1247–1252 (2021).

Article
PubMed
PubMed Central

Google Scholar
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

Article
CAS
PubMed

Google Scholar
Xiao, J. et al. Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat. Genet. 49, 1546–1552 (2017).

Article
CAS
PubMed

Google Scholar
Schmitz, R. J., Grotewold, E. & Stam, M. Cis-regulatory sequences in plants: their importance, discovery, and future challenges. Plant Cell 34, 718–741 (2022).

Article
PubMed

Google Scholar
Ouyang, W. et al. Haplotype mapping of H3K27me3-associated chromatin interactions defines topological regulation of gene silencing in rice. Cell Rep. 42, 112350 (2023).

Article
CAS
PubMed

Google Scholar
Minnoye, L. et al. Chromatin accessibility profiling methods. Nat. Rev. Methods Primers 1, 10 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Yu, Y., Zhang, H., Long, Y., Shu, Y. & Zhai, J. Plant public RNA‐seq database: a comprehensive online database for expression analysis of~ 45 000 plant public RNA‐seq libraries. Plant Biotechnol. J. 20, 806 (2022).

Article
CAS
PubMed
PubMed Central

Google Scholar
Bai, X. et al. Duplication of an upstream silencer of FZP increases grain yield in rice. Nat. Plants 3, 885–893 (2017).

Article
CAS
PubMed

Google Scholar
Wang, Z. et al. AraENCODE: a comprehensive epigenomic database of Arabidopsis thaliana. Mol. Plant 16, 1113–1116 (2023).

Article
CAS
PubMed

Google Scholar
Tonosaki, K. & Kinoshita, T. Possible roles for polycomb repressive complex 2 in cereal endosperm. Front. Plant Sci. 6, 144 (2015).

Article
PubMed
PubMed Central

Google Scholar
Tan, F.-Q. et al. A coiled-coil protein associates Polycomb Repressive Complex 2 with KNOX/BELL transcription factors to maintain silencing of cell differentiation-promoting genes in the shoot apex. Plant Cell 34, 2969–2988 (2022).

Article
PubMed
PubMed Central

Google Scholar
Zhao, L. et al. Integrative analysis of reference epigenomes in 20 rice varieties. Nat. Commun. 11, 2658 (2020).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhang, J. et al. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci. Data 3, 1–8 (2016).

Article

Google Scholar
Zilberman, D., Coleman-Derr, D., Ballinger, T. & Henikoff, S. Histone H2A. Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456, 125–129 (2008).

Article
CAS
PubMed
PubMed Central

Google Scholar
Hure, V., Piron-Prunier, F. & Déléris, A. DNA methylation either antagonizes or promotes Polycomb recruitment at transposable elements. Preprint at bioRxiv https://doi.org/10.1101/2024.10.11.617914 (2024).
Lv, Z., Zhao, W., Kong, S., Li, L. & Lin, S. Overview of molecular mechanisms of plant leaf development: a systematic review. Front. Plant Sci. 14, 1293424 (2023).

Article
PubMed
PubMed Central

Google Scholar
Le Hir, R. & Bellini, C. The plant-specific Dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis. Front. Plant Sci. 4, 164 (2013).

PubMed
PubMed Central

Google Scholar
Dai, X. et al. Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize. Plant J. 109, 675–692 (2022).

Article
CAS
PubMed

Google Scholar
Yanagisawa, S. Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant J. 21, 281–288 (2000).

Article
CAS
PubMed

Google Scholar
Yanagisawa, S. & Sheen, J. Involvement of maize Dof zinc finger proteins in tissue-specific and light-regulated gene expression. Plant Cell 10, 75–89 (1998).

Article
CAS
PubMed
PubMed Central

Google Scholar
Borba, A. R. et al. Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C₄ photosynthesis is based on an ancient code found in the ancestral C₃ state. Mol. Biol. Evol. 35, 1690–1705 (2018).

Article
CAS
PubMed
PubMed Central

Google Scholar
Wolfe, K. H., Gouy, M., Yang, Y.-W., Sharp, P. M. & Li, W.-H. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl Acad. Sci. USA 86, 6201–6205 (1989).

Article
CAS
PubMed
PubMed Central

Google Scholar
Gaut, B. S. & Doebley, J. F. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl Acad. Sci. USA 94, 6809–6814 (1997).

Article
CAS
PubMed
PubMed Central

Google Scholar
Chen, X. et al. SQUAMOSA promoter‐binding protein‐like transcription factors: star players for plant growth and development. J. Integr. Plant Biol. 52, 946–951 (2010).

Article
CAS
PubMed

Google Scholar
Denyer, T. et al. Spatiotemporal developmental trajectories in the Arabidopsis root revealed using high-throughput single-cell RNA sequencing. Dev. Cell 48, 840–852. e845 (2019).

Article
CAS
PubMed

Google Scholar
Fang, J. et al. The URL1–ROC5–TPL2 transcriptional repressor complex represses the ACL1 gene to modulate leaf rolling in rice. Plant Physiol. 185, 1722–1744 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Horstman, A. et al. AIL and HDG proteins act antagonistically to control cell proliferation. Development 142, 454–464 (2015).

CAS
PubMed

Google Scholar
Qing, L. & Aoyama, T. Pathways for epidermal cell differentiation via the homeobox gene GLABRA2: update on the roles of the classic regulator F. J. Integr. Plant Biol. 54, 729–737 (2012).

Article

Google Scholar
Rombolá-Caldentey, B., Rueda-Romero, P., Iglesias-Fernández, R., Carbonero, P. & Oñate-Sánchez, L. Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element. Plant Cell 26, 2905–2919 (2014).

Article
PubMed
PubMed Central

Google Scholar
Yu, L. H. et al. Arabidopsis EDT 1/HDG 11 improves drought and salt tolerance in cotton and poplar and increases cotton yield in the field. Plant Biotechnol. J. 14, 72–84 (2016).

Article
CAS
PubMed

Google Scholar
Hong, S.-Y., Kim, O.-K., Kim, S.-G., Yang, M.-S. & Park, C.-M. Nuclear import and DNA binding of the ZHD5 transcription factor is modulated by a competitive peptide inhibitor in Arabidopsis. J. Biol. Chem. 286, 1659–1668 (2011).

Article
CAS
PubMed

Google Scholar
Rosado, D., Ackermann, A., Spassibojko, O., Rossi, M. & Pedmale, U. V. WRKY transcription factors and ethylene signaling modify root growth during the shade-avoidance response. Plant Physiol. 188, 1294–1311 (2022).

Article
CAS
PubMed

Google Scholar
Brockington, S. F. et al. Evolutionary analysis of the MIXTA gene family highlights potential targets for the study of cellular differentiation. Mol. Biol. Evol. 30, 526–540 (2013).

Article
CAS
PubMed

Google Scholar
Huang, Y. et al. OsNCED5, a 9-cis-epoxycarotenoid dioxygenase gene, regulates salt and water stress tolerance and leaf senescence in rice. Plant Sci. 287, 110188 (2019).

Article
CAS
PubMed

Google Scholar
Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2005).

Article
PubMed

Google Scholar
Babarinde, I. A. & Saitou, N. Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Mol. Biol. Evol. 33, 1807–1817 (2016).

Article
CAS
PubMed

Google Scholar
Song, B. et al. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Res. 31, 1245–1257 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Nelson, A. C. & Wardle, F. C. Conserved non-coding elements and cis regulation: actions speak louder than words. Development 140, 1385–1395 (2013).

Article
CAS
PubMed

Google Scholar
Hendelman, A. et al. Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 184, 1724–1739. e1716 (2021).

Article
CAS
PubMed

Google Scholar
Wiles, E. T. & Selker, E. U. H3K27 methylation: a promiscuous repressive chromatin mark. Curr. Opin. Genet. Dev. 43, 31–37 (2017).

Article
CAS
PubMed

Google Scholar
Guillotin, B. et al. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 617, 785–791 (2023).

Article
CAS
PubMed
PubMed Central

Google Scholar
Goel, M. et al. The vast majority of somatic mutations in plants are layer-specific. Genome Biol. 25, 194 (2024).

Article
CAS
PubMed
PubMed Central

Google Scholar
Andrews, G. et al. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science 380, eabn7930 (2023).

Article
CAS
PubMed

Google Scholar
Engelhorn, J. et al. Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites. Preprint at bioRxiv https://doi.org/10.1101/2023.08.08.551183 (2023).
Zhao, T. & Schranz, M. E. Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes. Proc. Natl Acad. Sci. USA 116, 2165–2174 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Reineke, A. R., Bornberg-Bauer, E. & Gu, J. Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res. 39, 6029–6043 (2011).

Article
CAS
PubMed
PubMed Central

Google Scholar
Kaplinsky, N. J., Braun, D. M., Penterman, J., Goff, S. A. & Freeling, M. Utility and distribution of conserved noncoding sequences in the grasses. Proc. Natl Acad. Sci. USA 99, 6147–6151 (2002).

Article
CAS
PubMed
PubMed Central

Google Scholar
Guo, H. & Moose, S. P. Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15, 1143–1158 (2003).

Article
CAS
PubMed
PubMed Central

Google Scholar
Inada, D. C. et al. Conserved noncoding sequences in the grasses4. Genome Res. 13, 2030–2041 (2003).

Article
CAS
PubMed
PubMed Central

Google Scholar
Clark, J. W. & Donoghue, P. C. Whole-genome duplication and plant macroevolution. Trends Plant Sci. 23, 933–945 (2018).

Article
CAS
PubMed

Google Scholar
Del Pozo, J. C. & Ramirez-Parra, E. Whole genome duplications in plants: an overview from Arabidopsis. J. Exp. Bot. 66, 6991–7003 (2015).

Article
PubMed

Google Scholar
Jump, A. S., Marchant, R. & Peñuelas, J. Environmental change and the option value of genetic diversity. Trends Plant Sci. 14, 51–58 (2009).

Article
CAS
PubMed

Google Scholar
Vierstra, J. et al. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science 346, 1007–1012 (2014).

Article
CAS
PubMed
PubMed Central

Google Scholar
Ciren, D., Zebell, S. & Lippman, Z. B. Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genet. 20, e1011174 (2024).

Article
CAS
PubMed
PubMed Central

Google Scholar
Baumgart, L. A. et al. Recruitment, rewiring and deep conservation in flowering plant gene regulation. Nat. Plants 11, 1514–1527 (2025).

Article
PubMed

Google Scholar
Zhang, X., Marand, A. P., Yan, H. & Schmitz, R. J. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biol. 25, 90 (2024).

Article
CAS
PubMed
PubMed Central

Google Scholar
Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

Article
CAS
PubMed
PubMed Central

Google Scholar
Ouyang, S. et al. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35, D883–D887 (2007).

Article
CAS
PubMed

Google Scholar
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).

Article
CAS
PubMed
PubMed Central

Google Scholar
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291. e289 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

Article
CAS
PubMed

Google Scholar
Crow, M., Paul, A., Ballouz, S., Huang, Z. J. & Gillis, J. Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat. Commun. 9, 884 (2018).

Article
PubMed
PubMed Central

Google Scholar
Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Stickels, R. R. et al. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol. 39, 313–319 (2021).

Article
CAS
PubMed

Google Scholar
Satpathy, A. T. et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat. Biotechnol. 37, 925–936 (2019).

Article
CAS
PubMed
PubMed Central

Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Article
PubMed
PubMed Central

Google Scholar
Picard Toolkit. GitHub repository (Broad institute, 2019).
Nishimura, D. RepeatMasker. Biotech. Softw. Internet Rep. 1, 36–39 (2000).

Article

Google Scholar
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 1–9 (2009).

Article

Google Scholar
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, 1–9 (2008).

Article

Google Scholar
DeBruine, Z. J., Melcher, K. & Triche, T. J. Jr. Fast and robust non-negative matrix factorization for single-cell experiments. Preprint at bioRxiv https://doi.org/10.1101/2021.09.01.458620 (2021).
McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018).
Pettkó-Szandtner, A. et al. Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf. J. Plant Res. 128, 953–974 (2015).

Article
PubMed

Google Scholar
Schep, A. N. et al. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res. 25, 1757–1770 (2015).

Article
CAS
PubMed
PubMed Central

Google Scholar
Abney, S. Bootstrapping. In Proc. 40th Annual Meeting of the Association for Computational Linguistics (ACL) 360–367 (2002).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

Article
CAS
PubMed
PubMed Central

Google Scholar
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 1–11 (2015).

Article

Google Scholar
Kaul, A., Bhattacharyya, S. & Ay, F. Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nat. Protoc. 15, 991–1012 (2020).

Article
CAS
PubMed
PubMed Central

Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

Article
CAS
PubMed
PubMed Central

Google Scholar
Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).

Article
CAS
PubMed
PubMed Central

Google Scholar
Dijk, D. V. et al. MAGIC: a diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. Preprint at bioRxiv https://doi.org/10.1101/111591 (2017).
Alpert, A., Moore, L. S., Dubovik, T. & Shen-Orr, S. S. Alignment of single-cell trajectories to compare cellular expression dynamics. Nat. Methods 15, 267–270 (2018).

Article
CAS
PubMed

Google Scholar
Jin, J. et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 45, D1040–D1045 (2016).
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).

Article
CAS
PubMed
PubMed Central

Google Scholar
Castro-Mondragon, J. A. et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 50, D165–D173 (2022).

Article
CAS
PubMed

Google Scholar
Wagner-Menghin, M. M. Binomial test. in Encyclopedia of Statistics in Behavioral Science 1st edn (eds Everitt, B. S. & Howell, D. C.) 158–163 (John Wiley & Sons, 2005).
Bolstad, B. M. preprocessCore: A collection of pre-processing functions. R Package v1.40.0 (Bioconductor, 2017).
Lovell, J. T. et al. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. Elife 11, e78526 (2022).

Article
CAS
PubMed
PubMed Central

Google Scholar
Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 49, D10–D17 (2021).

Article
CAS
PubMed

Google Scholar
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).

Article
PubMed
PubMed Central

Google Scholar
Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110–121 (2010).

Article
CAS
PubMed
PubMed Central

Google Scholar
Siepel, A. & Haussler, D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21, 468–488 (2004).

Article
CAS
PubMed

Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

Article
CAS
PubMed
PubMed Central

Google Scholar
Stovner, E. B. & Sætrom, P. epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics 35, 4392–4393 (2019).

Article
CAS
PubMed

Google Scholar
Xie, L. et al. RiceENCODE: a comprehensive epigenomic database as a rice Encyclopedia of DNA Elements. Mol. Plant 14, 1604–1606 (2021).

Article
CAS
PubMed

Google Scholar
Noshay, J. M. et al. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 11, jkab190 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).

Article
CAS
PubMed
PubMed Central

Google Scholar
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).

Article
PubMed
PubMed Central

Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

Article
CAS
PubMed
PubMed Central

Google Scholar
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

Article
CAS
PubMed
PubMed Central

Google Scholar
Tian, T. et al. agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45, W122–W129 (2017).

Article
CAS
PubMed
PubMed Central

Google Scholar
Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T‐DNA. Plant J. 6, 271–282 (1994).

Article
CAS
PubMed

Google Scholar
Hofmeister, B. T. & Schmitz, R. J. Enhanced JBrowse plugins for epigenomics data visualization. BMC Bioinformatics 19, 1–6 (2018).

Article

Google Scholar
Shimadzu, S., Furuya, T. & Kondo, Y. Molecular mechanisms underlying the establishment and maintenance of vascular stem cells in Arabidopsis thaliana. Plant Cell Physiol. 64, 274–283 (2023).

Article
CAS
PubMed

Google Scholar
Otero, S. & Helariutta, Y. Companion cells: a diamond in the rough. J. Exp. Bot. 68, 71–78 (2016).

Article
PubMed

Google Scholar
Ramachandran, V. et al. Plant-specific Dof transcription factors VASCULAR-RELATED DOF1 and VASCULAR-RELATED DOF2 regulate vascular cell differentiation and lignin biosynthesis in Arabidopsis. Plant Mol. Biol. 104, 263–281 (2020).

Article
CAS
PubMed

Google Scholar
Kubo, H., Kishi, M. & Goto, K. Expression analysis of ANTHOCYANINLESS2 gene in Arabidopsis. Plant Sci. 175, 853–857 (2008).

Article
CAS

Google Scholar
Amanda, D. et al. DEFECTIVE KERNEL1 (DEK1) regulates cell walls in the leaf epidermis. Plant Physiol. 172, 2204–2218 (2016).

Article
CAS
PubMed
PubMed Central

Google Scholar
Alexandrov, N. et al. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 43, D1023–D1027 (2015).

Article
CAS
PubMed

Google Scholar